Keyword: models
2017 (1)
Analysis of the Association of Clubhouse Membership with Overall Costs of Care for Mental Health Treatment. Hwang, S., Woody, J., & Eaton, W. W. Community Mental Health Journal, 53(1):102--106, 2017.
doi abstract bibtex
doi abstract bibtex
We examined whether frequency of attendance at the B'More Clubhouse was associated with lower mental health care costs in the Medicaid database, and whether members in the B'More Clubhouse (n = 30) would have lower mental health care costs compared with a set of matched controls from the same claims database (n = 150). Participants who attended the Clubhouse 3 days or more per week had mean 1-year mental health care costs of US \$5697, compared to \$14,765 for those who attended less often. B'More Clubhouse members had significantly lower annual total mental health care costs than the matched comparison group (\$10,391 vs. \$15,511; p \textless 0.0001). Membership in the B'More Clubhouse is associated with a substantial beneficial influence on health care costs.
@article{hwang_analysis_2017,
title = {Analysis of the {Association} of {Clubhouse} {Membership} with {Overall} {Costs} of {Care} for {Mental} {Health} {Treatment}},
volume = {53},
issn = {1573-2789},
doi = {10.1007/s10597-016-0041-3},
abstract = {We examined whether frequency of attendance at the B'More Clubhouse was associated with lower mental health care costs in the Medicaid database, and whether members in the B'More Clubhouse (n = 30) would have lower mental health care costs compared with a set of matched controls from the same claims database (n = 150). Participants who attended the Clubhouse 3 days or more per week had mean 1-year mental health care costs of US \$5697, compared to \$14,765 for those who attended less often. B'More Clubhouse members had significantly lower annual total mental health care costs than the matched comparison group (\$10,391 vs. \$15,511; p {\textless} 0.0001). Membership in the B'More Clubhouse is associated with a substantial beneficial influence on health care costs.},
language = {eng},
number = {1},
journal = {Community Mental Health Journal},
author = {Hwang, Seungyoung and Woody, Jason and Eaton, William W.},
year = {2017},
pmid = {27380210},
keywords = {Adult, Clubhouse, Cost, Costs and Cost Analysis, Databases, Factual, Female, Health Care Costs, Humans, Male, Medicaid, Mental Disorders, Mental Health Services, Mental health, Middle Aged, Models, Theoretical, United States},
pages = {102--106}
}2016 (1)
Manta birostris, predator of the deep? Insight into the diet of the giant manta ray through stable isotope analysis. Burgess, K. B., Couturier, L. I. E., Marshall, A. D., Richardson, A. J., Weeks, S. J., & Bennett, M. B. Royal Society Open Science, 3(11):160717, November, 2016. 00000 WOS:000389244400052
doi abstract bibtex
doi abstract bibtex
The characterization of diet for the giant manta ray Manta birostris has been problematic given their large-scale movement patterns and the difficulty in obtaining stomach contents from this species. The large majority of existing information is based on observational data limited to feeding events at the sea surface during daylight. Recently discovered aggregation sites for the giant manta ray off mainland Ecuador are some of the most accessible to date and provide a unique opportunity for researchers to gather much needed information on this elusive species. To assess how important surface zooplankton is to giant manta ray diet, we conducted stable isotope analysis (N-15 and C-13) on M. birostris muscle and surface zooplankton. Trophic position estimates placed M. birostris overall at a secondary consumer level of approximately 3.4 but there was large variation in delta N-15 and delta C-13 values among individuals. Manta birostris muscle tissue delta C-13 values were also not consistent with this species feeding predominantly on surface zooplankton and suggest that the majority of dietary intake is of mesopelagic origin. Given the conservative life history and fisheries pressure on large planktivores, knowledge of their trophic role and foraging strategies is essential to better understand their ecology and develop effective conservation measures.
@article{burgess_manta_2016,
title = {Manta birostris, predator of the deep? {Insight} into the diet of the giant manta ray through stable isotope analysis},
volume = {3},
issn = {2054-5703},
shorttitle = {Manta birostris, predator of the deep?},
doi = {10.1098/rsos.160717},
abstract = {The characterization of diet for the giant manta ray Manta birostris has been problematic given their large-scale movement patterns and the difficulty in obtaining stomach contents from this species. The large majority of existing information is based on observational data limited to feeding events at the sea surface during daylight. Recently discovered aggregation sites for the giant manta ray off mainland Ecuador are some of the most accessible to date and provide a unique opportunity for researchers to gather much needed information on this elusive species. To assess how important surface zooplankton is to giant manta ray diet, we conducted stable isotope analysis (N-15 and C-13) on M. birostris muscle and surface zooplankton. Trophic position estimates placed M. birostris overall at a secondary consumer level of approximately 3.4 but there was large variation in delta N-15 and delta C-13 values among individuals. Manta birostris muscle tissue delta C-13 values were also not consistent with this species feeding predominantly on surface zooplankton and suggest that the majority of dietary intake is of mesopelagic origin. Given the conservative life history and fisheries pressure on large planktivores, knowledge of their trophic role and foraging strategies is essential to better understand their ecology and develop effective conservation measures.},
language = {English},
number = {11},
journal = {Royal Society Open Science},
author = {Burgess, Katherine B. and Couturier, Lydie I. E. and Marshall, Andrea D. and Richardson, Anthony J. and Weeks, Scarla J. and Bennett, Michael B.},
month = nov,
year = {2016},
note = {00000
WOS:000389244400052},
keywords = {Diet, Ecology, Mesopelagic, conservation, eastern tropical Pacific Ocean, ecosystem, elasmobranch, mesopelagic fishes, models, nitrogen isotopes, ocean, pacific, planktivore, trophic ecology, trophic position, whale sharks},
pages = {160717}
}2015 (2)
Anthropometric models of bone mineral content and areal bone mineral density based on the bone mineral density in childhood study. Short, D. F., Gilsanz, V., Kalkwarf, H. J., Lappe, J. M., Oberfield, S., Shepherd, J. A., Winer, K. K., Zemel, B. S., & Hangartner, T. N. Osteoporosis international: a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA, 26(3):1099–1108, March, 2015.
doi abstract bibtex
doi abstract bibtex
New models describing anthropometrically adjusted normal values of bone mineral density and content in children have been created for the various measurement sites. The inclusion of multiple explanatory variables in the models provides the opportunity to calculate Z-scores that are adjusted with respect to the relevant anthropometric parameters. INTRODUCTION: Previous descriptions of children's bone mineral measurements by age have focused on segmenting diverse populations by race and sex without adjusting for anthropometric variables or have included the effects of a single anthropometric variable. METHODS: We applied multivariate semi-metric smoothing to the various pediatric bone-measurement sites using data from the Bone Mineral Density in Childhood Study to evaluate which of sex, race, age, height, weight, percent body fat, and sexual maturity explain variations in the population's bone mineral values. By balancing high adjusted R(2) values with clinical needs, two models are examined. RESULTS: At the spine, whole body, whole body sub head, total hip, hip neck, and forearm sites, models were created using sex, race, age, height, and weight as well as an additional set of models containing these anthropometric variables and percent body fat. For bone mineral density, weight is more important than percent body fat, which is more important than height. For bone mineral content, the order varied by site with body fat being the weakest component. Including more anthropometrics in the model reduces the overlap of the critical groups, identified as those individuals with a Z-score below -2, from the standard sex, race, and age model. CONCLUSIONS: If body fat is not available, the simpler model including height and weight should be used. The inclusion of multiple explanatory variables in the models provides the opportunity to calculate Z-scores that are adjusted with respect to the relevant anthropometric parameters.
@article{short_anthropometric_2015,
title = {Anthropometric models of bone mineral content and areal bone mineral density based on the bone mineral density in childhood study},
volume = {26},
issn = {1433-2965},
doi = {10.1007/s00198-014-2916-x},
abstract = {New models describing anthropometrically adjusted normal values of bone mineral density and content in children have been created for the various measurement sites. The inclusion of multiple explanatory variables in the models provides the opportunity to calculate Z-scores that are adjusted with respect to the relevant anthropometric parameters.
INTRODUCTION: Previous descriptions of children's bone mineral measurements by age have focused on segmenting diverse populations by race and sex without adjusting for anthropometric variables or have included the effects of a single anthropometric variable.
METHODS: We applied multivariate semi-metric smoothing to the various pediatric bone-measurement sites using data from the Bone Mineral Density in Childhood Study to evaluate which of sex, race, age, height, weight, percent body fat, and sexual maturity explain variations in the population's bone mineral values. By balancing high adjusted R(2) values with clinical needs, two models are examined.
RESULTS: At the spine, whole body, whole body sub head, total hip, hip neck, and forearm sites, models were created using sex, race, age, height, and weight as well as an additional set of models containing these anthropometric variables and percent body fat. For bone mineral density, weight is more important than percent body fat, which is more important than height. For bone mineral content, the order varied by site with body fat being the weakest component. Including more anthropometrics in the model reduces the overlap of the critical groups, identified as those individuals with a Z-score below -2, from the standard sex, race, and age model.
CONCLUSIONS: If body fat is not available, the simpler model including height and weight should be used. The inclusion of multiple explanatory variables in the models provides the opportunity to calculate Z-scores that are adjusted with respect to the relevant anthropometric parameters.},
language = {eng},
number = {3},
journal = {Osteoporosis international: a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
author = {Short, D. F. and Gilsanz, V. and Kalkwarf, H. J. and Lappe, J. M. and Oberfield, S. and Shepherd, J. A. and Winer, K. K. and Zemel, B. S. and Hangartner, T. N.},
month = mar,
year = {2015},
pmid = {25311106},
pmcid = {PMC4768717},
keywords = {Absorptiometry, Photon, Adipose Tissue, Adolescent, Age Factors, Algorithms, Anthropometry, Body Height, Body Weight, Bone Density, Bone and Bones, Child, Child, Preschool, Continental Population Groups, Female, Humans, Longitudinal Studies, Male, Models, Theoretical, Sex Factors, Young Adult},
pages = {1099--1108}
}Models of primary care for frail patients. Frank, C. & Wilson, C., R. Canadian family physician Medecin de famille canadien, 61(7):601-606, 7, 2015.
abstract bibtex
abstract bibtex
OBJECTIVE: To discuss models of care for frail seniors provided in primary care settings and those developed by Canadian FPs. SOURCES OF INFORMATION: Ovid MEDLINE and the Cochrane database were searched from 2010 to January 2014 using the terms models of care, family medicine, elderly, and geriatrics. MAIN MESSAGE: New models of funding for primary care have opened opportunities for ways of caring for complex frail older patients. Severity of frailty is an important factor, and more severe frailty should prompt consideration of using an alternate model of care for a senior. In Canada, models in use include integrated care systems, shared care models, home-based care models, and family medicine specialty clinics. No one model should take precedence but FPs should be involved in developing and implementing strategies that meet the needs of individual patients and communities. Organizational and remunerative supports will need to be put in place to achieve widespread uptake of such models. CONCLUSION: Given the increased numbers of frail seniors and the decrease in access to hospital beds, prioritized care models should include ones focused on optimizing health, decreasing frailty, and helping to avoid hospitalization of frail and well seniors alike. The Health Care of the Elderly Program Committee at the College of Family Physicians of Canada is hosting a repository for models of care used by FPs and is asking physicians to submit their ideas for how to best care for frail seniors.
@article{
title = {Models of primary care for frail patients},
type = {article},
year = {2015},
identifiers = {[object Object]},
keywords = {Aged,Canada,Frail Elderly,Health Services for the Aged/organization & admini,Humans,Models, Nursing,Primary Health Care/methods},
pages = {601-606},
volume = {61},
month = {7},
city = {Canada},
id = {6a0a5f0f-ce4e-3c61-bee5-e77b7fc2bd29},
created = {2016-08-20T16:52:37.000Z},
file_attached = {false},
profile_id = {217ced55-4c79-38dc-838b-4b5ea8df5597},
group_id = {408d37d9-5f1b-3398-a9f5-5c1a487116d4},
last_modified = {2017-03-14T09:54:45.334Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {JOUR},
notes = {LR: 20150921; JID: 0120300; OID: NLM: PMC4501602; ppublish},
folder_uuids = {27325661-146f-41f6-bd41-67b2f73e4225},
private_publication = {false},
abstract = {OBJECTIVE: To discuss models of care for frail seniors provided in primary care settings and those developed by Canadian FPs. SOURCES OF INFORMATION: Ovid MEDLINE and the Cochrane database were searched from 2010 to January 2014 using the terms models of care, family medicine, elderly, and geriatrics. MAIN MESSAGE: New models of funding for primary care have opened opportunities for ways of caring for complex frail older patients. Severity of frailty is an important factor, and more severe frailty should prompt consideration of using an alternate model of care for a senior. In Canada, models in use include integrated care systems, shared care models, home-based care models, and family medicine specialty clinics. No one model should take precedence but FPs should be involved in developing and implementing strategies that meet the needs of individual patients and communities. Organizational and remunerative supports will need to be put in place to achieve widespread uptake of such models. CONCLUSION: Given the increased numbers of frail seniors and the decrease in access to hospital beds, prioritized care models should include ones focused on optimizing health, decreasing frailty, and helping to avoid hospitalization of frail and well seniors alike. The Health Care of the Elderly Program Committee at the College of Family Physicians of Canada is hosting a repository for models of care used by FPs and is asking physicians to submit their ideas for how to best care for frail seniors.},
bibtype = {article},
author = {Frank, C and Wilson, C R},
journal = {Canadian family physician Medecin de famille canadien},
number = {7}
}2014 (2)
Real-time simulation of three-dimensional shoulder girdle and arm dynamics. Chadwick, E. K., Blana, D., Kirsch, R. F., & van den Bogert, A. J. IEEE transactions on bio-medical engineering, 61(7):1947–1956, July, 2014.
doi abstract bibtex
doi abstract bibtex
Electrical stimulation is a promising technology for the restoration of arm function in paralyzed individuals. Control of the paralyzed arm under electrical stimulation, however, is a challenging problem that requires advanced controllers and command interfaces for the user. A real-time model describing the complex dynamics of the arm would allow user-in-the-loop type experiments where the command interface and controller could be assessed. Real-time models of the arm previously described have not included the ability to model the independently controlled scapula and clavicle, limiting their utility for clinical applications of this nature. The goal of this study therefore was to evaluate the performance and mechanical behavior of a real-time, dynamic model of the arm and shoulder girdle. The model comprises seven segments linked by eleven degrees of freedom and actuated by 138 muscle elements. Polynomials were generated to describe the muscle lines of action to reduce computation time, and an implicit, first-order Rosenbrock formulation of the equations of motion was used to increase simulation step-size. The model simulated flexion of the arm faster than real time, simulation time being 92% of actual movement time on standard desktop hardware. Modeled maximum isometric torque values agreed well with values from the literature, showing that the model simulates the moment-generating behavior of a real human arm. The speed of the model enables experiments where the user controls the virtual arm and receives visual feedback in real time. The ability to optimize potential solutions in simulation greatly reduces the burden on the user during development.
@article{chadwick_real-time_2014,
title = {Real-time simulation of three-dimensional shoulder girdle and arm dynamics},
volume = {61},
copyright = {All rights reserved},
issn = {1558-2531},
doi = {10.1109/TBME.2014.2309727},
abstract = {Electrical stimulation is a promising technology for the restoration of arm function in paralyzed individuals. Control of the paralyzed arm under electrical stimulation, however, is a challenging problem that requires advanced controllers and command interfaces for the user. A real-time model describing the complex dynamics of the arm would allow user-in-the-loop type experiments where the command interface and controller could be assessed. Real-time models of the arm previously described have not included the ability to model the independently controlled scapula and clavicle, limiting their utility for clinical applications of this nature. The goal of this study therefore was to evaluate the performance and mechanical behavior of a real-time, dynamic model of the arm and shoulder girdle. The model comprises seven segments linked by eleven degrees of freedom and actuated by 138 muscle elements. Polynomials were generated to describe the muscle lines of action to reduce computation time, and an implicit, first-order Rosenbrock formulation of the equations of motion was used to increase simulation step-size. The model simulated flexion of the arm faster than real time, simulation time being 92\% of actual movement time on standard desktop hardware. Modeled maximum isometric torque values agreed well with values from the literature, showing that the model simulates the moment-generating behavior of a real human arm. The speed of the model enables experiments where the user controls the virtual arm and receives visual feedback in real time. The ability to optimize potential solutions in simulation greatly reduces the burden on the user during development.},
language = {eng},
number = {7},
journal = {IEEE transactions on bio-medical engineering},
author = {Chadwick, Edward K. and Blana, Dimitra and Kirsch, Robert F. and van den Bogert, Antonie J.},
month = jul,
year = {2014},
pmid = {24956613},
pmcid = {PMC4068297},
keywords = {Biomechanical Phenomena, Computer Simulation, Humans, Models, Biological, Range of Motion, Articular, Shoulder, Upper Extremity},
pages = {1947--1956},
}Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity. Eguchi, A., Neymotin, S. A., & Stringer, S. M. Frontiers in Neural Circuits, 2014.
![Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex
Paper doi abstract bibtex Although many computational models have been proposed to explain orientation maps in primary visual cortex (V1), it is not yet known how similar clusters of color-selective neurons in macaque V1/V2 are connected and develop. In this work, we address the problem of understanding the cortical processing of color information with a possible mechanism of the development of the patchy distribution of color selectivity via computational modeling. Each color input is decomposed into a red, green, and blue representation and transmitted to the visual cortex via a simulated optic nerve in a luminance channel and red–green and blue–yellow opponent color channels. Our model of the early visual system consists of multiple topographically-arranged layers of excitatory and inhibitory neurons, with sparse intra-layer connectivity and feed-forward connectivity between layers. Layers are arranged based on anatomy of early visual pathways, and include a retina, lateral geniculate nucleus, and layered neocortex. Each neuron in the V1 output layer makes synaptic connections to neighboring neurons and receives the three types of signals in the different channels from the corresponding photoreceptor position. Synaptic weights are randomized and learned using spike-timing-dependent plasticity (STDP). After training with natural images, the neurons display heightened sensitivity to specific colors. Information-theoretic analysis reveals mutual information between particular stimuli and responses, and that the information reaches a maximum with fewer neurons in the higher layers, indicating that estimations of the input colors can be done using the output of fewer cells in the later stages of cortical processing. In addition, cells with similar color receptive fields form clusters. Analysis of spiking activity reveals increased firing synchrony between neurons when particular color inputs are presented or removed (ON-cell/OFF-cell).
@article{eguchi_color_2014,
title = {Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity},
volume = {8},
url = {http://journal.frontiersin.org/article/10.3389/fncir.2014.00016/abstract},
doi = {10.3389/fncir.2014.00016},
abstract = {Although many computational models have been proposed to explain orientation maps in primary visual cortex (V1), it is not yet known how similar clusters of color-selective neurons in macaque V1/V2 are connected and develop. In this work, we address the problem of understanding the cortical processing of color information with a possible mechanism of the development of the patchy distribution of color selectivity via computational modeling. Each color input is decomposed into a red, green, and blue representation and transmitted to the visual cortex via a simulated optic nerve in a luminance channel and red–green and blue–yellow opponent color channels. Our model of the early visual system consists of multiple topographically-arranged layers of excitatory and inhibitory neurons, with sparse intra-layer connectivity and feed-forward connectivity between layers. Layers are arranged based on anatomy of early visual pathways, and include a retina, lateral geniculate nucleus, and layered neocortex. Each neuron in the V1 output layer makes synaptic connections to neighboring neurons and receives the three types of signals in the different channels from the corresponding photoreceptor position. Synaptic weights are randomized and learned using spike-timing-dependent plasticity (STDP). After training with natural images, the neurons display heightened sensitivity to specific colors. Information-theoretic analysis reveals mutual information between particular stimuli and responses, and that the information reaches a maximum with fewer neurons in the higher layers, indicating that estimations of the input colors can be done using the output of fewer cells in the later stages of cortical processing. In addition, cells with similar color receptive fields form clusters. Analysis of spiking activity reveals increased firing synchrony between neurons when particular color inputs are presented or removed (ON-cell/OFF-cell).},
number = {16},
urldate = {2015-03-18TZ},
journal = {Frontiers in Neural Circuits},
author = {Eguchi, Akihiro and Neymotin, Samuel A. and Stringer, Simon M.},
year = {2014},
keywords = {Action Potentials, Animals, Brain modeling, Color, Color Perception, Computer Simulation, Geniculate Bodies, Models, Neurological, Neocortex, Neuronal Plasticity, Neurons, Photic Stimulation, STDP, Visual Cortex, Visual Pathways, color selectivity, self-organizing color maps, self-organizing feature maps}
}2013 (6)
Green-up dates in the Tibetan Plateau have continuously advanced from 1982 to 2011. Zhang, G., Zhang, Y., Dong, J., & Xiao, X. Proceedings of the National Academy of Sciences of the United States of America, 110(11):4309-14, 3, 2013.
![Green-up dates in the Tibetan Plateau have continuously advanced from 1982 to 2011. [pdf]](https://bibbase.org/img/filetypes/pdf.svg "pdf")
Paper Website abstract bibtex
Paper Website abstract bibtex As the Earth's third pole, the Tibetan Plateau has experienced a pronounced warming in the past decades. Recent studies reported that the start of the vegetation growing season (SOS) in the Plateau showed an advancing trend from 1982 to the late 1990s and a delay from the late 1990s to 2006. However, the findings regarding the SOS delay in the later period have been questioned, and the reasons causing the delay remain unknown. Here we explored the alpine vegetation SOS in the Plateau from 1982 to 2011 by integrating three long-term time-series datasets of Normalized Difference Vegetation Index (NDVI): Global Inventory Modeling and Mapping Studies (GIMMS, 1982-2006), SPOT VEGETATION (SPOT-VGT, 1998-2011), and Moderate Resolution Imaging Spectroradiometer (MODIS, 2000-2011). We found GIMMS NDVI in 2001-2006 differed substantially from SPOT-VGT and MODIS NDVIs and may have severe data quality issues in most parts of the western Plateau. By merging GIMMS-based SOSs from 1982 to 2000 with SPOT-VGT-based SOSs from 2001 to 2011 we found the alpine vegetation SOS in the Plateau experienced a continuous advancing trend at a rate of ∼1.04 d·y(-1) from 1982 to 2011, which was consistent with observed warming in springs and winters. The satellite-derived SOSs were proven to be reliable with observed phenology data at 18 sites from 2003 to 2011; however, comparison of their trends was inconclusive due to the limited temporal coverage of the observed data. Longer-term observed data are still needed to validate the phenology trend in the future.
@article{
title = {Green-up dates in the Tibetan Plateau have continuously advanced from 1982 to 2011.},
type = {article},
year = {2013},
identifiers = {[object Object]},
keywords = {Databases, Factual,Ecosystem,History, 20th Century,History, 21st Century,Models, Biological,Tibet},
pages = {4309-14},
volume = {110},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3600495&tool=pmcentrez&rendertype=abstract},
month = {3},
day = {12},
id = {4b196d1d-2802-39a5-a05a-1248ce2420b0},
created = {2015-05-08T02:33:35.000Z},
accessed = {2014-11-03},
file_attached = {true},
profile_id = {f8c267c4-4c39-31dc-80fa-3a9691373386},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2015-05-08T10:27:30.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {As the Earth's third pole, the Tibetan Plateau has experienced a pronounced warming in the past decades. Recent studies reported that the start of the vegetation growing season (SOS) in the Plateau showed an advancing trend from 1982 to the late 1990s and a delay from the late 1990s to 2006. However, the findings regarding the SOS delay in the later period have been questioned, and the reasons causing the delay remain unknown. Here we explored the alpine vegetation SOS in the Plateau from 1982 to 2011 by integrating three long-term time-series datasets of Normalized Difference Vegetation Index (NDVI): Global Inventory Modeling and Mapping Studies (GIMMS, 1982-2006), SPOT VEGETATION (SPOT-VGT, 1998-2011), and Moderate Resolution Imaging Spectroradiometer (MODIS, 2000-2011). We found GIMMS NDVI in 2001-2006 differed substantially from SPOT-VGT and MODIS NDVIs and may have severe data quality issues in most parts of the western Plateau. By merging GIMMS-based SOSs from 1982 to 2000 with SPOT-VGT-based SOSs from 2001 to 2011 we found the alpine vegetation SOS in the Plateau experienced a continuous advancing trend at a rate of ∼1.04 d·y(-1) from 1982 to 2011, which was consistent with observed warming in springs and winters. The satellite-derived SOSs were proven to be reliable with observed phenology data at 18 sites from 2003 to 2011; however, comparison of their trends was inconclusive due to the limited temporal coverage of the observed data. Longer-term observed data are still needed to validate the phenology trend in the future.},
bibtype = {article},
author = {Zhang, Geli and Zhang, Yangjian and Dong, Jinwei and Xiao, Xiangming},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {11}
}Structure-dynamics relationship in coherent transport through disordered systems. Mostarda, S., Levi, F., Prada-Gracia, D., Mintert, F., & Rao, F. Nature Communications, 4:2296, Nature Publishing Group, 2013.
Paper Website abstract bibtex
Paper Website abstract bibtex Quantum transport is strongly influenced by interference with phase relations that depend on the scattering medium. As even small changes in the geometry of the medium can turn constructive interference to destructive, a clear relation between structure and fast, efficient transport is difficult to identify. Here we present a complex network analysis of quantum transport through disordered systems to elucidate the relationship between transport efficiency and structural organization. Evidence is provided for the emergence of structural classes with different geometries but similar high efficiency. Specifically, a structural motif characterized by pair sites, which are not actively participating to the dynamics, renders transport properties robust against perturbations. Our results pave the way for a systematic rationalization of the design principles behind highly efficient transport, which is of paramount importance for technological applications as well as to address transport robustness in natural-light-harvesting complexes.
@article{
title = {Structure-dynamics relationship in coherent transport through disordered systems.},
type = {article},
year = {2013},
identifiers = {[object Object]},
keywords = {Biological Transport,Light-Harvesting Protein Complexes,Light-Harvesting Protein Complexes: metabolism,Models,Molecular,Quantum Theory,Structure-Activity Relationship},
pages = {2296},
volume = {4},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/23921601},
publisher = {Nature Publishing Group},
id = {3f87e940-7af8-3bcb-bed4-3d31f6134410},
created = {2015-09-16T08:16:33.000Z},
file_attached = {true},
profile_id = {11c803fe-e925-36b5-adf2-c0ec2ac564b7},
last_modified = {2017-03-15T14:59:46.881Z},
read = {false},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
citation_key = {Mostarda2013},
folder_uuids = {a7bd5854-c2ae-4826-9510-66f14b2d0d0c},
private_publication = {false},
abstract = {Quantum transport is strongly influenced by interference with phase relations that depend on the scattering medium. As even small changes in the geometry of the medium can turn constructive interference to destructive, a clear relation between structure and fast, efficient transport is difficult to identify. Here we present a complex network analysis of quantum transport through disordered systems to elucidate the relationship between transport efficiency and structural organization. Evidence is provided for the emergence of structural classes with different geometries but similar high efficiency. Specifically, a structural motif characterized by pair sites, which are not actively participating to the dynamics, renders transport properties robust against perturbations. Our results pave the way for a systematic rationalization of the design principles behind highly efficient transport, which is of paramount importance for technological applications as well as to address transport robustness in natural-light-harvesting complexes.},
bibtype = {article},
author = {Mostarda, Stefano and Levi, Federico and Prada-Gracia, Diego and Mintert, Florian and Rao, Francesco},
journal = {Nature Communications}
}An environmental scan of an aged care workplace using the PARiHS model: assessing preparedness for change. Gibb, H. Journal of nursing management, 21(2):293-303, Blackwell Publishing Ltd, 3, 2013.
abstract bibtex
abstract bibtex
AIM: The environmental scan aimed to deepen our understanding of the aged care work culture and to ascertain the readiness of the workers to advance towards team-based quality care provision. BACKGROUND: The workplace context was a high-care unit within a large residential aged care facility. METHODS: We used the Promoting Action on Research Implementation in Health Services (PARiHS) framework to assess workplace readiness via interviews, individual surveys and observation of practice. RESULTS: A profile of current culture emerged as mutually supportive and task focused, but at the same time lacking corporate team features of shared decision-making and feedback for practice improvement. However, latent within the frontline leaders and personal care staff, there was evidence of some embedded knowledge and capacity for corporate team performance. CONCLUSIONS: This study has validated an evidence-based method for conducting environmental scanning in aged care, recommended before any major change is introduced. IMPLICATIONS FOR NURSING MANAGEMENT: Environmental scanning helps gauge workforce capacity and limitations; this information can enable managers to capitalize on identified cultural strengths to fortify change and avoid pitfalls of personal and collective vulnerabilities.
@article{
title = {An environmental scan of an aged care workplace using the PARiHS model: assessing preparedness for change},
type = {article},
year = {2013},
identifiers = {[object Object]},
keywords = {Aged, 80 and over,Focus Groups,Homes for the Aged/organization & administration/s,Humans,Models, Theoretical,Organizational Culture,Organizational Innovation,Patient Care Team,Workplace},
pages = {293-303},
volume = {21},
month = {3},
publisher = {Blackwell Publishing Ltd},
city = {Research and Development Unit, Helping Hand Aged Inc Care, North Adelaide, South Australia, Australia. hgibb@helpinghand.org.au},
id = {3a4428f8-5de6-3767-8fb4-6836305e2b86},
created = {2016-08-21T22:18:08.000Z},
file_attached = {false},
profile_id = {217ced55-4c79-38dc-838b-4b5ea8df5597},
group_id = {408d37d9-5f1b-3398-a9f5-5c1a487116d4},
last_modified = {2017-03-14T09:54:45.334Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {JOUR},
notes = {ID: 68477; CI: (c) 2012; JID: 9306050; 2012/06/14 [aheadofprint]; ppublish},
folder_uuids = {cf78c658-6722-4a88-93c6-6a86fb55df05},
private_publication = {false},
abstract = {AIM: The environmental scan aimed to deepen our understanding of the aged care work culture and to ascertain the readiness of the workers to advance towards team-based quality care provision. BACKGROUND: The workplace context was a high-care unit within a large residential aged care facility. METHODS: We used the Promoting Action on Research Implementation in Health Services (PARiHS) framework to assess workplace readiness via interviews, individual surveys and observation of practice. RESULTS: A profile of current culture emerged as mutually supportive and task focused, but at the same time lacking corporate team features of shared decision-making and feedback for practice improvement. However, latent within the frontline leaders and personal care staff, there was evidence of some embedded knowledge and capacity for corporate team performance. CONCLUSIONS: This study has validated an evidence-based method for conducting environmental scanning in aged care, recommended before any major change is introduced. IMPLICATIONS FOR NURSING MANAGEMENT: Environmental scanning helps gauge workforce capacity and limitations; this information can enable managers to capitalize on identified cultural strengths to fortify change and avoid pitfalls of personal and collective vulnerabilities.},
bibtype = {article},
author = {Gibb, H},
journal = {Journal of nursing management},
number = {2}
}Economic Impacts of Using Switchgrass as a Feedstock for Ethanol Production: A Case Study Located in East Tennessee. English, B. C., Yu, Edward, T.H., Larson, J. A., Menard, Jamey, R., & Gao, Y. Economics Research International, 2013:14, December, 2013.
Paper doi abstract bibtex
Paper doi abstract bibtex One of the major motivations to establish a biobased energy sector in the United States is to promote economic development in the rural areas of the nation. This study estimated the economic impact of investing and operating a switchgrass-based ethanol plant in East Tennessee. Applying a spatially oriented mixed-integer mathematical programming model, we first determined the location of biorefinery, feedstock draw area, and the resources used in various feedstock supply systems by minimizing the total plant gate cost of feedstock. Based on the model output, an input-output model was utilized to determine the total economic impact, including direct, indirect, and induced effects of feedstock investment and annual production in the study region. Moreover, the economic impact of ethanol plant investment and annual conversion operation was analyzed. Results suggest that the total annual expenditures in an unprotected large round bale system generated a total \$92.5 million in economic output within the 13 counties of East Tennessee. In addition, an estimated \$234 million in overall economic output was generated through the operation of the biorefinery. This research showed that the least-cost configuration of the feedstock supply chain influenced the levels and types of economic impact of biorefinery.
@article{ english_economic_2013,
title = {Economic {Impacts} of {Using} {Switchgrass} as a {Feedstock} for {Ethanol} {Production}: {A} {Case} {Study} {Located} in {East} {Tennessee}},
volume = {2013},
issn = {2090-2123},
url = {http://dx.doi.org/10.1155/2013/138485},
doi = {10.1155/2013/138485},
abstract = {One of the major motivations to establish a biobased energy sector in the United States is to promote economic development in the rural areas of the nation. This study estimated the economic impact of investing and operating a switchgrass-based ethanol plant in East Tennessee. Applying a spatially oriented mixed-integer mathematical programming model, we first determined the location of biorefinery, feedstock draw area, and the resources used in various feedstock supply systems by minimizing the total plant gate cost of feedstock. Based on the model output, an input-output model was utilized to determine the total economic impact, including direct, indirect, and induced effects of feedstock investment and annual production in the study region. Moreover, the economic impact of ethanol plant investment and annual conversion operation was analyzed. Results suggest that the total annual expenditures in an unprotected large round bale system generated a total \$92.5 million in economic output within the 13 counties of East Tennessee. In addition, an estimated \$234 million in overall economic output was generated through the operation of the biorefinery. This research showed that the least-cost configuration of the feedstock supply chain influenced the levels and types of economic impact of biorefinery.},
journal = {Economics Research International},
author = {English, Burton C. and Yu, Tun-Hsiang Edward and Larson, James A. and Menard, R. Jamey and Gao, Yuan},
month = {December},
year = {2013},
keywords = {BIOFUELS, Bioenergy, Economic indicators, Economics, Farm inputs, Industry, Land Use, Models, Panicum virgatum, Storage},
pages = {14}
}Human and natural influences on the changing thermal structure of the atmosphere. Santer, B., D., Painter, J., F., Bonfils, C., Mears, C., a., Solomon, S., Wigley, T., M., L., Gleckler, P., J., Schmidt, G., a., Doutriaux, C., Gillett, N., P., Taylor, K., E., Thorne, P., W., & Wentz, F., J. Proceedings of the National Academy of Sciences of the United States of America, 110(43):17235-40, 10, 2013.
Paper Website abstract bibtex
Paper Website abstract bibtex Since the late 1970s, satellite-based instruments have monitored global changes in atmospheric temperature. These measurements reveal multidecadal tropospheric warming and stratospheric cooling, punctuated by short-term volcanic signals of reverse sign. Similar long- and short-term temperature signals occur in model simulations driven by human-caused changes in atmospheric composition and natural variations in volcanic aerosols. Most previous comparisons of modeled and observed atmospheric temperature changes have used results from individual models and individual observational records. In contrast, we rely on a large multimodel archive and multiple observational datasets. We show that a human-caused latitude/altitude pattern of atmospheric temperature change can be identified with high statistical confidence in satellite data. Results are robust to current uncertainties in models and observations. Virtually all previous research in this area has attempted to discriminate an anthropogenic signal from internal variability. Here, we present evidence that a human-caused signal can also be identified relative to the larger "total" natural variability arising from sources internal to the climate system, solar irradiance changes, and volcanic forcing. Consistent signal identification occurs because both internal and total natural variability (as simulated by state-of-the-art models) cannot produce sustained global-scale tropospheric warming and stratospheric cooling. Our results provide clear evidence for a discernible human influence on the thermal structure of the atmosphere.
@article{
title = {Human and natural influences on the changing thermal structure of the atmosphere.},
type = {article},
year = {2013},
identifiers = {[object Object]},
keywords = {Atmosphere,Atmosphere: chemistry,Climate,Computer Simulation,Ecosystem,Global Warming,Humans,Models, Theoretical,Sunlight,Temperature,Volcanic Eruptions},
pages = {17235-40},
volume = {110},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3808612&tool=pmcentrez&rendertype=abstract},
month = {10},
day = {22},
id = {791a92c6-8675-30af-b586-472dd6c42e45},
created = {2015-05-08T02:31:45.000Z},
accessed = {2014-01-23},
file_attached = {true},
profile_id = {f8c267c4-4c39-31dc-80fa-3a9691373386},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2015-05-08T09:06:22.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {Since the late 1970s, satellite-based instruments have monitored global changes in atmospheric temperature. These measurements reveal multidecadal tropospheric warming and stratospheric cooling, punctuated by short-term volcanic signals of reverse sign. Similar long- and short-term temperature signals occur in model simulations driven by human-caused changes in atmospheric composition and natural variations in volcanic aerosols. Most previous comparisons of modeled and observed atmospheric temperature changes have used results from individual models and individual observational records. In contrast, we rely on a large multimodel archive and multiple observational datasets. We show that a human-caused latitude/altitude pattern of atmospheric temperature change can be identified with high statistical confidence in satellite data. Results are robust to current uncertainties in models and observations. Virtually all previous research in this area has attempted to discriminate an anthropogenic signal from internal variability. Here, we present evidence that a human-caused signal can also be identified relative to the larger "total" natural variability arising from sources internal to the climate system, solar irradiance changes, and volcanic forcing. Consistent signal identification occurs because both internal and total natural variability (as simulated by state-of-the-art models) cannot produce sustained global-scale tropospheric warming and stratospheric cooling. Our results provide clear evidence for a discernible human influence on the thermal structure of the atmosphere.},
bibtype = {article},
author = {Santer, Benjamin D and Painter, Jeffrey F and Bonfils, Céline and Mears, Carl a and Solomon, Susan and Wigley, Tom M L and Gleckler, Peter J and Schmidt, Gavin a and Doutriaux, Charles and Gillett, Nathan P and Taylor, Karl E and Thorne, Peter W and Wentz, Frank J},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {43}
}Simple computation of reaction-diffusion processes on point clouds. Macdonald, C., B., Merriman, B., & Ruuth, S., J. Proceedings of the National Academy of Sciences of the United States of America, 110(23):9209-14, National Academy of Sciences, 6, 2013.
Paper Website abstract bibtex
Paper Website abstract bibtex The study of reaction-diffusion processes is much more complicated on general curved surfaces than on standard Cartesian coordinate spaces. Here we show how to formulate and solve systems of reaction-diffusion equations on surfaces in an extremely simple way, using only the standard Cartesian form of differential operators, and a discrete unorganized point set to represent the surface. Our method decouples surface geometry from the underlying differential operators. As a consequence, it becomes possible to formulate and solve rather general reaction-diffusion equations on general surfaces without having to consider the complexities of differential geometry or sophisticated numerical analysis. To illustrate the generality of the method, computations for surface diffusion, pattern formation, excitable media, and bulk-surface coupling are provided for a variety of complex point cloud surfaces.
@article{
title = {Simple computation of reaction-diffusion processes on point clouds.},
type = {article},
year = {2013},
identifiers = {[object Object]},
keywords = {Algorithms,Chemical Processes,Diffusion,Mathematics,Mathematics: methods,Models,Theoretical},
pages = {9209-14},
volume = {110},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/23690616,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3677480,http://www.pnas.org/content/110/23/9209.short},
month = {6},
publisher = {National Academy of Sciences},
day = {4},
id = {211ab4f0-8de4-3c16-9e7b-607c00a9239e},
created = {2017-09-01T09:28:56.947Z},
accessed = {2017-08-31},
file_attached = {true},
profile_id = {df40269a-9b9a-3554-bc8a-43d01382c51a},
group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
last_modified = {2017-09-01T12:38:21.645Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Macdonald2013},
folder_uuids = {8d6d2c18-9ff8-43ee-9c8c-92ccbd4f5542},
private_publication = {false},
abstract = {The study of reaction-diffusion processes is much more complicated on general curved surfaces than on standard Cartesian coordinate spaces. Here we show how to formulate and solve systems of reaction-diffusion equations on surfaces in an extremely simple way, using only the standard Cartesian form of differential operators, and a discrete unorganized point set to represent the surface. Our method decouples surface geometry from the underlying differential operators. As a consequence, it becomes possible to formulate and solve rather general reaction-diffusion equations on general surfaces without having to consider the complexities of differential geometry or sophisticated numerical analysis. To illustrate the generality of the method, computations for surface diffusion, pattern formation, excitable media, and bulk-surface coupling are provided for a variety of complex point cloud surfaces.},
bibtype = {article},
author = {Macdonald, Colin B and Merriman, Barry and Ruuth, Steven J},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {23}
}2012 (5)
A significant role for nitrate and peroxide groups on indoor secondary organic aerosol. Carslaw, N., Mota, T., Jenkin, M., E., Barley, M., H., & McFiggans, G. Environmental science & technology, 46(17):9290-8, 9, 2012.
Paper Website abstract bibtex
Paper Website abstract bibtex This paper reports indoor secondary organic aerosol, SOA, composition based on the results from an improved model for indoor air chemistry. The model uses a detailed chemical mechanism that is near-explicit to describe the gas-phase degradation of relevant indoor VOC species. In addition, gas-to-particle partitioning is included for oxygenated products formed from the degradation of limonene, the most ubiquitous terpenoid species in the indoor environment. The detail inherent in the chemical mechanism permits the indoor SOA composition to be reported in greater detail than currently possible using experimental techniques. For typical indoor conditions in the suburban UK, SOA concentrations are ~1 μg m(-3) and dominated by nitrated material (~85%), with smaller contributions from peroxide (12%), carbonyl (3%), and acidic (1%) material. During cleaning activities, SOA concentrations can reach 20 μg m(-3) with the composition dominated by peroxide material (73%), with a smaller contribution from nitrated material (21%). The relative importance of these different moieties depends crucially (in order) on the outdoor concentration of O(3), the deposition rates employed and the scaling factor value applied to the partitioning coefficient. There are currently few studies that report observation of aerosol composition indoors, and most of these have been carried out under conditions that are not directly relevant. This study highlights the need to investigate SOA composition in real indoor environments. Further, there is a need to measure deposition rates for key indoor air species on relevant indoor surfaces and to reduce the uncertainties that still exist in gas-to-particle phase parametrization for both indoor and outdoor air chemistry models.
@article{
title = {A significant role for nitrate and peroxide groups on indoor secondary organic aerosol.},
type = {article},
year = {2012},
identifiers = {[object Object]},
keywords = {Aerosols,Aerosols: analysis,Air Pollutants,Air Pollutants: analysis,Air Pollution,Chemical,Environmental Monitoring,Indoor,Indoor: analysis,Models,Nitrates,Nitrates: analysis,Peroxides,Peroxides: analysis},
pages = {9290-8},
volume = {46},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/22881450},
month = {9},
day = {4},
id = {fd411c91-c498-3878-b89c-bf763e7e96ee},
created = {2015-05-07T15:03:43.000Z},
file_attached = {true},
profile_id = {81af7548-db00-3f00-bfa0-1774347c59e1},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2015-05-07T16:01:31.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {This paper reports indoor secondary organic aerosol, SOA, composition based on the results from an improved model for indoor air chemistry. The model uses a detailed chemical mechanism that is near-explicit to describe the gas-phase degradation of relevant indoor VOC species. In addition, gas-to-particle partitioning is included for oxygenated products formed from the degradation of limonene, the most ubiquitous terpenoid species in the indoor environment. The detail inherent in the chemical mechanism permits the indoor SOA composition to be reported in greater detail than currently possible using experimental techniques. For typical indoor conditions in the suburban UK, SOA concentrations are ~1 μg m(-3) and dominated by nitrated material (~85%), with smaller contributions from peroxide (12%), carbonyl (3%), and acidic (1%) material. During cleaning activities, SOA concentrations can reach 20 μg m(-3) with the composition dominated by peroxide material (73%), with a smaller contribution from nitrated material (21%). The relative importance of these different moieties depends crucially (in order) on the outdoor concentration of O(3), the deposition rates employed and the scaling factor value applied to the partitioning coefficient. There are currently few studies that report observation of aerosol composition indoors, and most of these have been carried out under conditions that are not directly relevant. This study highlights the need to investigate SOA composition in real indoor environments. Further, there is a need to measure deposition rates for key indoor air species on relevant indoor surfaces and to reduce the uncertainties that still exist in gas-to-particle phase parametrization for both indoor and outdoor air chemistry models.},
bibtype = {article},
author = {Carslaw, Nicola and Mota, Tiago and Jenkin, Michael E and Barley, Mark H and McFiggans, Gordon},
journal = {Environmental science & technology},
number = {17}
}Advances in the science and application of body composition measurement. Baracos, V., Caserotti, P., Earthman, C. P., Fields, D., Gallagher, D., Hall, K. D., Heymsfield, S. B., Müller, M. J., Rosen, A. N., Pichard, C., Redman, L. M., Shen, W., Shepherd, J. A., & Thomas, D. JPEN. Journal of parenteral and enteral nutrition, 36(1):96–107, January, 2012.
doi bibtex
doi bibtex
@article{baracos_advances_2012,
title = {Advances in the science and application of body composition measurement},
volume = {36},
issn = {1941-2444},
doi = {10.1177/0148607111417448},
language = {eng},
number = {1},
journal = {JPEN. Journal of parenteral and enteral nutrition},
author = {Baracos, Vickie and Caserotti, Paolo and Earthman, Carrie P. and Fields, David and Gallagher, Dympna and Hall, Kevin D. and Heymsfield, Steven B. and Müller, Manfred J. and Rosen, Antonella Napolitano and Pichard, Claude and Redman, Leanne M. and Shen, Wei and Shepherd, John A. and Thomas, Diana},
month = jan,
year = {2012},
pmid = {22235108},
pmcid = {PMC4422066},
keywords = {Absorptiometry, Photon, Acute Disease, Adipose Tissue, Aging, Body Composition, Chronic Disease, Dielectric Spectroscopy, Energy Metabolism, Humans, Magnetic Resonance Imaging, Metabolic Diseases, Models, Biological, Neoplasms},
pages = {96--107}
}The scaffolding and signalling functions of a localization factor impact polar development. Curtis, P. D, Quardokus, E. M, Lawler, M. L, Guo, X., Klein, D., Chen, J. C, Arnold, R. J, & Brun, Y. V Molecular microbiology, 84(4):712--735, May, 2012.
doi abstract bibtex
doi abstract bibtex
In the differentiating alphaproteobacterium Caulobacter crescentus, organelle synthesis at cell poles is critical to forming different progeny after cell division. Co-ordination of polar organelle synthesis, including pili and holdfast, and flagellum ejection, is mediated in part by the scaffolding protein PodJ. At the time of cell division, PodJ undergoes regulated processing to a short form that persists at the flagellar pole of swarmer cells. This study analyses how PodJ's role in structural and signalling protein localization impacts organelle synthesis. A PodJ mutant with an internal deletion exhibits reduced sensitivity to pili-tropic phage ΦCbK, resulting from reduced pilA gene expression, which can be linked to altered signalling protein localization. The phage sensitivity defect of a ΔpodJ mutant can be partially suppressed by ectopic pilA expression. Induction of PodJ processing, by manipulation of podJ itself or controlled perP expression, resulted in decreased pilus biogenesis and, when coupled with a podJ mutation that reduced pilA expression, led to complete loss of phage sensitivity. As a whole, the results show that PodJ's scaffolding role for structural and signalling proteins both contribute to flagellar pole organelle development.
@article{curtis_scaffolding_2012,
title = {The scaffolding and signalling functions of a localization factor impact polar development},
volume = {84},
issn = {1365-2958},
doi = {10.1111/j.1365-2958.2012.08055.x},
abstract = {In the differentiating alphaproteobacterium Caulobacter crescentus, organelle synthesis at cell poles is critical to forming different progeny after cell division. Co-ordination of polar organelle synthesis, including pili and holdfast, and flagellum ejection, is mediated in part by the scaffolding protein PodJ. At the time of cell division, PodJ undergoes regulated processing to a short form that persists at the flagellar pole of swarmer cells. This study analyses how PodJ's role in structural and signalling protein localization impacts organelle synthesis. A PodJ mutant with an internal deletion exhibits reduced sensitivity to pili-tropic phage ΦCbK, resulting from reduced pilA gene expression, which can be linked to altered signalling protein localization. The phage sensitivity defect of a ΔpodJ mutant can be partially suppressed by ectopic pilA expression. Induction of PodJ processing, by manipulation of podJ itself or controlled perP expression, resulted in decreased pilus biogenesis and, when coupled with a podJ mutation that reduced pilA expression, led to complete loss of phage sensitivity. As a whole, the results show that PodJ's scaffolding role for structural and signalling proteins both contribute to flagellar pole organelle development.},
number = {4},
journal = {Molecular microbiology},
author = {Curtis, Patrick D and Quardokus, Ellen M and Lawler, Melanie L and Guo, Xiaoyun and Klein, David and Chen, Joseph C and Arnold, Randy J and Brun, Yves V},
month = may,
year = {2012},
pmid = {22512778},
keywords = {Amino Acid Sequence, Bacterial Proteins, Bacteriophages, Caulobacter crescentus, Cell Division, Fimbriae, Bacterial, Gene expression, Membrane Proteins, Models, Biological, Molecular Sequence Data, Sequence Deletion, Suppression, Genetic},
pages = {712--735}
}Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes. Höfinger, S., Yamamoto, E., Hirano, Y., Zerbetto, F., Narumi, T., Yasuoka, K., & Yasui, M. Biochim. Biophys. Acta, 1818(9):2234-43, 9, 2012.
Paper abstract bibtex
Paper abstract bibtex A limited class of aquaporins has been described to form regular arrays and junctions in membranes. The biological significance of these structures, however, remains uncertain. Here we analyze the underlying physical principles with the help of a computational procedure that takes into account protein-protein as well as protein-membrane interactions. Experimentally observed array/junction structures are systematically (dis)assembled and major driving forces identified. Aquaporin 4 was found to be markedly different from the non-junction forming aquaporin 1. The environmental stabilization resulting from embedding into the biomembrane was identified as the main driving force. This highlights the role of protein-membrane interactions in aquaporin 4. Analysis of the type presented here can help to decipher the biological role of membrane arrays and junctions formed by aquaporin.
@article{
id = {c833f827-d0f9-33bf-86c2-b8903285f617},
title = {Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes.},
type = {article},
year = {2012},
identifiers = {[object Object]},
keywords = {Animals,Aquaporin 4,Aquaporin 4: chemistry,Biophysics,Biophysics: methods,Cattle,Cell Membrane,Cell Membrane: metabolism,Lipids,Lipids: chemistry,Models, Molecular,Molecular Conformation,Molecular Dynamics Simulation,Protein Binding,Protein Interaction Mapping,Protein Interaction Mapping: methods,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Rats,Thermodynamics,Water,Water: chemistry},
created = {2014-12-10T04:09:01.000Z},
pages = {2234-43},
volume = {1818},
websites = {http://www.sciencedirect.com/science/article/pii/S0005273612001319},
month = {9},
accessed = {2014-06-23},
file_attached = {true},
profile_id = {6708b05a-e661-38c6-9bb8-cf4f304b6385},
group_id = {424eb3e1-9b50-35ed-91d3-65c78c3164d7},
last_modified = {2014-12-10T09:11:31.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Hofinger2012a},
abstract = {A limited class of aquaporins has been described to form regular arrays and junctions in membranes. The biological significance of these structures, however, remains uncertain. Here we analyze the underlying physical principles with the help of a computational procedure that takes into account protein-protein as well as protein-membrane interactions. Experimentally observed array/junction structures are systematically (dis)assembled and major driving forces identified. Aquaporin 4 was found to be markedly different from the non-junction forming aquaporin 1. The environmental stabilization resulting from embedding into the biomembrane was identified as the main driving force. This highlights the role of protein-membrane interactions in aquaporin 4. Analysis of the type presented here can help to decipher the biological role of membrane arrays and junctions formed by aquaporin.},
bibtype = {article},
author = {Höfinger, Siegfried and Yamamoto, Eiji and Hirano, Yoshinori and Zerbetto, Francesco and Narumi, Tetsu and Yasuoka, Kenji and Yasui, Masato},
journal = {Biochim. Biophys. Acta},
number = {9}
}A simple mathematical model based on the cancer stem cell hypothesis suggests kinetic commonalities in solid tumor growth. Molina-Peña, R. & Álvarez, M., M. PloS one, 7(2):e26233, 2012.
Paper Website abstract bibtex
Paper Website abstract bibtex BACKGROUND: The Cancer Stem Cell (CSC) hypothesis has gained credibility within the cancer research community. According to this hypothesis, a small subpopulation of cells within cancerous tissues exhibits stem-cell-like characteristics and is responsible for the maintenance and proliferation of cancer.\n\nMETHODOLOGIES/PRINCIPAL FINDINGS: We present a simple compartmental pseudo-chemical mathematical model for tumor growth, based on the CSC hypothesis, and derived using a "chemical reaction" approach. We defined three cell subpopulations: CSCs, transit progenitor cells, and differentiated cells. Each event related to cell division, differentiation, or death is then modeled as a chemical reaction. The resulting set of ordinary differential equations was numerically integrated to describe the time evolution of each cell subpopulation and the overall tumor growth. The parameter space was explored to identify combinations of parameter values that produce biologically feasible and consistent scenarios.\n\nCONCLUSIONS/SIGNIFICANCE: Certain kinetic relationships apparently must be satisfied to sustain solid tumor growth and to maintain an approximate constant fraction of CSCs in the tumor lower than 0.01 (as experimentally observed): (a) the rate of symmetrical and asymmetrical CSC renewal must be in the same order of magnitude; (b) the intrinsic rate of renewal and differentiation of progenitor cells must be half an order of magnitude higher than the corresponding intrinsic rates for cancer stem cells; (c) the rates of apoptosis of the CSC, transit amplifying progenitor (P) cells, and terminally differentiated (D) cells must be progressively higher by approximately one order of magnitude. Simulation results were consistent with reports that have suggested that encouraging CSC differentiation could be an effective therapeutic strategy for fighting cancer in addition to selective killing or inhibition of symmetric division of CSCs.
@article{
title = {A simple mathematical model based on the cancer stem cell hypothesis suggests kinetic commonalities in solid tumor growth.},
type = {article},
year = {2012},
identifiers = {[object Object]},
keywords = {Cell Death,Cell Proliferation,Databases as Topic,Disease Progression,Humans,Kinetics,Linear Models,Models, Biological,Neoplasms,Neoplasms: pathology,Neoplastic Stem Cells,Neoplastic Stem Cells: pathology},
pages = {e26233},
volume = {7},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3281810&tool=pmcentrez&rendertype=abstract},
id = {897c93cd-75db-3e30-92e4-b13bd2cc635e},
created = {2016-02-15T11:48:13.000Z},
file_attached = {true},
profile_id = {7ff501d0-9b93-3c0b-8624-3a271e09e231},
group_id = {e5b5af30-88cd-38f9-9b93-f6ad4b7f3758},
last_modified = {2017-07-17T10:42:05.204Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Molina-Pena2012},
abstract = {BACKGROUND: The Cancer Stem Cell (CSC) hypothesis has gained credibility within the cancer research community. According to this hypothesis, a small subpopulation of cells within cancerous tissues exhibits stem-cell-like characteristics and is responsible for the maintenance and proliferation of cancer.\n\nMETHODOLOGIES/PRINCIPAL FINDINGS: We present a simple compartmental pseudo-chemical mathematical model for tumor growth, based on the CSC hypothesis, and derived using a "chemical reaction" approach. We defined three cell subpopulations: CSCs, transit progenitor cells, and differentiated cells. Each event related to cell division, differentiation, or death is then modeled as a chemical reaction. The resulting set of ordinary differential equations was numerically integrated to describe the time evolution of each cell subpopulation and the overall tumor growth. The parameter space was explored to identify combinations of parameter values that produce biologically feasible and consistent scenarios.\n\nCONCLUSIONS/SIGNIFICANCE: Certain kinetic relationships apparently must be satisfied to sustain solid tumor growth and to maintain an approximate constant fraction of CSCs in the tumor lower than 0.01 (as experimentally observed): (a) the rate of symmetrical and asymmetrical CSC renewal must be in the same order of magnitude; (b) the intrinsic rate of renewal and differentiation of progenitor cells must be half an order of magnitude higher than the corresponding intrinsic rates for cancer stem cells; (c) the rates of apoptosis of the CSC, transit amplifying progenitor (P) cells, and terminally differentiated (D) cells must be progressively higher by approximately one order of magnitude. Simulation results were consistent with reports that have suggested that encouraging CSC differentiation could be an effective therapeutic strategy for fighting cancer in addition to selective killing or inhibition of symmetric division of CSCs.},
bibtype = {article},
author = {Molina-Peña, Rodolfo and Álvarez, Mario Moisés},
journal = {PloS one},
number = {2}
}2011 (5)
Microscale 3-D hydrogel scaffold for biomimetic gastrointestinal (GI) tract model. Sung, J., H., Yu, J., Luo, D., Shuler, M., L., & March, J., C. Lab on a chip, 11(3):389-92, The Royal Society of Chemistry, 2, 2011.
Website abstract bibtex
Website abstract bibtex Here we describe a simple and efficient method for fabricating natural and synthetic hydrogels into 3-D geometries with high aspect ratio and curvature. Fabricating soft hydrogels into such shapes using conventional techniques has been extremely difficult. Combination of laser ablation and sacrificial molding technique using calcium alginate minimizes the stress associated with separating the mold from the hydrogel structure, and therefore allows fabrication of complex structures without damaging them. As a demonstration of this technique, we have fabricated a microscale collagen structure mimicking the actual density and size of human intestinal villi. Colon carcinoma cell line, Caco-2 cells, was seeded onto the structure and cultured for 3 weeks until the whole structure was covered, forming finger-like structures mimicking the intestinal villi covered with epithelial cells. This method will enable construction of in vitro tissue models with physiologically realistic geometries at microscale resolutions.
@article{
title = {Microscale 3-D hydrogel scaffold for biomimetic gastrointestinal (GI) tract model.},
type = {article},
year = {2011},
identifiers = {[object Object]},
keywords = {Biomimetics,Biomimetics: methods,Caco-2 Cells,Cell Culture Techniques,Cells, Cultured,Collagen,Collagen: chemistry,Gastrointestinal Tract,Gastrointestinal Tract: cytology,Humans,Hydrogels,Hydrogels: chemistry,Microtechnology,Microtechnology: methods,Models, Biological},
pages = {389-92},
volume = {11},
websites = {http://pubs.rsc.org/en/content/articlehtml/2011/lc/c0lc00273a},
month = {2},
publisher = {The Royal Society of Chemistry},
day = {7},
id = {2e67e193-bbd9-35f1-9ead-02d11287a327},
created = {2016-06-24T20:49:43.000Z},
accessed = {2014-11-22},
file_attached = {false},
profile_id = {954a987f-819f-3985-95a4-2991e0cf0552},
group_id = {8440dcff-74cc-3783-aef7-fe2749cfc7ef},
last_modified = {2016-06-24T20:49:43.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Sung2011},
language = {en},
abstract = {Here we describe a simple and efficient method for fabricating natural and synthetic hydrogels into 3-D geometries with high aspect ratio and curvature. Fabricating soft hydrogels into such shapes using conventional techniques has been extremely difficult. Combination of laser ablation and sacrificial molding technique using calcium alginate minimizes the stress associated with separating the mold from the hydrogel structure, and therefore allows fabrication of complex structures without damaging them. As a demonstration of this technique, we have fabricated a microscale collagen structure mimicking the actual density and size of human intestinal villi. Colon carcinoma cell line, Caco-2 cells, was seeded onto the structure and cultured for 3 weeks until the whole structure was covered, forming finger-like structures mimicking the intestinal villi covered with epithelial cells. This method will enable construction of in vitro tissue models with physiologically realistic geometries at microscale resolutions.},
bibtype = {article},
author = {Sung, Jong Hwan and Yu, Jiajie and Luo, Dan and Shuler, Michael L and March, John C},
journal = {Lab on a chip},
number = {3}
}COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Wang, J. Molecular Ecology Resources, 11(1):141–145, January, 2011.
doi abstract bibtex
doi abstract bibtex
The software package COANCESTRY implements seven relatedness estimators and three inbreeding estimators to estimate relatedness and inbreeding coefficients from multilocus genotype data. Two likelihood estimators that allow for inbred individuals and account for genotyping errors are for the first time included in this user-friendly program for PCs running Windows operating system. A simulation module is built in the program to simulate multilocus genotype data of individuals with a predefined relationship, and to compare the estimators and the simulated relatedness values to facilitate the selection of the best estimator in a particular situation. Bootstrapping and permutations are used to obtain the 95% confidence intervals of each relatedness or inbreeding estimate, and to test the difference in averages between groups.
@article{wang_coancestry:_2011,
title = {{COANCESTRY}: a program for simulating, estimating and analysing relatedness and inbreeding coefficients},
volume = {11},
issn = {1755-0998},
shorttitle = {{COANCESTRY}},
doi = {10.1111/j.1755-0998.2010.02885.x},
abstract = {The software package COANCESTRY implements seven relatedness estimators and three inbreeding estimators to estimate relatedness and inbreeding coefficients from multilocus genotype data. Two likelihood estimators that allow for inbred individuals and account for genotyping errors are for the first time included in this user-friendly program for PCs running Windows operating system. A simulation module is built in the program to simulate multilocus genotype data of individuals with a predefined relationship, and to compare the estimators and the simulated relatedness values to facilitate the selection of the best estimator in a particular situation. Bootstrapping and permutations are used to obtain the 95\% confidence intervals of each relatedness or inbreeding estimate, and to test the difference in averages between groups.},
language = {eng},
number = {1},
journal = {Molecular Ecology Resources},
author = {Wang, Jinliang},
month = jan,
year = {2011},
pmid = {21429111},
keywords = {Computer Simulation, Genetics, Population, Humans, Inbreeding, Models, Genetic, Pedigree, Software},
pages = {141--145}
}Key characteristics of knowledge transfer and exchange in healthcare: integrative literature review. Pentland, D., Forsyth, K., Maciver, D., Walsh, M., Murray, R., Irvine, L., & Sikora, S. Journal of Advanced Nursing, 67(7):1408–1425, 2011.
Paper doi bibtex
Paper doi bibtex @article{pentland_key_2011,
title = {Key characteristics of knowledge transfer and exchange in healthcare: integrative literature review},
volume = {67},
issn = {1365-2648},
shorttitle = {Key characteristics of knowledge transfer and exchange in healthcare},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2648.2011.05631.x},
doi = {10/bbmtr4},
language = {en},
number = {7},
urldate = {2019-01-13},
journal = {Journal of Advanced Nursing},
author = {Pentland, Duncan and Forsyth, Kirsty and Maciver, Donald and Walsh, Mike and Murray, Richard and Irvine, Linda and Sikora, Simon},
year = {2011},
keywords = {\#à lire 📖},
pages = {1408--1425}
}Bacillus thuringiensis: A story of a successful bioinsecticide. Bravo, A., Likitvivatanavong, S., Gill, S., S., & Soberón, M. Insect biochemistry and molecular biology, 41(7):423-31, 7, 2011.
Paper abstract bibtex
Paper abstract bibtex Bacillus thuringiensis (Bt) bacteria are insect pathogens that rely on insecticidal pore forming proteins known as Cry and Cyt toxins to kill their insect larval hosts. At least four different non-structurally related families of proteins form the Cry toxin group of toxins. The expression of certain Cry toxins in transgenic crops has contributed to an efficient control of insect pests resulting in a significant reduction in chemical insecticide use. The mode of action of the three domain Cry toxin family involves sequential interaction of these toxins with several insect midgut proteins facilitating the formation of a pre-pore oligomer structure and subsequent membrane insertion that leads to the killing of midgut insect cells by osmotic shock. In this manuscript we review recent progress in understanding the mode of action of this family of proteins in lepidopteran, dipteran and coleopteran insects. Interestingly, similar Cry-binding proteins have been identified in the three insect orders, as cadherin, aminopeptidase-N and alkaline phosphatase suggesting a conserved mode of action. Also, recent data on insect responses to Cry toxin attack is discussed. Finally, we review the different Bt based products, including transgenic crops, that are currently used in agriculture.
@article{
title = {Bacillus thuringiensis: A story of a successful bioinsecticide.},
type = {article},
year = {2011},
identifiers = {[object Object]},
keywords = {Alkaline Phosphatase,Alkaline Phosphatase: metabolism,Animals,Antigens, CD13,Antigens, CD13: metabolism,Bacillus thuringiensis,Bacillus thuringiensis: chemistry,Bacillus thuringiensis: metabolism,Bacillus thuringiensis: pathogenicity,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Bacterial Proteins: toxicity,Biological,Biological: methods,CD13,CD13: metabolism,Cadherins,Cadherins: metabolism,Genetically Modified,Insect Proteins,Insect Proteins: metabolism,Insecticides,Insects,Insects: drug effects,Insects: genetics,Insects: metabolism,Models, Molecular,Molecular,Pest Control, Biological,Pest Control, Biological: methods,Plants, Genetically Modified,Pore Forming Cytotoxic Proteins,Pore Forming Cytotoxic Proteins: chemistry,Pore Forming Cytotoxic Proteins: genetics,Pore Forming Cytotoxic Proteins: metabolism,Pore Forming Cytotoxic Proteins: toxicity,Protein Binding},
pages = {423-31},
volume = {41},
websites = {http://www.sciencedirect.com/science/article/pii/S0965174811000543},
month = {7},
id = {4357d3cc-03d4-3da2-ba93-373cd60c04e6},
created = {2015-07-07T19:45:57.000Z},
accessed = {2014-09-18},
file_attached = {true},
profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
last_modified = {2015-07-07T19:56:59.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Bravo2011},
abstract = {Bacillus thuringiensis (Bt) bacteria are insect pathogens that rely on insecticidal pore forming proteins known as Cry and Cyt toxins to kill their insect larval hosts. At least four different non-structurally related families of proteins form the Cry toxin group of toxins. The expression of certain Cry toxins in transgenic crops has contributed to an efficient control of insect pests resulting in a significant reduction in chemical insecticide use. The mode of action of the three domain Cry toxin family involves sequential interaction of these toxins with several insect midgut proteins facilitating the formation of a pre-pore oligomer structure and subsequent membrane insertion that leads to the killing of midgut insect cells by osmotic shock. In this manuscript we review recent progress in understanding the mode of action of this family of proteins in lepidopteran, dipteran and coleopteran insects. Interestingly, similar Cry-binding proteins have been identified in the three insect orders, as cadherin, aminopeptidase-N and alkaline phosphatase suggesting a conserved mode of action. Also, recent data on insect responses to Cry toxin attack is discussed. Finally, we review the different Bt based products, including transgenic crops, that are currently used in agriculture.},
bibtype = {article},
author = {Bravo, Alejandra and Likitvivatanavong, Supaporn and Gill, Sarjeet S and Soberón, Mario},
journal = {Insect biochemistry and molecular biology},
number = {7}
}Optimizing clinical environments for knowledge translation: strategies for nursing leaders. Scott, S., D., VandenBeld, B., & Cummings, G., G. Nursing leadership (Toronto, Ont.), 24(3):73-85, 2011.
Website abstract bibtex
Website abstract bibtex Using findings from our recent study that found that a context of uncertainty in the work environment hindered nurses' research utilization, we suggest strategies for nurse managers and leaders to optimize clinical environments and support efforts to put research into clinical practice (knowledge translation). Two important sources of uncertainty were the complexity of teamwork and inconsistency in management and leadership styles. To reduce the uncertainty arising from teamwork, we propose (a) clarifying nurses' scopes of practice, (b) increasing knowledge sharing through supporting journal clubs and enhanced computer access and (c) creating safe venues for multidisciplinary dialogue. To reduce uncertainty arising from variations in management and leadership, we propose (a) developing policies that enhance the consistency of leadership and clarify the strategic direction of the management team, (b) clearly communicating those policies to nurses and (c) providing explicit rationales for treatment changes. Small, incremental steps can be taken to realize substantive changes in clinical environments in order to optimize nursing work environments for knowledge translation.
@article{
title = {Optimizing clinical environments for knowledge translation: strategies for nursing leaders.},
type = {article},
year = {2011},
identifiers = {[object Object]},
keywords = {Evidence-Based Nursing,Humans,Models, Nursing,Models, Organizational,Nurse Administrators,Nursing, Supervisory,Organizational Culture,Patient Care Team,evidence based nursing,human,leadership,methodology,model,nonbiological model,nurse administrator,nursing,nursing research,organization,organization and management,patient care,psychological aspect,review,social environment,uncertainty},
pages = {73-85},
volume = {24},
websites = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84857378230&partnerID=40&md5=01153990c31273801d8559dc71b43d25},
city = {Affiliation: Faculty of Nursing, University of Alberta, Edmonton, AB, Canada.; Correspondence Address: Scott, S.D.email: Shannon.scott@ualberta.ca},
id = {dd7d9064-764b-3047-b4c2-a2fbc91d7611},
created = {2016-08-21T22:17:39.000Z},
file_attached = {false},
profile_id = {217ced55-4c79-38dc-838b-4b5ea8df5597},
group_id = {408d37d9-5f1b-3398-a9f5-5c1a487116d4},
last_modified = {2017-03-14T09:54:45.334Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {JOUR},
folder_uuids = {028056a6-dab5-46a4-b9bf-02542e7cfa2b},
private_publication = {false},
abstract = {Using findings from our recent study that found that a context of uncertainty in the work environment hindered nurses' research utilization, we suggest strategies for nurse managers and leaders to optimize clinical environments and support efforts to put research into clinical practice (knowledge translation). Two important sources of uncertainty were the complexity of teamwork and inconsistency in management and leadership styles. To reduce the uncertainty arising from teamwork, we propose (a) clarifying nurses' scopes of practice, (b) increasing knowledge sharing through supporting journal clubs and enhanced computer access and (c) creating safe venues for multidisciplinary dialogue. To reduce uncertainty arising from variations in management and leadership, we propose (a) developing policies that enhance the consistency of leadership and clarify the strategic direction of the management team, (b) clearly communicating those policies to nurses and (c) providing explicit rationales for treatment changes. Small, incremental steps can be taken to realize substantive changes in clinical environments in order to optimize nursing work environments for knowledge translation.},
bibtype = {article},
author = {Scott, S D and VandenBeld, B and Cummings, G G},
journal = {Nursing leadership (Toronto, Ont.)},
number = {3}
}2010 (7)
iqr: A Tool for the Construction of Multi-level Simulations of Brain and Behaviour. Bernardet, U. & Verschure, P., F. Neuroinformatics, 8(2):113-34, Humana Press Inc., 2010.
Paper Website abstract bibtex
Paper Website abstract bibtex The brain is the most complex system we know of. Despite the wealth of data available in neuroscience, our understanding of this system is still very limited. Here we argue that an essential component in our arsenal of methods to advance our understanding of the brain is the construction of artificial brain-like systems. In this way we can encompass the multi-level organisation of the brain and its role in the context of the complete embodied real-world and real-time perceiving and behaving system. Hence, on the one hand, we must be able to develop and validate theories of brains as closing the loop between perception and action, and on the other hand as interacting with the real world. Evidence is growing that one of the sources of the computational power of neuronal systems lies in the massive and specific connectivity, rather than the complexity of single elements. To meet these challenges-multiple levels of organisation, sophisticated connectivity, and the interaction of neuronal models with the real-world-we have developed a multi-level neuronal simulation environment, iqr. This framework deals with these requirements by directly transforming them into the core elements of the simulation environment itself. iqr provides a means to design complex neuronal models graphically, and to visualise and analyse their properties on-line. In iqr connectivity is defined in a flexible, yet compact way, and simulations run at a high speed, which allows the control of real-world devices-robots in the broader sense-in real-time. The architecture of iqr is modular, providing the possibility to write new neuron, and synapse types, and custom interfaces to other hardware systems. The code of iqr is publicly accessible under the GNU General Public License (GPL). iqr has been in use since 1996 and has been the core tool for a large number of studies ranging from detailed models of neuronal systems like the cerebral cortex, and the cerebellum, to robot based models of perception, cognition and action to large-scale real-world systems. In addition, iqr has been widely used over many years to introduce students to neuronal simulation and neuromorphic control. In this paper we outline the conceptual and methodological background of iqr and its design philosophy. Thereafter we present iqr's main features and computational properties. Finally, we describe a number of projects using iqr, singling out how iqr is used for building a "synthetic insect".
@article{
title = {iqr: A Tool for the Construction of Multi-level Simulations of Brain and Behaviour.},
type = {article},
year = {2010},
identifiers = {[object Object]},
keywords = {Access to Information,Animal,Animals,Behavior,Behavior: physiology,Brain,Brain: physiology,Computer Simulation,Humans,Insects,Internet,Memory,Memory: physiology,Models,Neurological,Neurons,Neurons: physiology,Robotics,Software,Synapses,Synapses: physiology,Time Factors,User-Computer Interface},
pages = {113-34},
volume = {8},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/20502987},
publisher = {Humana Press Inc.},
id = {59515ef3-1a82-3d32-b933-751e65c1b13e},
created = {2016-02-18T20:36:44.000Z},
file_attached = {true},
profile_id = {666a093a-6015-3506-8b43-c65cadb20ea2},
last_modified = {2017-03-09T23:31:28.082Z},
read = {true},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
citation_key = {Bernardet2010},
source_type = {article},
folder_uuids = {2e9f9bfc-4801-4871-9757-39a0ad79563e,79387ff2-9353-4bd0-8477-6c81b81f953f},
abstract = {The brain is the most complex system we know of. Despite the wealth of data available in neuroscience, our understanding of this system is still very limited. Here we argue that an essential component in our arsenal of methods to advance our understanding of the brain is the construction of artificial brain-like systems. In this way we can encompass the multi-level organisation of the brain and its role in the context of the complete embodied real-world and real-time perceiving and behaving system. Hence, on the one hand, we must be able to develop and validate theories of brains as closing the loop between perception and action, and on the other hand as interacting with the real world. Evidence is growing that one of the sources of the computational power of neuronal systems lies in the massive and specific connectivity, rather than the complexity of single elements. To meet these challenges-multiple levels of organisation, sophisticated connectivity, and the interaction of neuronal models with the real-world-we have developed a multi-level neuronal simulation environment, iqr. This framework deals with these requirements by directly transforming them into the core elements of the simulation environment itself. iqr provides a means to design complex neuronal models graphically, and to visualise and analyse their properties on-line. In iqr connectivity is defined in a flexible, yet compact way, and simulations run at a high speed, which allows the control of real-world devices-robots in the broader sense-in real-time. The architecture of iqr is modular, providing the possibility to write new neuron, and synapse types, and custom interfaces to other hardware systems. The code of iqr is publicly accessible under the GNU General Public License (GPL). iqr has been in use since 1996 and has been the core tool for a large number of studies ranging from detailed models of neuronal systems like the cerebral cortex, and the cerebellum, to robot based models of perception, cognition and action to large-scale real-world systems. In addition, iqr has been widely used over many years to introduce students to neuronal simulation and neuromorphic control. In this paper we outline the conceptual and methodological background of iqr and its design philosophy. Thereafter we present iqr's main features and computational properties. Finally, we describe a number of projects using iqr, singling out how iqr is used for building a "synthetic insect".},
bibtype = {article},
author = {Bernardet, Ulysses and Verschure, Paul F.M.J.},
journal = {Neuroinformatics},
number = {2}
}Estimating risk factors for farm-level transmission of disease: foot and mouth disease during the 2001 epidemic in Great Britain. Bessell, P. R., Shaw, D. J., Savill, N. J., & Woolhouse, M. E. J. Epidemics, 2(3):109--115, September, 2010.
doi abstract bibtex
doi abstract bibtex
Controlling an epidemic would be aided by establishing whether particular individuals in infected populations are more likely to transmit infection. However, few analyses have characterised such individuals. Such analyses require both data on who infected whom and on the likely determinants of transmission; data that are available at the farm level for the 2001 Foot and Mouth Disease epidemic in Great Britain. Using these data a putative number of daughter infected premises (IPs) resulting from each IP was calculated where these daughters were within 3km of the IP. A set of possible epidemiological, demographic, spatial and temporal risk factors were analysed, with the final multivariate generalised linear model (Poisson error term) having 6 statistically significant (p\textless0.05) main effects including geographic area, local cattle and sheep densities, and the number of non-IP culls. This model demonstrates that farms are heterogeneous in their propensity to transmit infection to other farms and, importantly, that it may be possible to identify holdings that are at high risk of spreading disease a priori. Such information could be used to help prioritise the response to an epidemic.
@article{bessell_estimating_2010,
title = {Estimating risk factors for farm-level transmission of disease: foot and mouth disease during the 2001 epidemic in {Great} {Britain}.},
volume = {2},
copyright = {Copyright (c) 2010 Elsevier B.V. All rights reserved.},
issn = {1878-0067 1878-0067},
doi = {10.1016/j.epidem.2010.06.002},
abstract = {Controlling an epidemic would be aided by establishing whether particular individuals in infected populations are more likely to transmit infection. However, few analyses have characterised such individuals. Such analyses require both data on who infected whom and on the likely determinants of transmission; data that are available at the farm level for the 2001 Foot and Mouth Disease epidemic in Great Britain. Using these data a putative number of daughter infected premises (IPs) resulting from each IP was calculated where these daughters were within 3km of the IP. A set of possible epidemiological, demographic, spatial and temporal risk factors were analysed, with the final multivariate generalised linear model (Poisson error term) having 6 statistically significant (p{\textless}0.05) main effects including geographic area, local cattle and sheep densities, and the number of non-IP culls. This model demonstrates that farms are heterogeneous in their propensity to transmit infection to other farms and, importantly, that it may be possible to identify holdings that are at high risk of spreading disease a priori. Such information could be used to help prioritise the response to an epidemic.},
language = {eng},
number = {3},
journal = {Epidemics},
author = {Bessell, Paul R. and Shaw, Darren J. and Savill, Nicholas J. and Woolhouse, Mark E. J.},
month = sep,
year = {2010},
pmid = {21352781},
keywords = {Animal Husbandry, Animals, Cattle, Epidemics/prevention \& control/statistics \& numerical data/*veterinary, Foot-and-Mouth Disease Virus/physiology, Foot-and-Mouth Disease/epidemiology/*transmission, Models, Biological, Multivariate Analysis, Poisson Distribution, Risk Factors, Sheep, United Kingdom/epidemiology},
pages = {109--115}
}An artificial vector model for generating abnormal electrocardiographic rhythms. Clifford, G. D., Nemati, S., & Sameni, R. Physiological Measurement, 31(5):595--609, May, 2010.
doi abstract bibtex
doi abstract bibtex
We present generalizations of our previously published artificial models for generating multi-channel ECG to provide simulations of abnormal cardiac rhythms. Using a three-dimensional vectorcardiogram (VCG) formulation, we generate the normal cardiac dipole for a patient using a sum of Gaussian kernels, fitted to real VCG recordings. Abnormal beats are specified either as perturbations to the normal dipole or as new dipole trajectories. Switching between normal and abnormal beat types is achieved using a first-order Markov chain. Probability transitions can be learned from real data or modeled by coupling to heart rate and sympathovagal balance. Natural morphology changes from beat-to-beat are incorporated by varying the angular frequency of the dipole as a function of the inter-beat (RR) interval. The RR interval time series is generated using our previously described model whereby time- and frequency-domain heart rate (HR) and heart rate variability characteristics can be specified. QT-HR hysteresis is simulated by coupling the Gaussian kernels associated with the T-wave in the model with a nonlinear factor related to the local HR (determined from the last n RR intervals). Morphology changes due to respiration are simulated by introducing a rotation matrix couple to the respiratory frequency. We demonstrate an example of the use of this model by simulating HR-dependent T-wave alternans (TWA) with and without phase-switching due to ectopy. Application of our model also reveals previously unreported effects of common TWA estimation methods.
@article{clifford_artificial_2010,
title = {An artificial vector model for generating abnormal electrocardiographic rhythms},
volume = {31},
issn = {1361-6579},
doi = {10.1088/0967-3334/31/5/001},
abstract = {We present generalizations of our previously published artificial models for generating multi-channel ECG to provide simulations of abnormal cardiac rhythms. Using a three-dimensional vectorcardiogram (VCG) formulation, we generate the normal cardiac dipole for a patient using a sum of Gaussian kernels, fitted to real VCG recordings. Abnormal beats are specified either as perturbations to the normal dipole or as new dipole trajectories. Switching between normal and abnormal beat types is achieved using a first-order Markov chain. Probability transitions can be learned from real data or modeled by coupling to heart rate and sympathovagal balance. Natural morphology changes from beat-to-beat are incorporated by varying the angular frequency of the dipole as a function of the inter-beat (RR) interval. The RR interval time series is generated using our previously described model whereby time- and frequency-domain heart rate (HR) and heart rate variability characteristics can be specified. QT-HR hysteresis is simulated by coupling the Gaussian kernels associated with the T-wave in the model with a nonlinear factor related to the local HR (determined from the last n RR intervals). Morphology changes due to respiration are simulated by introducing a rotation matrix couple to the respiratory frequency. We demonstrate an example of the use of this model by simulating HR-dependent T-wave alternans (TWA) with and without phase-switching due to ectopy. Application of our model also reveals previously unreported effects of common TWA estimation methods.},
language = {eng},
number = {5},
journal = {Physiological Measurement},
author = {Clifford, Gari D. and Nemati, Shamim and Sameni, Reza},
month = may,
year = {2010},
pmid = {20308774},
pmcid = {PMC2927500},
keywords = {Arrhythmias, Cardiac, Electrocardiography, Heart Rate, Humans, Models, Cardiovascular},
pages = {595--609}
}Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes. Matsunaga, A. & Ziemann, P., J. Proceedings of the National Academy of Sciences of the United States of America, 107(15):6664-6669, 4, 2010.
Paper Website abstract bibtex
Paper Website abstract bibtex Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates, in particles formed from OH radical-initiated reactions of C(9)-C(15) 2-methyl-1-alkenes in the presence of NO(x) were measured by using a thermal desorption particle beam mass spectrometer coupled to a high-performance liquid chromatograph with a UV-visible (UV-vis) detector. Yields of beta-hydroxynitrates and dihydroxynitrates increased with carbon number primarily due to enhanced gas-to-particle partitioning before reaching plateaus at approximately C(14)-C(15), where the compounds were essentially entirely in the particle phase. Plateau yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates were 0.183 +/- 0.005, 0.045 +/- 0.005, and 0.034 +/- 0.005, and, after normalization for OH radical addition to the C = C double bond, were 0.225 +/- 0.007, 0.055 +/- 0.006, and 0.042 +/- 0.006. The fractions of 1-hydroxy and 2-hydroxy beta-hydroxynitrate isomers were 0.90/0.10. Yields measured here and in our previous study of reactions of linear internal alkenes and linear 1-alkenes indicate that, for these alkene classes, the relative branching ratios for forming tertiary, secondary, and primary beta-hydroxyalkyl radicals by OH radical addition to the C=C double bond are 4.3/1.9/1.0, and the branching ratios for forming beta-hydroxynitrates from reactions of tertiary, secondary, and primary beta-hydroxyperoxy radicals with NO are 0.25, 0.15, and 0.12. The effects of H(2)O vapor and NH(3) on yields were also explored.
@article{
title = {Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes.},
type = {article},
year = {2010},
identifiers = {[object Object]},
keywords = {*Hydroxyl Radical,Aerosols,Aerosols/chemistry,Aerosols: chemistry,Alkenes,Alkenes/*chemistry,Alkenes: chemistry,Ammonia,Ammonia/chemistry,Ammonia: chemistry,Atmosphere,Carbon,Carbon/chemistry,Carbon: chemistry,Chemical,Chemistry,Chromatography,Environmental Monitoring,Environmental Monitoring/methods,Environmental Monitoring: methods,High Pressure Liquid,High Pressure Liquid/methods,High Pressure Liquid: methods,Hydroxyl Radical,Mass Spectrometry,Mass Spectrometry/methods,Mass Spectrometry: methods,Models,Nitrates,Nitrates/*chemistry,Nitrates: chemistry,Organic,Organic/methods,Organic: methods,Particle Size,Ultraviolet Rays,Water,Water/chemistry,Water: chemistry},
pages = {6664-6669},
volume = {107},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2872378&tool=pmcentrez&rendertype=abstract,http://www.ncbi.nlm.nih.gov/pubmed/20080570},
month = {4},
day = {13},
edition = {2010/01/19},
id = {ed2248e9-15ec-3605-95cf-1651be7ffd2f},
created = {2015-10-30T20:07:32.000Z},
accessed = {2013-05-28},
file_attached = {true},
profile_id = {5a758209-74fb-3a9c-b322-2ae7f22f7b6c},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2015-10-30T20:22:36.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
language = {eng},
notes = {<b>From Duplicate 2 (<i>Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes</i> - Matsunaga, Aiko; Ziemann, Paul J)<br/></b><br/><b>From Duplicate 1 (<i>Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes</i> - Matsunaga, Aiko; Ziemann, Paul J)<br/></b><br/><b>From Duplicate 2 (<i>Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes</i> - Matsunaga, Aiko; Ziemann, Paul J)<br/></b><br/><b>From Duplicate 2 (<i>Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes</i> - Matsunaga, A; Ziemann, P J)<br/>And Duplicate 3 (<i>Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes</i> - Matsunaga, A; Ziemann, P J)<br/></b><br/>Matsunaga, Aiko<br/>Ziemann, Paul J<br/>Research Support, U.S. Gov't, Non-P.H.S.<br/>United States<br/>Proceedings of the National Academy of Sciences of the United States of America<br/>Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6664-9. doi: 10.1073/pnas.0910585107. Epub 2009 Dec 31.},
abstract = {Yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates, in particles formed from OH radical-initiated reactions of C(9)-C(15) 2-methyl-1-alkenes in the presence of NO(x) were measured by using a thermal desorption particle beam mass spectrometer coupled to a high-performance liquid chromatograph with a UV-visible (UV-vis) detector. Yields of beta-hydroxynitrates and dihydroxynitrates increased with carbon number primarily due to enhanced gas-to-particle partitioning before reaching plateaus at approximately C(14)-C(15), where the compounds were essentially entirely in the particle phase. Plateau yields of beta-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates were 0.183 +/- 0.005, 0.045 +/- 0.005, and 0.034 +/- 0.005, and, after normalization for OH radical addition to the C = C double bond, were 0.225 +/- 0.007, 0.055 +/- 0.006, and 0.042 +/- 0.006. The fractions of 1-hydroxy and 2-hydroxy beta-hydroxynitrate isomers were 0.90/0.10. Yields measured here and in our previous study of reactions of linear internal alkenes and linear 1-alkenes indicate that, for these alkene classes, the relative branching ratios for forming tertiary, secondary, and primary beta-hydroxyalkyl radicals by OH radical addition to the C=C double bond are 4.3/1.9/1.0, and the branching ratios for forming beta-hydroxynitrates from reactions of tertiary, secondary, and primary beta-hydroxyperoxy radicals with NO are 0.25, 0.15, and 0.12. The effects of H(2)O vapor and NH(3) on yields were also explored.},
bibtype = {article},
author = {Matsunaga, Aiko and Ziemann, Paul J},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {15}
}The edges of understanding. Lander, A., D. BMC biology, 8:40, 1, 2010.
Paper Website abstract bibtex
Paper Website abstract bibtex A culture's icons are a window onto its soul. Few would disagree that, in the culture of molecular biology that dominated much of the life sciences for the last third of the 20th century, the dominant icon was the double helix. In the present, post-modern, 'systems biology' era, however, it is, arguably, the hairball.
@article{
title = {The edges of understanding.},
type = {article},
year = {2010},
identifiers = {[object Object]},
keywords = {Comprehension,Models, Theoretical,Systems Biology,Systems Biology: methods,Systems Biology: trends},
pages = {40},
volume = {8},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2864098&tool=pmcentrez&rendertype=abstract},
month = {1},
id = {a7e90c2f-c8ca-3051-baa8-17b92b2b43e9},
created = {2016-04-08T12:19:35.000Z},
file_attached = {true},
profile_id = {994bc413-6766-31df-917a-32165aa30f6c},
group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
last_modified = {2017-03-14T10:42:46.538Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Lander2010b},
folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
private_publication = {false},
abstract = {A culture's icons are a window onto its soul. Few would disagree that, in the culture of molecular biology that dominated much of the life sciences for the last third of the 20th century, the dominant icon was the double helix. In the present, post-modern, 'systems biology' era, however, it is, arguably, the hairball.},
bibtype = {article},
author = {Lander, Arthur D},
journal = {BMC biology}
}Acoustic microstreaming around an encapsulated particle. Doinikov, A. & Bouakaz, A. The Journal of the Acoustical Society of America, 127(3):1218--27, March, 2010.
Paper doi abstract bibtex
Paper doi abstract bibtex A theory is suggested to calculate acoustic microstreaming that develops around an encapsulated particle in an ultrasound field. It is assumed that the particle is suspended in an unbounded fluid and can have a gas core or a liquid core. Fluids outside and inside the particle are assumed to be viscous and compressible. No restrictions are imposed on the size of the particle relative to the sound and viscous wavelengths in the outer and inner fluids, and all modes of the particle's motion, including the surface ones, are taken into account. The shell of the particle is assumed to be an elastic viscous compressible medium. Solutions for the sound field within the shell are also valid for any ratio between the particle size and the sound and viscous wavelengths in the shell material. Numerical examples for the cases of an encapsulated gas bubble and an encapsulated particle with a liquid core are presented.
@article{Doinikov2010b,
abstract = {A theory is suggested to calculate acoustic microstreaming that develops around an encapsulated particle in an ultrasound field. It is assumed that the particle is suspended in an unbounded fluid and can have a gas core or a liquid core. Fluids outside and inside the particle are assumed to be viscous and compressible. No restrictions are imposed on the size of the particle relative to the sound and viscous wavelengths in the outer and inner fluids, and all modes of the particle's motion, including the surface ones, are taken into account. The shell of the particle is assumed to be an elastic viscous compressible medium. Solutions for the sound field within the shell are also valid for any ratio between the particle size and the sound and viscous wavelengths in the shell material. Numerical examples for the cases of an encapsulated gas bubble and an encapsulated particle with a liquid core are presented.},
author = {Doinikov, Alexander and Bouakaz, Ayache},
doi = {10.1121/1.3290997},
file = {:C$\backslash$:/Users/emnicolas/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Doinikov, Bouakaz - 2010 - Acoustic microstreaming around an encapsulated particle.pdf:pdf},
issn = {1520-8524},
journal = {The Journal of the Acoustical Society of America},
keywords = {Elasticity,Microbubbles,Models, Theoretical,Particle Size,Ultrasonics,Viscosity,Water},
month = mar,
number = {3},
pages = {1218--27},
pmid = {20329820},
title = {{Acoustic microstreaming around an encapsulated particle.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20329820},
volume = {127},
year = {2010}
}Anatomy of large animal spines and its comparison to the human spine: a systematic review. Sheng, S. R., Wang, X. Y., Xu, H. Z., Zhu, G. Q., & Zhou, Y. F. Eur Spine J, 19(1):46--56, January, 2010.
abstract bibtex
abstract bibtex
Animal models have been commonly used for in vivo and in vitro spinal research. However, the extent to which animal models resemble the human spine has not been well known. We conducted a systematic review to compare the morphometric features of vertebrae between human and animal species, so as to give some suggestions on how to choose an appropriate animal model in spine research. A literature search of all English language peer-reviewed publications was conducted using PubMed, OVID, Springer and Elsevier (Science Direct) for the years 1980-2008. Two reviewers extracted data on the anatomy of large animal spines from the identified articles. Each anatomical study of animals had to include at least three vertebral levels. The anatomical data from all animal studies were compared with the existing data of the human spine in the literature. Of the papers retrieved, seven were included in the review. The animals in the studies involved baboon, sheep, porcine, calf and deer. Distinct anatomical differences of vertebrae were found between the human and each large animal spine. In cervical region, spines of the baboon and human are more similar as compared to other animals. In thoracic and lumbar regions, the mean pedicle height of all animals was greater than the human pedicles. There was similar mean pedicle width between animal and the human specimens, except in thoracic segments of sheep. The human spinal canal was wider and deeper in the anteroposterior plane than any of the animals. The mean human vertebral body width and depth were greater than that of the animals except in upper thoracic segments of the deer. However, the mean vertebral body height was lower than that of all animals. This paper provides a comprehensive review to compare vertebrae geometries of experimental animal models to the human vertebrae, and will help for choosing animal model in vivo and in vitro spine research. When the animal selected for spine research, the structural similarities and differences found in the animal studies must be kept in mind.
@article{sheng_anatomy_2010,
title = {Anatomy of large animal spines and its comparison to the human spine: a systematic review},
volume = {19},
issn = {1432-0932 (Electronic)0940-6719 (Linking)},
shorttitle = {Anatomy of large animal spines and its comparison to the human spine: a systematic review},
abstract = {Animal models have been commonly used for in vivo and in vitro spinal research. However, the extent to which animal models resemble the human spine has not been well known. We conducted a systematic review to compare the morphometric features of vertebrae between human and animal species, so as to give some suggestions on how to choose an appropriate animal model in spine research. A literature search of all English language peer-reviewed publications was conducted using PubMed, OVID, Springer and Elsevier (Science Direct) for the years 1980-2008. Two reviewers extracted data on the anatomy of large animal spines from the identified articles. Each anatomical study of animals had to include at least three vertebral levels. The anatomical data from all animal studies were compared with the existing data of the human spine in the literature. Of the papers retrieved, seven were included in the review. The animals in the studies involved baboon, sheep, porcine, calf and deer. Distinct anatomical differences of vertebrae were found between the human and each large animal spine. In cervical region, spines of the baboon and human are more similar as compared to other animals. In thoracic and lumbar regions, the mean pedicle height of all animals was greater than the human pedicles. There was similar mean pedicle width between animal and the human specimens, except in thoracic segments of sheep. The human spinal canal was wider and deeper in the anteroposterior plane than any of the animals. The mean human vertebral body width and depth were greater than that of the animals except in upper thoracic segments of the deer. However, the mean vertebral body height was lower than that of all animals. This paper provides a comprehensive review to compare vertebrae geometries of experimental animal models to the human vertebrae, and will help for choosing animal model in vivo and in vitro spine research. When the animal selected for spine research, the structural similarities and differences found in the animal studies must be kept in mind.},
language = {eng},
number = {1},
journal = {Eur Spine J},
author = {Sheng, S. R. and Wang, X. Y. and Xu, H. Z. and Zhu, G. Q. and Zhou, Y. F.},
month = jan,
year = {2010},
keywords = {Anatomy, Comparative/methods/ trends, Animals, Anthropometry, Humans, Mammals/ anatomy \& histology/surgery, Models, Animal, Neurosurgical Procedures/education/methods, Species Specificity, Spinal Diseases/surgery, Spine/ anatomy \& histology/surgery},
pages = {46--56}
}2009 (9)
Processing the H3K36me3 signature. Sims, R. J & Reinberg, D. Nature genetics, 41(3):270--1, March, 2009.
Paper doi bibtex
Paper doi bibtex @article{sims_processing_2009,
title = {Processing the {H}3K36me3 signature.},
volume = {41},
issn = {1546-1718},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19240748},
doi = {10.1038/ng0309-270},
number = {3},
journal = {Nature genetics},
author = {Sims, Robert J and Reinberg, Danny},
month = mar,
year = {2009},
pmid = {19240748},
keywords = {Animals, Biological, Caenorhabditis elegans, Caenorhabditis elegans: metabolism, Gene Expression Profiling, Gene Expression Regulation, Histone-Lysine N-Methyltransferase, Histones, Histones: chemistry, Histones: metabolism, Histones: physiology, Humans, Lysine, Lysine: metabolism, Metabolic Networks and Pathways, Metabolic Networks and Pathways: physiology, Methylation, Models, Post-Translational, Post-Translational: physiology, Protein Methyltransferases, Protein Methyltransferases: metabolism, Protein Processing},
pages = {270--1}
}Developing the next-generation climate system models: challenges and achievements. Slingo, J., Bates, K., Nikiforakis, N., Piggott, M., Roberts, M. J., Shaffrey, L. C., Stevens, I., Vidale, Luigi, P., & Weller, H. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 367(1890):815--31, March, 2009.
Paper doi abstract bibtex
Paper doi abstract bibtex Although climate models have been improving in accuracy and efficiency over the past few decades, it now seems that these incremental improvements may be slowing. As tera/petascale computing becomes massively parallel, our legacy codes are less suitable, and even with the increased resolution that we are now beginning to use, these models cannot represent the multiscale nature of the climate system. This paper argues that it may be time to reconsider the use of adaptive mesh refinement for weather and climate forecasting in order to achieve good scaling and representation of the wide range of spatial scales in the atmosphere and ocean. Furthermore, the challenge of introducing living organisms and human responses into climate system models is only just beginning to be tackled. We do not yet have a clear framework in which to approach the problem, but it is likely to cover such a huge number of different scales and processes that radically different methods may have to be considered. The challenges of multiscale modelling and petascale computing provide an opportunity to consider a fresh approach to numerical modelling of the climate (or Earth) system, which takes advantage of the computational fluid dynamics developments in other fields and brings new perspectives on how to incorporate Earth system processes. This paper reviews some of the current issues in climate (and, by implication, Earth) system modelling, and asks the question whether a new generation of models is needed to tackle these problems.
@article{ Slingo2009a,
author = {Slingo, Julia and Bates, Kevin and Nikiforakis, Nikos and Piggott,
Matthew and Roberts, Malcolm J. and Shaffrey, Len C. and Stevens,
Ian and Vidale, Pier Luigi and Weller, Hilary},
title = {{Developing the next-generation climate system models: challenges
and achievements.}},
journal = {Philosophical transactions. Series A, Mathematical, physical, and
engineering sciences},
year = {2009},
volume = {367},
pages = {815--31},
number = {1890},
month = {March},
abstract = {Although climate models have been improving in accuracy and efficiency
over the past few decades, it now seems that these incremental improvements
may be slowing. As tera/petascale computing becomes massively parallel,
our legacy codes are less suitable, and even with the increased resolution
that we are now beginning to use, these models cannot represent the
multiscale nature of the climate system. This paper argues that it
may be time to reconsider the use of adaptive mesh refinement for
weather and climate forecasting in order to achieve good scaling
and representation of the wide range of spatial scales in the atmosphere
and ocean. Furthermore, the challenge of introducing living organisms
and human responses into climate system models is only just beginning
to be tackled. We do not yet have a clear framework in which to approach
the problem, but it is likely to cover such a huge number of different
scales and processes that radically different methods may have to
be considered. The challenges of multiscale modelling and petascale
computing provide an opportunity to consider a fresh approach to
numerical modelling of the climate (or Earth) system, which takes
advantage of the computational fluid dynamics developments in other
fields and brings new perspectives on how to incorporate Earth system
processes. This paper reviews some of the current issues in climate
(and, by implication, Earth) system modelling, and asks the question
whether a new generation of models is needed to tackle these problems.},
doi = {10.1098/rsta.2008.0207},
file = {:Users/reinhard/Documents/articles/mendeley/Slingo et al‥ 2009. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences.pdf:pdf},
issn = {1364-503X},
keywords = {Climate,Climatic Processes,Computer Simulation,Ecology,Ecology: methods,Ecology:
trends,Internet,Models,Research,Research: trends,Science,Science:
methods,Science: trends,Theoretical},
pmid = {19087925},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19087925}
}Scaling rules for the final decline to extinction. Griffen, B., D. & Drake, J., M. Proceedings of the Royal Society, Series B, 276(1660):1361-1367, 4, 2009.
Paper Website abstract bibtex
Paper Website abstract bibtex Space-time scaling rules are ubiquitous in ecological phenomena. Current theory postulates three scaling rules that describe the duration of a population's final decline to extinction, although these predictions have not previously been empirically confirmed. We examine these scaling rules across a broader set of conditions, including a wide range of density-dependent patterns in the underlying population dynamics. We then report on tests of these predictions from experiments using the cladoceran Daphnia magna as a model. Our results support two predictions that: (i) the duration of population persistence is much greater than the duration of the final decline to extinction and (ii) the duration of the final decline to extinction increases with the logarithm of the population's estimated carrying capacity. However, our results do not support a third prediction that the duration of the final decline scales inversely with population growth rate. These findings not only support the current standard theory of population extinction but also introduce new empirical anomalies awaiting a theoretical explanation.
@article{
title = {Scaling rules for the final decline to extinction.},
type = {article},
year = {2009},
identifiers = {[object Object]},
keywords = {Animals,Biological,Daphnia,Extinction,Models,Population Dynamics},
pages = {1361-1367},
volume = {276},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2660959&tool=pmcentrez&rendertype=abstract},
month = {4},
day = {7},
id = {194e4705-4398-3e27-b8ac-d3d2484ae811},
created = {2012-03-21T15:22:14.000Z},
accessed = {2012-03-03},
file_attached = {true},
profile_id = {8988cb35-8a91-3e80-98d8-a7359f954673},
last_modified = {2016-09-02T19:26:59.000Z},
tags = {drake-lab,nsf-nipt},
read = {false},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
citation_key = {Griffen2009},
abstract = {Space-time scaling rules are ubiquitous in ecological phenomena. Current theory postulates three scaling rules that describe the duration of a population's final decline to extinction, although these predictions have not previously been empirically confirmed. We examine these scaling rules across a broader set of conditions, including a wide range of density-dependent patterns in the underlying population dynamics. We then report on tests of these predictions from experiments using the cladoceran Daphnia magna as a model. Our results support two predictions that: (i) the duration of population persistence is much greater than the duration of the final decline to extinction and (ii) the duration of the final decline to extinction increases with the logarithm of the population's estimated carrying capacity. However, our results do not support a third prediction that the duration of the final decline scales inversely with population growth rate. These findings not only support the current standard theory of population extinction but also introduce new empirical anomalies awaiting a theoretical explanation.},
bibtype = {article},
author = {Griffen, Blaine D and Drake, John M},
journal = {Proceedings of the Royal Society, Series B},
number = {1660}
}Prevention of breast cancer in postmenopausal women: approaches to estimating and reducing risk. Cummings, S. R., Tice, J. A., Bauer, S., Browner, W. S., Cuzick, J., Ziv, E., Vogel, V., Shepherd, J., Vachon, C., Smith-Bindman, R., & Kerlikowske, K. Journal of the National Cancer Institute, 101(6):384–398, March, 2009.
doi abstract bibtex
doi abstract bibtex
BACKGROUND: It is uncertain whether evidence supports routinely estimating a postmenopausal woman's risk of breast cancer and intervening to reduce risk. METHODS: We systematically reviewed prospective studies about models and sex hormone levels to assess breast cancer risk and used meta-analysis with random effects models to summarize the predictive accuracy of breast density. We also reviewed prospective studies of the effects of exercise, weight management, healthy diet, moderate alcohol consumption, and fruit and vegetable intake on breast cancer risk, and used random effects models for a meta-analyses of tamoxifen and raloxifene for primary prevention of breast cancer. All studies reviewed were published before June 2008, and all statistical tests were two-sided. RESULTS: Risk models that are based on demographic characteristics and medical history had modest discriminatory accuracy for estimating breast cancer risk (c-statistics range = 0.58-0.63). Breast density was strongly associated with breast cancer (relative risk [RR] = 4.03, 95% confidence interval [CI] = 3.10 to 5.26, for Breast Imaging Reporting and Data System category IV vs category I; RR = 4.20, 95% CI = 3.61 to 4.89, for \textgreater75% vs \textless5% of dense area), and adding breast density to models improved discriminatory accuracy (c-statistics range = 0.63-0.66). Estradiol was also associated with breast cancer (RR range = 2.0-2.9, comparing the highest vs lowest quintile of estradiol, P \textless .01). Most studies found that exercise, weight reduction, low-fat diet, and reduced alcohol intake were associated with a decreased risk of breast cancer. Tamoxifen and raloxifene reduced the risk of estrogen receptor-positive invasive breast cancer and invasive breast cancer overall. CONCLUSIONS: Evidence from this study supports screening for breast cancer risk in all postmenopausal women by use of risk factors and breast density and considering chemoprevention for those found to be at high risk. Several lifestyle changes with the potential to prevent breast cancer should be recommended regardless of risk.
@article{cummings_prevention_2009,
title = {Prevention of breast cancer in postmenopausal women: approaches to estimating and reducing risk},
volume = {101},
issn = {1460-2105},
shorttitle = {Prevention of breast cancer in postmenopausal women},
doi = {10.1093/jnci/djp018},
abstract = {BACKGROUND: It is uncertain whether evidence supports routinely estimating a postmenopausal woman's risk of breast cancer and intervening to reduce risk.
METHODS: We systematically reviewed prospective studies about models and sex hormone levels to assess breast cancer risk and used meta-analysis with random effects models to summarize the predictive accuracy of breast density. We also reviewed prospective studies of the effects of exercise, weight management, healthy diet, moderate alcohol consumption, and fruit and vegetable intake on breast cancer risk, and used random effects models for a meta-analyses of tamoxifen and raloxifene for primary prevention of breast cancer. All studies reviewed were published before June 2008, and all statistical tests were two-sided.
RESULTS: Risk models that are based on demographic characteristics and medical history had modest discriminatory accuracy for estimating breast cancer risk (c-statistics range = 0.58-0.63). Breast density was strongly associated with breast cancer (relative risk [RR] = 4.03, 95\% confidence interval [CI] = 3.10 to 5.26, for Breast Imaging Reporting and Data System category IV vs category I; RR = 4.20, 95\% CI = 3.61 to 4.89, for {\textgreater}75\% vs {\textless}5\% of dense area), and adding breast density to models improved discriminatory accuracy (c-statistics range = 0.63-0.66). Estradiol was also associated with breast cancer (RR range = 2.0-2.9, comparing the highest vs lowest quintile of estradiol, P {\textless} .01). Most studies found that exercise, weight reduction, low-fat diet, and reduced alcohol intake were associated with a decreased risk of breast cancer. Tamoxifen and raloxifene reduced the risk of estrogen receptor-positive invasive breast cancer and invasive breast cancer overall.
CONCLUSIONS: Evidence from this study supports screening for breast cancer risk in all postmenopausal women by use of risk factors and breast density and considering chemoprevention for those found to be at high risk. Several lifestyle changes with the potential to prevent breast cancer should be recommended regardless of risk.},
language = {eng},
number = {6},
journal = {Journal of the National Cancer Institute},
author = {Cummings, Steven R. and Tice, Jeffrey A. and Bauer, Scott and Browner, Warren S. and Cuzick, Jack and Ziv, Elad and Vogel, Victor and Shepherd, John and Vachon, Celine and Smith-Bindman, Rebecca and Kerlikowske, Karla},
month = mar,
year = {2009},
pmid = {19276457},
pmcid = {PMC2720698},
keywords = {Aged, Antineoplastic Agents, Hormonal, Biomarkers, Tumor, Breast, Breast Neoplasms, Case-Control Studies, Confidence Intervals, Confounding Factors (Epidemiology), Estrogen Receptor Modulators, Female, Gonadal Steroid Hormones, Humans, Life Style, Middle Aged, Models, Statistical, Odds Ratio, Postmenopause, Predictive Value of Tests, Prospective Studies, Raloxifene Hydrochloride, Randomized Controlled Trials as Topic, Research Design, Risk Assessment, Risk Factors, Risk Reduction Behavior, Tamoxifen},
pages = {384--398}
}Spike inference from calcium imaging using sequential Monte Carlo methods. Vogelstein, J., T., Watson, B., O., Packer, A., M., Yuste, R., Jedynak, B., M., & Paninski, L. Biophysical Journal, 97(2):636-655, 7, 2009.
abstract bibtex
abstract bibtex
As recent advances in calcium sensing technologies facilitate simultaneously imaging action potentials in neuronal populations, complementary analytical tools must also be developed to maximize the utility of this experimental paradigm. Although the observations here are fluorescence movies, the signals of interest--spike trains and/or time varying intracellular calcium concentrations--are hidden. Inferring these hidden signals is often problematic due to noise, nonlinearities, slow imaging rate, and unknown biophysical parameters. We overcome these difficulties by developing sequential Monte Carlo methods (particle filters) based on biophysical models of spiking, calcium dynamics, and fluorescence. We show that even in simple cases, the particle filters outperform the optimal linear (i.e., Wiener) filter, both by obtaining better estimates and by providing error bars. We then relax a number of our model assumptions to incorporate nonlinear saturation of the fluorescence signal, as well external stimulus and spike history dependence (e.g., refractoriness) of the spike trains. Using both simulations and in vitro fluorescence observations, we demonstrate temporal superresolution by inferring when within a frame each spike occurs. Furthermore, the model parameters may be estimated using expectation maximization with only a very limited amount of data (e.g., approximately 5-10 s or 5-40 spikes), without the requirement of any simultaneous electrophysiology or imaging experiments.
@article{
title = {Spike inference from calcium imaging using sequential Monte Carlo methods.},
type = {article},
year = {2009},
identifiers = {[object Object]},
keywords = {animals,biological,calcium,calcium metabolism,cytology/metabolism,fluorescence,inbred c57bl,intracellular space,intracellular space metabolism,metabolism,mice,models,monte carlo method,neurons,neurons cytology,neurons metabolism,probability,time factors},
pages = {636-655},
volume = {97},
websites = {http://dx.doi.org/10.1016/j.bpj.2008.08.005},
month = {7},
institution = {Department of Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA. joshuav@jhu.edu},
id = {ea71e181-8857-33ea-b063-d3d46eb47138},
created = {2015-06-19T07:45:09.000Z},
file_attached = {false},
profile_id = {182bbbf9-24a3-3af3-9ed6-563e8f89259b},
group_id = {8d229673-0aec-3014-b0f6-eda47f83e147},
last_modified = {2015-06-19T07:45:23.000Z},
read = {false},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
citation_key = {smc-oopsi},
source_type = {article},
abstract = {As recent advances in calcium sensing technologies facilitate simultaneously imaging action potentials in neuronal populations, complementary analytical tools must also be developed to maximize the utility of this experimental paradigm. Although the observations here are fluorescence movies, the signals of interest--spike trains and/or time varying intracellular calcium concentrations--are hidden. Inferring these hidden signals is often problematic due to noise, nonlinearities, slow imaging rate, and unknown biophysical parameters. We overcome these difficulties by developing sequential Monte Carlo methods (particle filters) based on biophysical models of spiking, calcium dynamics, and fluorescence. We show that even in simple cases, the particle filters outperform the optimal linear (i.e., Wiener) filter, both by obtaining better estimates and by providing error bars. We then relax a number of our model assumptions to incorporate nonlinear saturation of the fluorescence signal, as well external stimulus and spike history dependence (e.g., refractoriness) of the spike trains. Using both simulations and in vitro fluorescence observations, we demonstrate temporal superresolution by inferring when within a frame each spike occurs. Furthermore, the model parameters may be estimated using expectation maximization with only a very limited amount of data (e.g., approximately 5-10 s or 5-40 spikes), without the requirement of any simultaneous electrophysiology or imaging experiments.},
bibtype = {article},
author = {Vogelstein, Joshua T. and Watson, Brendon O and Packer, Adam M and Yuste, Rafael and Jedynak, Bruno M and Paninski, Liam},
journal = {Biophysical Journal},
number = {2}
}Assessing the environmental impacts of freshwater consumption in LCA. Pfister, S., Koehler, A., & Hellweg, S. Environmental science & technology, 43(11):4098-104, 6, 2009.
Paper Website abstract bibtex
Paper Website abstract bibtex A method for assessing the environmental impacts of freshwater consumption was developed. This method considers damages to three areas of protection: human health, ecosystem quality, and resources. The method can be used within most existing life-cycle impact assessment (LCIA) methods. The relative importance of water consumption was analyzed by integrating the method into the Eco-indicator-99 LCIA method. The relative impact of water consumption in LCIA was analyzed with a case study on worldwide cotton production. The importance of regionalized characterization factors for water use was also examined in the case study. In arid regions, water consumption may dominate the aggregated life-cycle impacts of cotton-textile production. Therefore, the consideration of water consumption is crucial in life-cycle assessment (LCA) studies that include water-intensive products, such as agricultural goods. A regionalized assessment is necessary, since the impacts of water use vary greatly as a function of location. The presented method is useful for environmental decision-support in the production of water-intensive products as well as for environmentally responsible value-chain management.
@article{
title = {Assessing the environmental impacts of freshwater consumption in LCA.},
type = {article},
year = {2009},
identifiers = {[object Object]},
keywords = {Agriculture,Conservation of Natural Resources,Cotton Fiber,Environment,Environmental Monitoring,Fresh Water,Humans,Models,Textile Industry,Theoretical,Water Supply},
pages = {4098-104},
volume = {43},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/19569336},
month = {6},
day = {1},
id = {5ea3532c-30f3-3993-be4b-dfcacd2d4e14},
created = {2012-01-26T16:47:48.000Z},
file_attached = {true},
profile_id = {3cddc622-545e-3931-8da7-74f4edefee8f},
group_id = {36e61195-3063-323c-b879-d6d31394db8a},
last_modified = {2017-03-14T14:39:23.619Z},
tags = {Ajouté par PL},
read = {true},
starred = {true},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Pfister2009},
folder_uuids = {1d1b23d4-a2f3-459c-a05a-d1b85060a546,51be121f-a309-44ad-ad90-bb8af078bd19},
private_publication = {false},
abstract = {A method for assessing the environmental impacts of freshwater consumption was developed. This method considers damages to three areas of protection: human health, ecosystem quality, and resources. The method can be used within most existing life-cycle impact assessment (LCIA) methods. The relative importance of water consumption was analyzed by integrating the method into the Eco-indicator-99 LCIA method. The relative impact of water consumption in LCIA was analyzed with a case study on worldwide cotton production. The importance of regionalized characterization factors for water use was also examined in the case study. In arid regions, water consumption may dominate the aggregated life-cycle impacts of cotton-textile production. Therefore, the consideration of water consumption is crucial in life-cycle assessment (LCA) studies that include water-intensive products, such as agricultural goods. A regionalized assessment is necessary, since the impacts of water use vary greatly as a function of location. The presented method is useful for environmental decision-support in the production of water-intensive products as well as for environmentally responsible value-chain management.},
bibtype = {article},
author = {Pfister, Stephan and Koehler, Annette and Hellweg, Stefanie},
journal = {Environmental science & technology},
number = {11}
}Structured variability of muscle activations supports the minimal intervention principle of motor control. Valero-Cuevas, J, F., Venkadesan, M., & Todorov, E. Journal of neurophysiology, 102:59-68, 2009 Jul, 2009.
Paper doi abstract bibtex
Paper doi abstract bibtex Numerous observations of structured motor variability indicate that the sensorimotor system preferentially controls task-relevant parameters while allowing task-irrelevant ones to fluctuate. Optimality models show that controlling a redundant musculo-skeletal system in this manner meets task demands while minimizing control effort. Although this line of inquiry has been very productive, the data are mostly behavioral with no direct physiological evidence on the level of muscle or neural activity. Furthermore, biomechanical coupling, signal-dependent noise, and alternative causes of trial-to-trial variability confound behavioral studies. Here we address those confounds and present evidence that the nervous system preferentially controls task-relevant parameters on the muscle level. We asked subjects to produce vertical fingertip force vectors of prescribed constant or time-varying magnitudes while maintaining a constant finger posture. We recorded intramuscular electromyograms (EMGs) simultaneously from all seven index finger muscles during this task. The experiment design and selective fine-wire muscle recordings allowed us to account for a median of 91% of the variance of fingertip forces given the EMG signals. By analyzing muscle coordination in the seven-dimensional EMG signal space, we find that variance-per-dimension is consistently smaller in the task-relevant subspace than in the task-irrelevant subspace. This first direct physiological evidence on the muscle level for preferential control of task-relevant parameters strongly suggest the use of a neural control strategy compatible with the principle of minimal intervention. Additionally, variance is nonnegligible in all seven dimensions, which is at odds with the view that muscle activation patterns are composed from a small number of synergies.
@article{ 71,
title = {Structured variability of muscle activations supports the minimal intervention principle of motor control.},
journal = {Journal of neurophysiology},
volume = {102},
year = {2009},
month = {2009 Jul},
pages = {59-68},
abstract = {Numerous observations of structured motor variability indicate that the sensorimotor system preferentially controls task-relevant parameters while allowing task-irrelevant ones to fluctuate. Optimality models show that controlling a redundant musculo-skeletal system in this manner meets task demands while minimizing control effort. Although this line of inquiry has been very productive, the data are mostly behavioral with no direct physiological evidence on the level of muscle or neural activity. Furthermore, biomechanical coupling, signal-dependent noise, and alternative causes of trial-to-trial variability confound behavioral studies. Here we address those confounds and present evidence that the nervous system preferentially controls task-relevant parameters on the muscle level. We asked subjects to produce vertical fingertip force vectors of prescribed constant or time-varying magnitudes while maintaining a constant finger posture. We recorded intramuscular electromyograms (EMGs) simultaneously from all seven index finger muscles during this task. The experiment design and selective fine-wire muscle recordings allowed us to account for a median of 91% of the variance of fingertip forces given the EMG signals. By analyzing muscle coordination in the seven-dimensional EMG signal space, we find that variance-per-dimension is consistently smaller in the task-relevant subspace than in the task-irrelevant subspace. This first direct physiological evidence on the muscle level for preferential control of task-relevant parameters strongly suggest the use of a neural control strategy compatible with the principle of minimal intervention. Additionally, variance is nonnegligible in all seven dimensions, which is at odds with the view that muscle activation patterns are composed from a small number of synergies.},
keywords = {Adolescent, Adult, Biological, Biomechanics, Electromyography, Female, Fingers, Humans, Male, Models, Movement, Muscle, Muscle Contraction, Muscle Strength, Posture, Principal Component Analysis, Psychomotor Performance, Skeletal, Time Factors, Young Adult},
issn = {0022-3077},
doi = {10.1152/jn.90324.2008},
url = {http://jn.physiology.org/content/102/1/59.long},
author = {Valero-Cuevas, Francisco J and Venkadesan, Madhusudhan and Todorov, Emanuel}
}A filter bank-based source extraction algorithm for heart sound removal in respiratory sounds. Jin, F., Sattar, F., & Goh, D., Y., T. Computers in biology and medicine, 39(9):768-77, 9, 2009.
Paper abstract bibtex
Paper abstract bibtex In this paper, we consider the problem of heart sounds (HS) removal from respiratory sounds (RS), and a novel semi-blind single-channel source extraction algorithm is proposed. The proposed method is able to extract the underlying pure RS from the HS corrupted noisy input signals by incorporating the filter banks and template-based matching using FIR filters. For performance evaluation of the presented method, the average power spectral densities (PSD) of the input RS segments without HS have been compared with the PSD of the reconstructed signals over six selected frequency bands from 20 to 800Hz. The proposed method is tested for various types of RS recordings and found effective by yielding an overall maximum spectral difference of 2.8707+/-0.9875dB for a frequency range below 800Hz.
@article{
id = {5b67cb62-1514-37d8-870e-c9c99f983a14},
title = {A filter bank-based source extraction algorithm for heart sound removal in respiratory sounds.},
type = {article},
year = {2009},
identifiers = {[object Object]},
keywords = {Algorithms,Auscultation,Auscultation: statistics & numerical data,Biomedical Engineering,Computer Simulation,Heart Sounds,Humans,Models, Biological,Respiratory Sounds,Respiratory Tract Diseases,Respiratory Tract Diseases: diagnosis,Signal Processing, Computer-Assisted},
created = {2010-05-05T19:40:37.000Z},
pages = {768-77},
volume = {39},
websites = {http://dx.doi.org/10.1016/j.compbiomed.2009.06.005},
month = {9},
file_attached = {true},
profile_id = {6d353feb-efe4-367e-84a2-0815eb9ca878},
group_id = {7f22d395-e966-3e55-9f90-9d0061e6682a},
last_modified = {2013-07-09T23:56:13.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Jin2009},
client_data = {"desktop_id":"4fd6a237-8203-439e-bb5b-5a732ed8198c"},
abstract = {In this paper, we consider the problem of heart sounds (HS) removal from respiratory sounds (RS), and a novel semi-blind single-channel source extraction algorithm is proposed. The proposed method is able to extract the underlying pure RS from the HS corrupted noisy input signals by incorporating the filter banks and template-based matching using FIR filters. For performance evaluation of the presented method, the average power spectral densities (PSD) of the input RS segments without HS have been compared with the PSD of the reconstructed signals over six selected frequency bands from 20 to 800Hz. The proposed method is tested for various types of RS recordings and found effective by yielding an overall maximum spectral difference of 2.8707+/-0.9875dB for a frequency range below 800Hz.},
bibtype = {article},
author = {Jin, F and Sattar, F and Goh, D Y T},
journal = {Computers in biology and medicine},
number = {9}
}The role of pre-emptive culling in the control of foot-and-mouth disease. Tildesley, M. J., Bessell, P. R., Keeling, M. J., & Woolhouse, M. E. J. Proceedings. Biological sciences, 276(1671):3239--3248, September, 2009.
doi abstract bibtex
doi abstract bibtex
The 2001 foot-and-mouth disease epidemic was controlled by culling of infectious premises and pre-emptive culling intended to limit the spread of disease. Of the control strategies adopted, routine culling of farms that were contiguous to infected premises caused the most controversy. Here we perform a retrospective analysis of the culling of contiguous premises as performed in 2001 and a simulation study of the effects of this policy on reducing the number of farms affected by disease. Our simulation results support previous studies and show that a national policy of contiguous premises (CPs) culling leads to fewer farms losing livestock. The optimal national policy for controlling the 2001 epidemic is found to be the targeting of all contiguous premises, whereas for localized outbreaks in high animal density regions, more extensive fixed radius ring culling is optimal. Analysis of the 2001 data suggests that the lowest-risk CPs were generally prioritized for culling, however, even in this case, the policy is predicted to be effective. A sensitivity analysis and the development of a spatially heterogeneous policy show that the optimal culling level depends upon the basic reproductive ratio of the infection and the width of the dispersal kernel. These analyses highlight an important and probably quite general result: optimal control is highly dependent upon the distance over which the pathogen can be transmitted, the transmission rate of infection and local demography where the disease is introduced.
@article{tildesley_role_2009,
title = {The role of pre-emptive culling in the control of foot-and-mouth disease.},
volume = {276},
issn = {0962-8452 0962-8452},
doi = {10.1098/rspb.2009.0427},
abstract = {The 2001 foot-and-mouth disease epidemic was controlled by culling of infectious premises and pre-emptive culling intended to limit the spread of disease. Of the control strategies adopted, routine culling of farms that were contiguous to infected premises caused the most controversy. Here we perform a retrospective analysis of the culling of contiguous premises as performed in 2001 and a simulation study of the effects of this policy on reducing the number of farms affected by disease. Our simulation results support previous studies and show that a national policy of contiguous premises (CPs) culling leads to fewer farms losing livestock. The optimal national policy for controlling the 2001 epidemic is found to be the targeting of all contiguous premises, whereas for localized outbreaks in high animal density regions, more extensive fixed radius ring culling is optimal. Analysis of the 2001 data suggests that the lowest-risk CPs were generally prioritized for culling, however, even in this case, the policy is predicted to be effective. A sensitivity analysis and the development of a spatially heterogeneous policy show that the optimal culling level depends upon the basic reproductive ratio of the infection and the width of the dispersal kernel. These analyses highlight an important and probably quite general result: optimal control is highly dependent upon the distance over which the pathogen can be transmitted, the transmission rate of infection and local demography where the disease is introduced.},
language = {eng},
number = {1671},
journal = {Proceedings. Biological sciences},
author = {Tildesley, Michael J. and Bessell, Paul R. and Keeling, Matt J. and Woolhouse, Mark E. J.},
month = sep,
year = {2009},
pmid = {19570791},
pmcid = {PMC2817163},
keywords = {Animals, Computer Simulation, Disease Outbreaks/prevention \& control/*veterinary, Foot-and-Mouth Disease/epidemiology/*prevention \& control, Geography, Models, Theoretical, United Kingdom},
pages = {3239--3248}
}2008 (6)
Ordered mesoporous alumina-supported metal oxides. Morris, S., M., Fulvio, P., F., & Jaroniec, M. Journal of the American Chemical Society, 130(45):15210-15216, 11, 2008.
Website abstract bibtex
Website abstract bibtex The one-pot synthesis of alumina-supported metal oxides via self-assembly of a metal precursor and aluminum isopropoxide in the presence of triblock copolymer (as a structure directing agent) is described in detail for nickel oxide. The resulting mesoporous mixed metal oxides possess p6 mm hexagonal symmetry, well-developed mesoporosity, relatively high BET surface area, large pore widths, and crystalline pore walls. In comparison to pure alumina, nickel aluminum oxide samples exhibited larger mesopores and improved thermal stability. Also, long-range ordering of the aforementioned samples was observed for nickel molar percentages as high as 20%. The generality of the recipe used for the synthesis of mesoporous nickel aluminum oxide was demonstrated by preparation of other alumina-supported metal oxides such as MgO, CaO, TiO 2, and Cr 2O 3. This method represents an important step toward the facile and reproducible synthesis of ordered mesoporous alumina-supported materials for various applications where large and accessible pores with high loading of catalytically active metal oxides are needed.
@article{
title = {Ordered mesoporous alumina-supported metal oxides.},
type = {article},
year = {2008},
identifiers = {[object Object]},
keywords = {Adsorption,Aluminum Oxide,Aluminum Oxide: chemistry,Magnetic Resonance Spectroscopy,Magnetic Resonance Spectroscopy: methods,Models,Molecular,Nickel,Nickel: chemistry,Nitrogen,Nitrogen: chemistry,Thermogravimetry,X-Ray Diffraction},
pages = {15210-15216},
volume = {130},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/18921999},
month = {11},
day = {12},
id = {2e834a44-1d53-395d-8219-28df16f794cb},
created = {2013-11-19T15:58:18.000Z},
file_attached = {false},
profile_id = {b9c5c1e6-09ce-3d53-9dcd-cde5fd0daa6e},
group_id = {4a031295-8de8-39cf-9e88-45764d428e4b},
last_modified = {2015-01-15T02:26:53.000Z},
read = {true},
starred = {true},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Morris2008a},
source_type = {article},
notes = {<b>From Duplicate 2 ( </b><br/><b><br/><i>Ordered mesoporous alumina-supported metal oxides.</i><br/></b><br/><b>- Morris, Stacy M; Fulvio, Pasquale F; Jaroniec, Mietek )<br/><br/></b><br/><br/><br/><b>From Duplicate 2 ( </b><br/><b><br/><i>Ordered mesoporous alumina-supported metal oxides.</i><br/></b><br/><b>- Morris, Stacy M; Fulvio, Pasquale F; Jaroniec, Mietek )<br/><br/></b><br/><br/><br/><b>From Duplicate 2 ( </b><br/><br/><b><br/><i>Ordered mesoporous alumina-supported metal oxides.</i><br/></b><br/><br/><b>- Morris, Stacy M; Fulvio, Pasquale F; Jaroniec, Mietek )<br/><br/></b>},
folder_uuids = {c32e54a8-cdc5-443e-b903-55c929dd6ca9},
abstract = {The one-pot synthesis of alumina-supported metal oxides via self-assembly of a metal precursor and aluminum isopropoxide in the presence of triblock copolymer (as a structure directing agent) is described in detail for nickel oxide. The resulting mesoporous mixed metal oxides possess p6 mm hexagonal symmetry, well-developed mesoporosity, relatively high BET surface area, large pore widths, and crystalline pore walls. In comparison to pure alumina, nickel aluminum oxide samples exhibited larger mesopores and improved thermal stability. Also, long-range ordering of the aforementioned samples was observed for nickel molar percentages as high as 20%. The generality of the recipe used for the synthesis of mesoporous nickel aluminum oxide was demonstrated by preparation of other alumina-supported metal oxides such as MgO, CaO, TiO 2, and Cr 2O 3. This method represents an important step toward the facile and reproducible synthesis of ordered mesoporous alumina-supported materials for various applications where large and accessible pores with high loading of catalytically active metal oxides are needed.},
bibtype = {article},
author = {Morris, Stacy M and Fulvio, Pasquale F and Jaroniec, Mietek},
journal = {Journal of the American Chemical Society},
number = {45}
}The predicted impact of immunosuppression upon population age-intensity profiles for schistosomiasis. Mitchell, K. M., Mutapi, F., & Woolhouse, M. E. J. Parasite immunology, 30(9):462--470, September, 2008.
doi abstract bibtex
doi abstract bibtex
The slow development of acquired immunity is thought to be responsible for the characteristic convex age-intensity curve seen in human schistosome infection, which peaks earlier in more heavily infected populations (this is described as a peak shift). Schistosomes are able to suppress protective host responses, and it is hypothesized that this suppression is responsible for the delayed development of protective responses. A deterministic mathematical model is used to describe levels of infection and immunity in an endemic population, incorporating protective immune responses which either reduce adult worm burden or reduce superinfection. Suppression, related to current worm burden, is also included and acts against one or both protective responses. If suppression acts against the entire protective response, it is able to delay the development of protective immunity, and the peak shift is predicted to be reversed at higher infection intensities, with removal of the peaks altogether at the highest levels of infection and/or suppression. If only the anti-adult worm protective immune response is vulnerable to suppression, while the anti-reinfection response remains intact, then suppression does not remove the peak in the age-intensity curve. These findings are discussed in the light of existing field and experimental data.
@article{mitchell_predicted_2008,
title = {The predicted impact of immunosuppression upon population age-intensity profiles for schistosomiasis.},
volume = {30},
issn = {1365-3024 0141-9838},
doi = {10.1111/j.1365-3024.2008.01043.x},
abstract = {The slow development of acquired immunity is thought to be responsible for the characteristic convex age-intensity curve seen in human schistosome infection, which peaks earlier in more heavily infected populations (this is described as a peak shift). Schistosomes are able to suppress protective host responses, and it is hypothesized that this suppression is responsible for the delayed development of protective responses. A deterministic mathematical model is used to describe levels of infection and immunity in an endemic population, incorporating protective immune responses which either reduce adult worm burden or reduce superinfection. Suppression, related to current worm burden, is also included and acts against one or both protective responses. If suppression acts against the entire protective response, it is able to delay the development of protective immunity, and the peak shift is predicted to be reversed at higher infection intensities, with removal of the peaks altogether at the highest levels of infection and/or suppression. If only the anti-adult worm protective immune response is vulnerable to suppression, while the anti-reinfection response remains intact, then suppression does not remove the peak in the age-intensity curve. These findings are discussed in the light of existing field and experimental data.},
language = {eng},
number = {9},
journal = {Parasite immunology},
author = {Mitchell, K. M. and Mutapi, F. and Woolhouse, M. E. J.},
month = sep,
year = {2008},
pmid = {18522703},
keywords = {*Immune Tolerance, Age Factors, Animals, Antibodies, Helminth/immunology, Humans, Models, Biological, Schistosoma/*immunology, Schistosomiasis/epidemiology/*immunology},
pages = {462--470}
}Relationships of thoracic aortic wall calcification to cardiovascular risk factors: The Multi-Ethnic Study of Atherosclerosis (MESA). Takasu, J., Katz, R., Nasir, K., Carr, J. J., Wong, N., Detrano, R., & Budoff, M. J. American Heart Journal, 155(4):765-71, 2008.
bibtex
bibtex
@Article{Takasu_2008_782,
author = {Takasu, J. and Katz, R. and Nasir, K. and Carr, J. J. and Wong, N. and Detrano, R. and Budoff, M. J.},
journal = {American Heart Journal},
number = {4},
pages = {765-71},
title = {Relationships of thoracic aortic wall calcification to cardiovascular risk factors: {T}he {M}ulti-{E}thnic {S}tudy of {A}therosclerosis ({MESA})},
volume = {155},
year = {2008},
keywords = {African, Americans, Age, Distribution, Aged, Aged, 80, and, over, Aorta, Thoracic, Aortic, Diseases/, ethnology, Calcinosis/, ethnology, Cardiovascular, Diseases, China/ethnology, Cross-Sectional, Studies, European, Continental, Ancestry, Group, Female, Hispanic, Americans, Humans, Logistic, Models, Male, Middle, Aged, Prevalence, Risk, Factors, Sex, Distribution, United, States/epidemiology},
title_with_no_special_chars = {Relationships of thoracic aortic wall calcification to cardiovascular risk factors The MultiEthnic Study of Atherosclerosis MESA}
}Conscientious objection: a potential neonatal nursing response to care orders that cause suffering at the end of life? Study of a concept. Catlin, A., Armigo, C., Volat, D., Vale, E., Hadley, Ann, M., Gong, W., Bassir, R., & Anderson, K. Neonatal network: NN, 27(2):101--108, April, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex This article is an exploratory effort meant to solicit and provoke dialog. Conscientious objection is proposed as a potential response to the moral distress experienced by neonatal nurses. The most commonly reported cause of distress for all nurses is following orders to support patients at the end of their lives with advanced technology when palliative or comfort care would be more humane. Nurses report that they feel they are harming patients or causing suffering when they could be comforting instead. We examined the literature on moral distress, futility, and the concept of conscientious objection from the perspective of the nurse's potential response to performing advanced technologic interventions for the dying patient. We created a small pilot study to engage in clinical verification of the use of our concept of conscientious objection. Data from 66 neonatal intensive care and pediatric intensive care unit nurses who responded in a one-month period are reported here. Interest in conscientious objection to care that causes harm or suffering was very high. This article reports the analysis of conscientious objection use in neonatal care.
@article{ catlin_conscientious_2008-1,
title = {Conscientious objection: a potential neonatal nursing response to care orders that cause suffering at the end of life? Study of a concept},
volume = {27},
issn = {0730-0832},
shorttitle = {Conscientious objection},
url = {http://www.sonoma.edu/users/c/catlin/conscientious%20objection.pdf},
doi = {10.1891/0730-0832.27.2.101},
abstract = {This article is an exploratory effort meant to solicit and provoke dialog. Conscientious objection is proposed as a potential response to the moral distress experienced by neonatal nurses. The most commonly reported cause of distress for all nurses is following orders to support patients at the end of their lives with advanced technology when palliative or comfort care would be more humane. Nurses report that they feel they are harming patients or causing suffering when they could be comforting instead. We examined the literature on moral distress, futility, and the concept of conscientious objection from the perspective of the nurse's potential response to performing advanced technologic interventions for the dying patient. We created a small pilot study to engage in clinical verification of the use of our concept of conscientious objection. Data from 66 neonatal intensive care and pediatric intensive care unit nurses who responded in a one-month period are reported here. Interest in conscientious objection to care that causes harm or suffering was very high. This article reports the analysis of conscientious objection use in neonatal care.},
language = {eng},
number = {2},
journal = {Neonatal network: {NN}},
author = {Catlin, Anita and Armigo, Christine and Volat, Deborah and Vale, Elnora and Hadley, Mary Ann and Gong, Wendy and Bassir, Ranginah and Anderson, Kelly},
month = {April},
year = {2008},
pmid = {18431964},
keywords = {Attitude of Health Personnel, Conflict (Psychology), Conscience, Health Knowledge, Attitudes, Practice, Humans, Infant, Newborn, Intensive Care, Neonatal, Medical Futility, Models, Nursing, Morals, Neonatal Nursing, Nurse's Role, Nursing Methodology Research, Nursing Staff, Hospital, Palliative Care, Patient Advocacy, Pilot Projects, Questionnaires, Stress, Psychological},
pages = {101--108}
}Grid-free models of multicellular systems, with an application to large-scale vortices accompanying primitive streak formation. Newman, T., J. Current topics in developmental biology, 81(07):157-82, 1, 2008.
Paper Website abstract bibtex
Paper Website abstract bibtex This paper is comprised of two parts. In the first we provide a brief overview of grid-free methods for modeling multicellular systems. We focus on an approach based on Langevin equations, in which inertia is ignored, and stochastic effects on cell motion are included. The discussion starts with simpler models, in which cells are modeled as adhesive spheres. We then turn to more sophisticated approaches in which nontrivial cell shape is accommodated, including the recently introduced Subcellular Element Model, in which each cell is described as a cluster of adhesively coupled over-damped subcellular elements, representing patches of cytoskeleton. In the second part of the paper we illustrate the use of a standard grid-free cell-based model to computationally probe interesting new features associated with primitive streak formation in the chick embryo. Streak formation is a key developmental step in amniotes (i.e., birds, reptiles, and mammals), and can be observed in detail in the chick embryo, where the streak extends across a tightly-packed two-dimensional sheet (the epiblast) comprised of about 50,000 cells. The Weijer group [Cui, Yang, Chuai, Glazier, and Weijer, Dev. Biol. 284 (2005) 37-47] recently observed that streak formation is accompanied by coordinated cell movement lateral to the streak, resulting in two large counter-rotating vortices. We study a mechanism based on cell polarity (in the plane of the epiblast) that provides an explanation for these vortices, and test it successfully using computer simulations. This mechanism is robust, since the emergent vortex formation depends only on the gross features of the initial spatial distribution of planar polarity in the epiblast.
@article{
title = {Grid-free models of multicellular systems, with an application to large-scale vortices accompanying primitive streak formation.},
type = {article},
year = {2008},
identifiers = {[object Object]},
keywords = {Animals,Cell Adhesion,Cell Movement,Cell Polarity,Cell Shape,Chick Embryo,Computer Simulation,Cyclic AMP,Cyclic AMP: metabolism,Dictyostelium,Dictyostelium: cytology,Dictyostelium: metabolism,Ferric Compounds,Germ Layers,Germ Layers: cytology,Models, Biological,Primitive Streak,Primitive Streak: cytology,Primitive Streak: embryology,Stochastic Processes},
pages = {157-82},
volume = {81},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/18023727},
month = {1},
id = {e3671b8e-592a-3bce-8010-0a966527d736},
created = {2016-02-10T15:06:25.000Z},
accessed = {2014-12-01},
file_attached = {true},
profile_id = {397d75f1-832d-36e0-bbe6-b6878f88c402},
group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
last_modified = {2017-03-14T10:42:46.538Z},
read = {true},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Newman2008},
folder_uuids = {8010415f-2a72-427e-8a93-e658ed2fb621},
private_publication = {false},
abstract = {This paper is comprised of two parts. In the first we provide a brief overview of grid-free methods for modeling multicellular systems. We focus on an approach based on Langevin equations, in which inertia is ignored, and stochastic effects on cell motion are included. The discussion starts with simpler models, in which cells are modeled as adhesive spheres. We then turn to more sophisticated approaches in which nontrivial cell shape is accommodated, including the recently introduced Subcellular Element Model, in which each cell is described as a cluster of adhesively coupled over-damped subcellular elements, representing patches of cytoskeleton. In the second part of the paper we illustrate the use of a standard grid-free cell-based model to computationally probe interesting new features associated with primitive streak formation in the chick embryo. Streak formation is a key developmental step in amniotes (i.e., birds, reptiles, and mammals), and can be observed in detail in the chick embryo, where the streak extends across a tightly-packed two-dimensional sheet (the epiblast) comprised of about 50,000 cells. The Weijer group [Cui, Yang, Chuai, Glazier, and Weijer, Dev. Biol. 284 (2005) 37-47] recently observed that streak formation is accompanied by coordinated cell movement lateral to the streak, resulting in two large counter-rotating vortices. We study a mechanism based on cell polarity (in the plane of the epiblast) that provides an explanation for these vortices, and test it successfully using computer simulations. This mechanism is robust, since the emergent vortex formation depends only on the gross features of the initial spatial distribution of planar polarity in the epiblast.},
bibtype = {article},
author = {Newman, Timothy J},
journal = {Current topics in developmental biology},
number = {07}
}Phenotypic plasticity, costs of phenotypes, and costs of plasticity: toward an integrative view. Callahan, H. S, Maughan, H., & Steiner, U. K Annals of the New York Academy of Sciences, 1133:44--66, 2008.
doi abstract bibtex
doi abstract bibtex
Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic basis of plasticity. In this vein, microbial work is especially illuminating and has three additional strengths. First, information about the machinery underlying plasticity--such as structural and regulatory genes, sensory proteins, and biochemical pathways--helps link population-level studies with underlying physiological and genetic mechanisms. Second, microbial studies involve many generations, large populations, and replication. Finally, empirical estimation of key parameters (e.g., mutation rates) is tractable. Together, these allow for rigorous investigation of gene interactions, drift, mutation, and selection--all potential factors influencing the maintenance or loss of inducible traits along with phenotypic and plasticity costs. Messages emerging from microbial work can guide future efforts to understand the evolution of plastic traits in diverse organisms.
@article{callahan_phenotypic_2008,
title = {Phenotypic plasticity, costs of phenotypes, and costs of plasticity: toward an integrative view},
volume = {1133},
issn = {0077-8923},
shorttitle = {Phenotypic plasticity, costs of phenotypes, and costs of plasticity},
doi = {10.1196/annals.1438.008},
abstract = {Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic basis of plasticity. In this vein, microbial work is especially illuminating and has three additional strengths. First, information about the machinery underlying plasticity--such as structural and regulatory genes, sensory proteins, and biochemical pathways--helps link population-level studies with underlying physiological and genetic mechanisms. Second, microbial studies involve many generations, large populations, and replication. Finally, empirical estimation of key parameters (e.g., mutation rates) is tractable. Together, these allow for rigorous investigation of gene interactions, drift, mutation, and selection--all potential factors influencing the maintenance or loss of inducible traits along with phenotypic and plasticity costs. Messages emerging from microbial work can guide future efforts to understand the evolution of plastic traits in diverse organisms.},
language = {eng},
journal = {Annals of the New York Academy of Sciences},
author = {Callahan, Hilary S and Maughan, Heather and Steiner, Ulrich K},
year = {2008},
pmid = {18559815},
keywords = {Adaptation, Physiological, Animals, Directed Molecular Evolution, Food Chain, Genetic Variation, Genome, Models, Biological, Models, Genetic, Phenotype, Predatory Behavior, Selection, Genetic},
pages = {44--66}
}2007 (8)
The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Watters, A. L, Deka, P., Corrent, C., Callender, D., Varani, G., Sosnick, T., & Baker, D. Cell, 128(3):613--624, February, 2007.
doi abstract bibtex
doi abstract bibtex
To illuminate the evolutionary pressure acting on the folding free energy landscapes of naturally occurring proteins, we have systematically characterized the folding free energy landscape of Top7, a computationally designed protein lacking an evolutionary history. Stopped-flow kinetics, circular dichroism, and NMR experiments reveal that there are at least three distinct phases in the folding of Top7, that a nonnative conformation is stable at equilibrium, and that multiple fragments of Top7 are stable in isolation. These results indicate that the folding of Top7 is significantly less cooperative than the folding of similarly sized naturally occurring proteins, suggesting that the cooperative folding and smooth free energy landscapes observed for small naturally occurring proteins are not general properties of polypeptide chains that fold to unique stable structures but are instead a product of natural selection.
@article{watters_highly_2007,
title = {The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection},
volume = {128},
issn = {0092-8674},
doi = {10.1016/j.cell.2006.12.042},
abstract = {To illuminate the evolutionary pressure acting on the folding free energy landscapes of naturally occurring proteins, we have systematically characterized the folding free energy landscape of Top7, a computationally designed protein lacking an evolutionary history. Stopped-flow kinetics, circular dichroism, and NMR experiments reveal that there are at least three distinct phases in the folding of Top7, that a nonnative conformation is stable at equilibrium, and that multiple fragments of Top7 are stable in isolation. These results indicate that the folding of Top7 is significantly less cooperative than the folding of similarly sized naturally occurring proteins, suggesting that the cooperative folding and smooth free energy landscapes observed for small naturally occurring proteins are not general properties of polypeptide chains that fold to unique stable structures but are instead a product of natural selection.},
language = {eng},
number = {3},
journal = {Cell},
author = {Watters, Alexander L and Deka, Pritilekha and Corrent, Colin and Callender, David and Varani, Gabriele and Sosnick, Tobin and Baker, David},
month = feb,
year = {2007},
pmid = {17289578},
keywords = {Circular Dichroism, Kinetics, Models, Chemical, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Point Mutation, Protein Folding, Protein Structure, Secondary, Proteins, Selection, Genetic, Thermodynamics},
pages = {613--624}
}The flexural stiffness of superficial neuromasts in the zebrafish (Danio rerio) lateral line. McHenry, M., J. & van Netten, S., M. The Journal of experimental biology, 210(Pt 23):4244-53, 12, 2007.
Paper Website abstract bibtex
Paper Website abstract bibtex Superficial neuromasts are structures that detect water flow on the surface of the body of fish and amphibians. As a component of the lateral line system, these receptors are distributed along the body, where they sense flow patterns that mediate a wide variety of behaviors. Their ability to detect flow is governed by their structural properties, yet the micromechanics of superficial neuromasts are not well understood. The aim of this study was to examine these mechanics in zebrafish (Danio rerio) larvae by measuring the flexural stiffness of individual neuromasts. Each neuromast possesses a gelatinous cupula that is anchored to hair cells by kinocilia. Using quasi-static bending tests of the proximal region of the cupula, we found that flexural stiffness is proportional to the number of hair cells, and consequently the number of kinocilia, within a neuromast. From this relationship, the flexural stiffness of an individual kinocilium was found to be 2.4 x 10(-20) N m2. Using this value, we estimate that the 11 kinocilia in an average cupula generate more than four-fifths of the total flexural stiffness in the proximal region. The relatively minor contribution of the cupular matrix may be attributed to its highly compliant material composition (Young's modulus of approximately 21 Pa). The distal tip of the cupula is entirely composed of this material and is consequently predicted to be at least an order of magnitude more flexible than the proximal region. These findings suggest that the transduction of flow by a superficial neuromast depends on structural dynamics that are dominated by the number and height of kinocilia.
@article{
title = {The flexural stiffness of superficial neuromasts in the zebrafish (Danio rerio) lateral line.},
type = {article},
year = {2007},
identifiers = {[object Object]},
keywords = {Animals,Biomechanics,Cilia,Cilia: physiology,Larva,Larva: anatomy & histology,Lateral Line System,Lateral Line System: anatomy & histology,Lateral Line System: physiology,Models, Biological,Zebrafish,Zebrafish: anatomy & histology,Zebrafish: physiology},
pages = {4244-53},
volume = {210},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/18025022},
month = {12},
id = {8868854a-7353-3c9b-ac4d-81317f75c261},
created = {2012-12-06T09:13:40.000Z},
accessed = {2010-08-18},
file_attached = {true},
profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
last_modified = {2017-03-14T17:27:14.020Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {McHenry2007a},
abstract = {Superficial neuromasts are structures that detect water flow on the surface of the body of fish and amphibians. As a component of the lateral line system, these receptors are distributed along the body, where they sense flow patterns that mediate a wide variety of behaviors. Their ability to detect flow is governed by their structural properties, yet the micromechanics of superficial neuromasts are not well understood. The aim of this study was to examine these mechanics in zebrafish (Danio rerio) larvae by measuring the flexural stiffness of individual neuromasts. Each neuromast possesses a gelatinous cupula that is anchored to hair cells by kinocilia. Using quasi-static bending tests of the proximal region of the cupula, we found that flexural stiffness is proportional to the number of hair cells, and consequently the number of kinocilia, within a neuromast. From this relationship, the flexural stiffness of an individual kinocilium was found to be 2.4 x 10(-20) N m2. Using this value, we estimate that the 11 kinocilia in an average cupula generate more than four-fifths of the total flexural stiffness in the proximal region. The relatively minor contribution of the cupular matrix may be attributed to its highly compliant material composition (Young's modulus of approximately 21 Pa). The distal tip of the cupula is entirely composed of this material and is consequently predicted to be at least an order of magnitude more flexible than the proximal region. These findings suggest that the transduction of flow by a superficial neuromast depends on structural dynamics that are dominated by the number and height of kinocilia.},
bibtype = {article},
author = {McHenry, Matthew J and van Netten, Sietse M},
journal = {The Journal of experimental biology},
number = {Pt 23}
}Computer-aided drug design: the next 20 years. Van Drie, J. H. Journal of Computer-Aided Molecular Design, 21(10-11):591–601, November, 2007.
doi abstract bibtex
doi abstract bibtex
This perspectives article has been taken from a talk the author gave at the symposium in honor of Yvonne C. Martin's retirement, held at the American Chemical Society spring meeting in Chicago on March 25, 2007. The talk was intended as a somewhat lighthearted attempt to gaze into the future; inevitably, in print, things will come across more seriously than was intended. As we all know-the past is rarely predictive of the future.
@article{van_drie_computer-aided_2007,
title = {Computer-aided drug design: the next 20 years},
volume = {21},
issn = {0920-654X},
shorttitle = {Computer-aided drug design},
doi = {10.1007/s10822-007-9142-y},
abstract = {This perspectives article has been taken from a talk the author gave at the symposium in honor of Yvonne C. Martin's retirement, held at the American Chemical Society spring meeting in Chicago on March 25, 2007. The talk was intended as a somewhat lighthearted attempt to gaze into the future; inevitably, in print, things will come across more seriously than was intended. As we all know-the past is rarely predictive of the future.},
language = {eng},
number = {10-11},
journal = {Journal of Computer-Aided Molecular Design},
author = {Van Drie, John H.},
month = nov,
year = {2007},
pmid = {17989929},
keywords = {Computer-Aided Design, Drug Design, Drug Evaluation, Preclinical, History, 20th Century, History, 21st Century, Ligands, Models, Molecular, Quantitative Structure-Activity Relationship, Software, Thermodynamics, User-Computer Interface},
pages = {591--601},
}Data-driven grasp synthesis using shape matching and task-based pruning. Li, Y., Fu, J., L., & Pollard, N., S. IEEE transactions on visualization and computer graphics, 13(4):732-47, 1, 2007.
Paper Website abstract bibtex
Paper Website abstract bibtex Human grasps, especially whole-hand grasps, are difficult to animate because of the high number of degrees of freedom of the hand and the need for the hand to conform naturally to the object surface. Captured human motion data provides us with a rich source of examples of natural grasps. However, for each new object, we are faced with the problem of selecting the best grasp from the database and adapting it to that object. This paper presents a data-driven approach to grasp synthesis. We begin with a database of captured human grasps. To identify candidate grasps for a new object, we introduce a novel shape matching algorithm that matches hand shape to object shape by identifying collections of features having similar relative placements and surface normals. This step returns many grasp candidates, which are clustered and pruned by choosing the grasp best suited for the intended task. For pruning undesirable grasps, we develop an anatomically-based grasp quality measure specific to the human hand. Examples of grasp synthesis are shown for a variety of objects not present in the original database. This algorithm should be useful both as an animator tool for posing the hand and for automatic grasp synthesis in virtual environments.
@article{
title = {Data-driven grasp synthesis using shape matching and task-based pruning.},
type = {article},
year = {2007},
identifiers = {[object Object]},
keywords = {Algorithms,Artificial Intelligence,Computer Graphics,Computer Simulation,Databases, Factual,Hand,Hand Strength,Hand Strength: physiology,Hand: anatomy & histology,Hand: physiology,Humans,Image Enhancement,Image Enhancement: methods,Image Interpretation, Computer-Assisted,Image Interpretation, Computer-Assisted: methods,Imaging, Three-Dimensional,Imaging, Three-Dimensional: methods,Information Storage and Retrieval,Information Storage and Retrieval: methods,Models, Biological,Numerical Analysis, Computer-Assisted,Pattern Recognition, Automated,Pattern Recognition, Automated: methods,Task Performance and Analysis,User-Computer Interface},
pages = {732-47},
volume = {13},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/17495333},
month = {1},
id = {ec6d4de5-0837-33ee-800a-bb66a2178f4d},
created = {2015-11-11T21:03:58.000Z},
accessed = {2015-11-11},
file_attached = {true},
profile_id = {49ab3d8e-c22b-36d3-a37b-6ec3833fa8a0},
group_id = {eeef833e-cee4-3b2a-b33a-aec5e9ea9601},
last_modified = {2015-11-11T21:05:17.000Z},
tags = {data driven,grasp synthesis,survey},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
short_title = {Visualization and Computer Graphics, IEEE Transact},
abstract = {Human grasps, especially whole-hand grasps, are difficult to animate because of the high number of degrees of freedom of the hand and the need for the hand to conform naturally to the object surface. Captured human motion data provides us with a rich source of examples of natural grasps. However, for each new object, we are faced with the problem of selecting the best grasp from the database and adapting it to that object. This paper presents a data-driven approach to grasp synthesis. We begin with a database of captured human grasps. To identify candidate grasps for a new object, we introduce a novel shape matching algorithm that matches hand shape to object shape by identifying collections of features having similar relative placements and surface normals. This step returns many grasp candidates, which are clustered and pruned by choosing the grasp best suited for the intended task. For pruning undesirable grasps, we develop an anatomically-based grasp quality measure specific to the human hand. Examples of grasp synthesis are shown for a variety of objects not present in the original database. This algorithm should be useful both as an animator tool for posing the hand and for automatic grasp synthesis in virtual environments.},
bibtype = {article},
author = {Li, Ying and Fu, Jiaxin L and Pollard, Nancy S},
journal = {IEEE transactions on visualization and computer graphics},
number = {4}
}Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms. Kültz, D., Fiol, D., Valkova, N., Gomez-Jimenez, S., Chan, S., Y., & Lee, J. The Journal of experimental biology, 210(Pt 9):1593-601, 5, 2007.
Paper Website abstract bibtex
Paper Website abstract bibtex All organisms are adapted to well-defined extracellular salinity ranges. Osmoregulatory mechanisms spanning all levels of biological organization, from molecules to behavior, are central to salinity adaptation. Functional genomics and proteomics approaches represent powerful tools for gaining insight into the molecular basis of salinity adaptation and euryhalinity in animals. In this review, we discuss our experience in applying such tools to so-called 'non-model' species, including euryhaline animals that are well-suited for studies of salinity adaptation. Suppression subtractive hybridization, RACE-PCR and mass spectrometry-driven proteomics can be used to identify genes and proteins involved in salinity adaptation or other environmental stress responses in tilapia, sharks and sponges. For protein identification in non-model species, algorithms based on sequence homology searches such as MSBLASTP2 are most powerful. Subsequent gene ontology and pathway analysis can then utilize sets of identified genes and proteins for modeling molecular mechanisms of environmental adaptation. Current limitations for proteomics in non-model species can be overcome by improving sequence coverage, N- and C-terminal sequencing and analysis of intact proteins. Dependence on information about biochemical pathways and gene ontology databases for model species represents a more severe barrier for work with non-model species. To minimize such dependence, focusing on a single biological process (rather than attempting to describe the system as a whole) is key when applying 'omics' approaches to non-model organisms.
@article{
title = {Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms.},
type = {article},
year = {2007},
identifiers = {[object Object]},
keywords = {Adaptation, Physiological,Adaptation, Physiological: genetics,Animals,Computational Biology,Computational Biology: methods,Databases, Genetic,Electrophoresis, Gel, Two-Dimensional,Electrophoresis, Gel, Two-Dimensional: methods,Gene Regulatory Networks,Gene Regulatory Networks: genetics,Genomics,Genomics: methods,Models, Biological,Nucleic Acid Hybridization,Nucleic Acid Hybridization: methods,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Protein Interaction Mapping,Protein Interaction Mapping: methods,Proteomics,Proteomics: methods,Species Specificity,Water-Electrolyte Balance,Water-Electrolyte Balance: genetics},
pages = {1593-601},
volume = {210},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/17449824},
month = {5},
id = {b6d25d99-c033-3a18-9605-0f4802f65569},
created = {2012-12-06T09:12:59.000Z},
file_attached = {true},
profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
last_modified = {2017-03-14T17:27:14.020Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Kultz2007},
abstract = {All organisms are adapted to well-defined extracellular salinity ranges. Osmoregulatory mechanisms spanning all levels of biological organization, from molecules to behavior, are central to salinity adaptation. Functional genomics and proteomics approaches represent powerful tools for gaining insight into the molecular basis of salinity adaptation and euryhalinity in animals. In this review, we discuss our experience in applying such tools to so-called 'non-model' species, including euryhaline animals that are well-suited for studies of salinity adaptation. Suppression subtractive hybridization, RACE-PCR and mass spectrometry-driven proteomics can be used to identify genes and proteins involved in salinity adaptation or other environmental stress responses in tilapia, sharks and sponges. For protein identification in non-model species, algorithms based on sequence homology searches such as MSBLASTP2 are most powerful. Subsequent gene ontology and pathway analysis can then utilize sets of identified genes and proteins for modeling molecular mechanisms of environmental adaptation. Current limitations for proteomics in non-model species can be overcome by improving sequence coverage, N- and C-terminal sequencing and analysis of intact proteins. Dependence on information about biochemical pathways and gene ontology databases for model species represents a more severe barrier for work with non-model species. To minimize such dependence, focusing on a single biological process (rather than attempting to describe the system as a whole) is key when applying 'omics' approaches to non-model organisms.},
bibtype = {article},
author = {Kültz, Dietmar and Fiol, Diego and Valkova, Nelly and Gomez-Jimenez, Silvia and Chan, Stephanie Y and Lee, Jinoo},
journal = {The Journal of experimental biology},
number = {Pt 9}
}Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 1. Noviello, C. M., Pond, S. L. K., Lewis, M. J., Richman, D. D., Pillai, S. K., Yang, O. O., Little, S. J., Smith, D. M., & Guatelli, J. C. Journal of Virology, 81(9):4776–4786, May, 2007.
doi abstract bibtex
doi abstract bibtex
Viruses encounter changing selective pressures during transmission between hosts, including host-specific immune responses and potentially varying functional demands on specific proteins. The human immunodeficiency virus type 1 Nef protein performs several functions potentially important for successful infection, including immune escape via down-regulation of class I major histocompatibility complex (MHC-I) and direct enhancement of viral infectivity and replication. Nef is also a major target of the host cytotoxic T-lymphocyte (CTL) response. To examine the impact of changing selective pressures on Nef functions following sexual transmission, we analyzed genetic and functional changes in nef clones from six transmission events. Phylogenetic analyses indicated that the diversity of nef was similar in both sources and acutely infected recipients, the patterns of selection across transmission were variable, and regions of Nef associated with distinct functions evolved similarly in sources and recipients. These results weighed against the selection of specific Nef functions by transmission or during acute infection. Measurement of Nef function provided no evidence that the down-regulation of either CD4 or MHC-I was optimized by transmission or during acute infection, although rare nef clones from sources that were impaired in these activities were not detected in recipients. Nef-specific CTL activity was detected as early as 3 weeks after infection and appeared to be an evolutionary force driving the diversification of nef. Despite the change in selective pressure between the source and recipient immune systems and concomitant genetic diversity, the majority of Nef proteins maintained robust abilities to down-regulate MHC-I and CD4. These data suggest that both functions are important for the successful establishment of infection in a new host.
@article{noviello_maintenance_2007,
title = {Maintenance of {Nef}-mediated modulation of major histocompatibility complex class {I} and {CD4} after sexual transmission of human immunodeficiency virus type 1},
volume = {81},
issn = {0022-538X},
doi = {10.1128/JVI.01793-06},
abstract = {Viruses encounter changing selective pressures during transmission between hosts, including host-specific immune responses and potentially varying functional demands on specific proteins. The human immunodeficiency virus type 1 Nef protein performs several functions potentially important for successful infection, including immune escape via down-regulation of class I major histocompatibility complex (MHC-I) and direct enhancement of viral infectivity and replication. Nef is also a major target of the host cytotoxic T-lymphocyte (CTL) response. To examine the impact of changing selective pressures on Nef functions following sexual transmission, we analyzed genetic and functional changes in nef clones from six transmission events. Phylogenetic analyses indicated that the diversity of nef was similar in both sources and acutely infected recipients, the patterns of selection across transmission were variable, and regions of Nef associated with distinct functions evolved similarly in sources and recipients. These results weighed against the selection of specific Nef functions by transmission or during acute infection. Measurement of Nef function provided no evidence that the down-regulation of either CD4 or MHC-I was optimized by transmission or during acute infection, although rare nef clones from sources that were impaired in these activities were not detected in recipients. Nef-specific CTL activity was detected as early as 3 weeks after infection and appeared to be an evolutionary force driving the diversification of nef. Despite the change in selective pressure between the source and recipient immune systems and concomitant genetic diversity, the majority of Nef proteins maintained robust abilities to down-regulate MHC-I and CD4. These data suggest that both functions are important for the successful establishment of infection in a new host.},
language = {eng},
number = {9},
journal = {Journal of Virology},
author = {Noviello, C. M. and Pond, S. L. Kosakovsky and Lewis, M. J. and Richman, D. D. and Pillai, S. K. and Yang, O. O. and Little, S. J. and Smith, D. M. and Guatelli, J. C.},
month = may,
year = {2007},
pmid = {17329339},
pmcid = {PMC1900175},
keywords = {Amino Acid Sequence, Base Sequence, Blotting, Western, CD4 Antigens, Evolution, Molecular, Flow Cytometry, Gene Expression Regulation, Viral, Gene Products, nef, Genes, MHC Class I, Genetic Variation, HIV Infections, HIV-1, Humans, Likelihood Functions, Models, Genetic, Molecular Sequence Data, Phylogeny, Selection, Genetic, Sequence Alignment, Sequence Analysis, DNA, T-Lymphocytes, Cytotoxic, nef Gene Products, Human Immunodeficiency Virus},
pages = {4776--4786},
}Invariant object recognition with trace learning and multiple stimuli present during training. Stringer, S M, Rolls, E T, & Tromans, J M Network (Bristol, England), 18(2):161--187, June, 2007.
doi abstract bibtex
doi abstract bibtex
Over successive stages, the ventral visual system develops neurons that respond with view, size and position invariance to objects including faces. A major challenge is to explain how invariant representations of individual objects could develop given visual input from environments containing multiple objects. Here we show that the neurons in a 1-layer competitive network learn to represent combinations of three objects simultaneously present during training if the number of objects in the training set is low (e.g. 4), to represent combinations of two objects as the number of objects is increased to for e.g. 10, and to represent individual objects as the number of objects in the training set is increased further to for e.g. 20. We next show that translation invariant representations can be formed even when multiple stimuli are always present during training, by including a temporal trace in the learning rule. Finally, we show that these concepts can be extended to a multi-layer hierarchical network model (VisNet) of the ventral visual system. This approach provides a way to understand how a visual system can, by self-organizing competitive learning, form separate invariant representations of each object even when each object is presented in a scene with multiple other objects present, as in natural visual scenes.
@article{stringer_invariant_2007,
title = {Invariant object recognition with trace learning and multiple stimuli present during training},
volume = {18},
issn = {0954-898X},
doi = {10.1080/09548980701556055},
abstract = {Over successive stages, the ventral visual system develops neurons that respond with view, size and position invariance to objects including faces. A major challenge is to explain how invariant representations of individual objects could develop given visual input from environments containing multiple objects. Here we show that the neurons in a 1-layer competitive network learn to represent combinations of three objects simultaneously present during training if the number of objects in the training set is low (e.g. 4), to represent combinations of two objects as the number of objects is increased to for e.g. 10, and to represent individual objects as the number of objects in the training set is increased further to for e.g. 20. We next show that translation invariant representations can be formed even when multiple stimuli are always present during training, by including a temporal trace in the learning rule. Finally, we show that these concepts can be extended to a multi-layer hierarchical network model (VisNet) of the ventral visual system. This approach provides a way to understand how a visual system can, by self-organizing competitive learning, form separate invariant representations of each object even when each object is presented in a scene with multiple other objects present, as in natural visual scenes.},
language = {eng},
number = {2},
journal = {Network (Bristol, England)},
author = {Stringer, S M and Rolls, E T and Tromans, J M},
month = jun,
year = {2007},
pmid = {17966074},
keywords = {Animals, Computer Simulation, Generalization (Psychology), Humans, Learning, Models, Neurological, Neural Networks (Computer), Neurons, Pattern Recognition, Visual, Photic Stimulation, Visual Cortex, Visual Pathways},
pages = {161--187}
}Executable cell biology. Fisher, J. & Henzinger, T., A. Nat. Biotechnol., 25(11):1239-1249, 2007.
bibtex
bibtex
@article{
title = {Executable cell biology},
type = {article},
year = {2007},
pages = {1239-1249},
volume = {25},
id = {1d7c5593-0a7d-38b3-a959-385f3b3464c0},
created = {2017-04-26T09:06:19.807Z},
file_attached = {false},
profile_id = {93e9c71a-776d-397a-8da2-55f5d4b0425c},
group_id = {337127a6-4a46-3af3-a559-f76746200fef},
last_modified = {2017-04-26T09:06:19.807Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Henzinger2007},
source_type = {article},
bibtype = {article},
author = {Fisher, J and Henzinger, T A},
journal = {Nat. Biotechnol.},
number = {11}
}2006 (4)
Biosorption of heavy metals by Saccharomyces cerevisiae: a review. Wang, J. & Chen, C. Biotechnology Advances, 24(5):427--451, October, 2006.
Paper doi abstract bibtex
Paper doi abstract bibtex Heavy metal pollution has become one of the most serious environmental problems today. Biosorption, using biomaterials such as bacteria, fungi, yeast and algae, is regarded as a cost-effective biotechnology for the treatment of high volume and low concentration complex wastewaters containing heavy metal(s) in the order of 1 to 100 mg/L. Among the promising biosorbents for heavy metal removal which have been researched during the past decades, Saccharomyces cerevisiae has received increasing attention due to the unique nature in spite of its mediocre capacity for metal uptake compared with other fungi. S. cerevisiae is widely used in food and beverage production, is easily cultivated using cheap media, is also a by-product in large quantity as a waste of the fermentation industry, and is easily manipulated at molecular level. The state of the art in the field of biosorption of heavy metals by S. cerevisiae not only in China, but also worldwide, is reviewed in this paper, based on a substantial number of relevant references published recently on the background of biosorption achievements and development. Characteristics of S. cerevisiae in heavy metal biosorption are extensively discussed. The yeast can be studied in various forms for different purposes. Metal-binding capacity for various heavy metals by S. cerevisiae under different conditions is compared. Lead and uranium, for instances, could be removed from dilute solutions more effectively in comparison with other metals. The yeast biosorption largely depends on parameters such as pH, the ratio of the initial metal ion and initial biomass concentration, culture conditions, presence of various ligands and competitive metal ions in solution and to a limited extent on temperature. An assessment of the isotherm equilibrium model, as well as kinetics was performed. The mechanisms of biosorption are understood only to a limited extent. Elucidation of the mechanism of metal uptake is a real challenge in the field of biosorption. Various mechanism assumptions of metal uptake by S. cerevisiae are summarized.
@article{wang_biosorption_2006,
title = {Biosorption of heavy metals by {Saccharomyces} cerevisiae: a review},
volume = {24},
issn = {0734-9750},
shorttitle = {Biosorption of heavy metals by {Saccharomyces} cerevisiae},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16737792},
doi = {10.1016/j.biotechadv.2006.03.001},
abstract = {Heavy metal pollution has become one of the most serious environmental problems today. Biosorption, using biomaterials such as bacteria, fungi, yeast and algae, is regarded as a cost-effective biotechnology for the treatment of high volume and low concentration complex wastewaters containing heavy metal(s) in the order of 1 to 100 mg/L. Among the promising biosorbents for heavy metal removal which have been researched during the past decades, Saccharomyces cerevisiae has received increasing attention due to the unique nature in spite of its mediocre capacity for metal uptake compared with other fungi. S. cerevisiae is widely used in food and beverage production, is easily cultivated using cheap media, is also a by-product in large quantity as a waste of the fermentation industry, and is easily manipulated at molecular level. The state of the art in the field of biosorption of heavy metals by S. cerevisiae not only in China, but also worldwide, is reviewed in this paper, based on a substantial number of relevant references published recently on the background of biosorption achievements and development. Characteristics of S. cerevisiae in heavy metal biosorption are extensively discussed. The yeast can be studied in various forms for different purposes. Metal-binding capacity for various heavy metals by S. cerevisiae under different conditions is compared. Lead and uranium, for instances, could be removed from dilute solutions more effectively in comparison with other metals. The yeast biosorption largely depends on parameters such as pH, the ratio of the initial metal ion and initial biomass concentration, culture conditions, presence of various ligands and competitive metal ions in solution and to a limited extent on temperature. An assessment of the isotherm equilibrium model, as well as kinetics was performed. The mechanisms of biosorption are understood only to a limited extent. Elucidation of the mechanism of metal uptake is a real challenge in the field of biosorption. Various mechanism assumptions of metal uptake by S. cerevisiae are summarized.},
number = {5},
urldate = {2009-11-02TZ},
journal = {Biotechnology Advances},
author = {Wang, Jianlong and Chen, Can},
month = oct,
year = {2006},
pmid = {16737792},
keywords = {Environmental Pollutants, Metals, Heavy, Models, Theoretical, Saccharomyces cerevisiae},
pages = {427--451}
}PM source apportionment and health effects. 3. Investigation of inter-method variations in associations between estimated source contributions of PM2.5 and daily mortality in Phoenix, AZ. Mar, T., F., Ito, K., Koenig, J., Q., Larson, T., V., Eatough, D., J., Henry, R., C., Kim, E., Laden, F., Lall, R., Neas, L., Stölzel, M., Paatero, P., Hopke, P., K., & Thurston, G., D. Journal of exposure science & environmental epidemiology, 16(4):311-20, 7, 2006.
Paper Website abstract bibtex
Paper Website abstract bibtex As part of an EPA-sponsored workshop to investigate the use of source apportionment in health effects analyses, the associations between the participant's estimated source contributions of PM(2.5) for Phoenix, AZ for the period from 1995-1997 and cardiovascular and total nonaccidental mortality were analyzed using Poisson generalized linear models (GLM). The base model controlled for extreme temperatures, relative humidity, day of week, and time trends using natural spline smoothers. The same mortality model was applied to all of the apportionment results to provide a consistent comparison across source components and investigators/methods. Of the apportioned anthropogenic PM(2.5) source categories, secondary sulfate, traffic, and copper smelter-derived particles were most consistently associated with cardiovascular mortality. The sources with the largest cardiovascular mortality effect size were secondary sulfate (median estimate=16.0% per 5th-to-95th percentile increment at lag 0 day among eight investigators/methods) and traffic (median estimate=13.2% per 5th-to-95th percentile increment at lag 1 day among nine investigators/methods). For total mortality, the associations were weaker. Sea salt was also found to be associated with both total and cardiovascular mortality, but at 5 days lag. Fine particle soil and biomass burning factors were not associated with increased risks. Variations in the maximum effect lag varied by source category suggesting that past analyses considering only single lags of PM(2.5) may have underestimated health impact contributions at different lags. Further research is needed on the possibility that different PM(2.5) source components may have different effect lag structure. There was considerable consistency in the health effects results across source apportionments in their effect estimates and their lag structures. Variations in results across investigators/methods were small compared to the variations across source categories. These results indicate reproducibility of source apportionment results across investigative groups and support applicability of these methods to effects studies. However, future research will also need to investigate a number of other important issues including accuracy of results.
@article{
title = {PM source apportionment and health effects. 3. Investigation of inter-method variations in associations between estimated source contributions of PM2.5 and daily mortality in Phoenix, AZ.},
type = {article},
year = {2006},
identifiers = {[object Object]},
keywords = {Air Pollutants,Air Pollutants: analysis,Air Pollutants: toxicity,Arizona,Arizona: epidemiology,Environmental Exposure,Humans,Models, Theoretical,Mortality,Particle Size,Urban Health},
pages = {311-20},
volume = {16},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/16288316},
month = {7},
id = {f5937c72-c789-3949-8931-a64cd949f37d},
created = {2014-05-31T04:12:14.000Z},
accessed = {2013-05-26},
file_attached = {true},
profile_id = {9edae5ec-3a23-3830-8934-2c27bef6ccbe},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2014-11-19T06:01:10.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {As part of an EPA-sponsored workshop to investigate the use of source apportionment in health effects analyses, the associations between the participant's estimated source contributions of PM(2.5) for Phoenix, AZ for the period from 1995-1997 and cardiovascular and total nonaccidental mortality were analyzed using Poisson generalized linear models (GLM). The base model controlled for extreme temperatures, relative humidity, day of week, and time trends using natural spline smoothers. The same mortality model was applied to all of the apportionment results to provide a consistent comparison across source components and investigators/methods. Of the apportioned anthropogenic PM(2.5) source categories, secondary sulfate, traffic, and copper smelter-derived particles were most consistently associated with cardiovascular mortality. The sources with the largest cardiovascular mortality effect size were secondary sulfate (median estimate=16.0% per 5th-to-95th percentile increment at lag 0 day among eight investigators/methods) and traffic (median estimate=13.2% per 5th-to-95th percentile increment at lag 1 day among nine investigators/methods). For total mortality, the associations were weaker. Sea salt was also found to be associated with both total and cardiovascular mortality, but at 5 days lag. Fine particle soil and biomass burning factors were not associated with increased risks. Variations in the maximum effect lag varied by source category suggesting that past analyses considering only single lags of PM(2.5) may have underestimated health impact contributions at different lags. Further research is needed on the possibility that different PM(2.5) source components may have different effect lag structure. There was considerable consistency in the health effects results across source apportionments in their effect estimates and their lag structures. Variations in results across investigators/methods were small compared to the variations across source categories. These results indicate reproducibility of source apportionment results across investigative groups and support applicability of these methods to effects studies. However, future research will also need to investigate a number of other important issues including accuracy of results.},
bibtype = {article},
author = {Mar, Therese F and Ito, Kazuhiko and Koenig, Jane Q and Larson, Timothy V and Eatough, Delbert J and Henry, Ronald C and Kim, Eugene and Laden, Francine and Lall, Ramona and Neas, Lucas and Stölzel, Matthias and Paatero, Pentti and Hopke, Philip K and Thurston, George D},
journal = {Journal of exposure science & environmental epidemiology},
number = {4}
}Automatic vessel wall contour detection and quantification of wall thickness in in-vivo MR images of the human aorta. Adame, I., van der Geest, R., Bluemke, D., Lima, J., Reiber, J., & Lelieveldt, B. Journal of Magnetic Resonance Imaging, 24(3):595-602, 2006.
bibtex
bibtex
@Article{Adame_2006_954,
author = {Adame, I.M. and van der Geest, R.J. and Bluemke, D.A. and Lima, J.A. and Reiber, J.H. and Lelieveldt, B.P.},
journal = {Journal of Magnetic Resonance Imaging},
number = {3},
pages = {595-602},
title = {Automatic vessel wall contour detection and quantification of wall thickness in in-vivo {MR} images of the human aorta},
volume = {24},
year = {2006},
keywords = {Aged, Aged, 80, and, over, Algorithms, Aorta/, pathology, Atherosclerosis/pathology, Automation, Endothelium, Vascular/, pathology, Humans, Image, Processing, Computer-Assisted, Magnetic, Resonance, Imaging/, methods, Middle, Aged, Models, Theoretical, Regression, Analysis, Reproducibility, of, Results, Time, Factors},
title_with_no_special_chars = {Automatic vessel wall contour detection and quantification of wall thickness in invivo MR images of the human aorta}
}A simple rule for the evolution of cooperation on graphs and social networks. Ohtsuki, H., Hauert, C., Lieberman, E., & Nowak, M., a. Nature, 441(7092):502-5, 5, 2006.
Paper Website abstract bibtex
Paper Website abstract bibtex A fundamental aspect of all biological systems is cooperation. Cooperative interactions are required for many levels of biological organization ranging from single cells to groups of animals. Human society is based to a large extent on mechanisms that promote cooperation. It is well known that in unstructured populations, natural selection favours defectors over cooperators. There is much current interest, however, in studying evolutionary games in structured populations and on graphs. These efforts recognize the fact that who-meets-whom is not random, but determined by spatial relationships or social networks. Here we describe a surprisingly simple rule that is a good approximation for all graphs that we have analysed, including cycles, spatial lattices, random regular graphs, random graphs and scale-free networks: natural selection favours cooperation, if the benefit of the altruistic act, b, divided by the cost, c, exceeds the average number of neighbours, k, which means b/c > k. In this case, cooperation can evolve as a consequence of 'social viscosity' even in the absence of reputation effects or strategic complexity.
@article{
title = {A simple rule for the evolution of cooperation on graphs and social networks.},
type = {article},
year = {2006},
identifiers = {[object Object]},
keywords = {Altruism,Animals,Biological Evolution,Cooperative Behavior,Costs and Cost Analysis,Game Theory,Humans,Models, Biological,Selection, Genetic,Social Support},
pages = {502-5},
volume = {441},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2430087&tool=pmcentrez&rendertype=abstract},
month = {5},
day = {25},
id = {394b9e2a-eb7d-3260-be1b-97b4b67534dc},
created = {2014-11-13T17:56:03.000Z},
accessed = {2014-05-30},
file_attached = {true},
profile_id = {5a758209-74fb-3a9c-b322-2ae7f22f7b6c},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2014-11-18T21:16:27.000Z},
read = {false},
starred = {true},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {A fundamental aspect of all biological systems is cooperation. Cooperative interactions are required for many levels of biological organization ranging from single cells to groups of animals. Human society is based to a large extent on mechanisms that promote cooperation. It is well known that in unstructured populations, natural selection favours defectors over cooperators. There is much current interest, however, in studying evolutionary games in structured populations and on graphs. These efforts recognize the fact that who-meets-whom is not random, but determined by spatial relationships or social networks. Here we describe a surprisingly simple rule that is a good approximation for all graphs that we have analysed, including cycles, spatial lattices, random regular graphs, random graphs and scale-free networks: natural selection favours cooperation, if the benefit of the altruistic act, b, divided by the cost, c, exceeds the average number of neighbours, k, which means b/c > k. In this case, cooperation can evolve as a consequence of 'social viscosity' even in the absence of reputation effects or strategic complexity.},
bibtype = {article},
author = {Ohtsuki, Hisashi and Hauert, Christoph and Lieberman, Erez and Nowak, Martin a},
journal = {Nature},
number = {7092}
}2005 (7)
Endovascular needle injection of cholesteryl linoleate into the arterial wall produces complex vascular lesions identifiable by intravascular ultrasound: Early development in a porcine model of vulnerable plaque. Granada, J., Moreno, P., Burke, A., Schulz, D., Raizner, A., & Kaluza, G. Coronary Artery Dispatch, 16(4):217-224, 2005. DA - 20050525 NOT IN FILE
bibtex
bibtex
@Article{Granada_2005_989,
author = {Granada, J.F. and Moreno, P.R. and Burke, A.P. and Schulz, D.G. and Raizner, A.E. and Kaluza, G.L.},
journal = {Coronary Artery Dispatch},
note = {DA - 20050525 NOT IN FILE},
number = {4},
pages = {217-224},
title = {Endovascular needle injection of cholesteryl linoleate into the arterial wall produces complex vascular lesions identifiable by intravascular ultrasound: {E}arly development in a porcine model of vulnerable plaque},
volume = {16},
year = {2005},
keywords = {analysis, Animals, Arteriosclerosis, Biopsy, Needle, Cholesterol, Esters, Comparative, Study, Coronary, Vessels, Disease, Models, Animal, Iliac, Artery, Immunohistochemistry, Injections, Intra-Arterial, methods, pathology, Probability, Research, Support, Non-U.S.Gov't, Sensitivity, and, Specificity, Sus, scrofa, Tunica, Intima, ultrasonography, Ultrasonography, Interventional},
title_with_no_special_chars = {Endovascular needle injection of cholesteryl linoleate into the arterial wall produces complex vascular lesions identifiable by intravascular ultrasound Early development in a porcine model of vulnerable plaque}
}Comparison between back-trajectory based modeling and Lagrangian backward dispersion modeling for locating sources of reactive gaseous mercury. Han, Y., Holsen, T., M., Hopke, P., K., & Yi, S. Environmental science & technology, 39(6):1715-23, 3, 2005.
Paper Website abstract bibtex
Paper Website abstract bibtex Reactive gaseous mercury (RGM) was measured using an annular denuder coated with potassium chloride at three rural sites (Potsdam, Stockton, and Sterling) in New York State from April 2002 to April 2003. Concentrations of RGM ranged from 0.1 to 84.6 pg m(-3) with large spatial and temporal variation. Potential source contribution function (PSCF), a common receptor modeling tool, was used with these measurements, and source-receptor relationships were calculated using back-dispersion and deposition as well as back-trajectories. Modeling results were compared with the RGM emissions inventory, and Spearman rank-order correlation coefficients were calculated. PSCF results incorporating backward dispersion and deposition were better correlated with the emissions inventory than PSCF based on back-trajectories alone. This difference was determined to be mainly due to the inclusion of dispersion rather than deposition. The main sources of RGM were suggested to be coal-fired power plants in New York and Pennsylvania, the large copper smelter in Quebec, and the taconite mining areas around the Great Lakes.
@article{
title = {Comparison between back-trajectory based modeling and Lagrangian backward dispersion modeling for locating sources of reactive gaseous mercury.},
type = {article},
year = {2005},
identifiers = {[object Object]},
keywords = {Air Movements,Air Pollutants,Air Pollutants: analysis,Coal,Environmental Monitoring,Gases,Mercury,Mercury: analysis,Mercury: chemistry,Models, Theoretical,New York,Power Plants},
pages = {1715-23},
volume = {39},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/15819229},
month = {3},
day = {15},
id = {70b063a1-7c9e-39d3-9e21-ee1359ced920},
created = {2014-05-31T04:12:14.000Z},
file_attached = {true},
profile_id = {9edae5ec-3a23-3830-8934-2c27bef6ccbe},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2014-11-19T06:00:52.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {Reactive gaseous mercury (RGM) was measured using an annular denuder coated with potassium chloride at three rural sites (Potsdam, Stockton, and Sterling) in New York State from April 2002 to April 2003. Concentrations of RGM ranged from 0.1 to 84.6 pg m(-3) with large spatial and temporal variation. Potential source contribution function (PSCF), a common receptor modeling tool, was used with these measurements, and source-receptor relationships were calculated using back-dispersion and deposition as well as back-trajectories. Modeling results were compared with the RGM emissions inventory, and Spearman rank-order correlation coefficients were calculated. PSCF results incorporating backward dispersion and deposition were better correlated with the emissions inventory than PSCF based on back-trajectories alone. This difference was determined to be mainly due to the inclusion of dispersion rather than deposition. The main sources of RGM were suggested to be coal-fired power plants in New York and Pennsylvania, the large copper smelter in Quebec, and the taconite mining areas around the Great Lakes.},
bibtype = {article},
author = {Han, Young-Ji and Holsen, Thomas M and Hopke, Philip K and Yi, Seung-Muk},
journal = {Environmental science & technology},
number = {6}
}Comparison of different mathematical models to analyze diminution kinetics of ultrasound contrast enhancement in a flow phantom. Meyer-Wiethe, K., Cangur, H., & Seidel, G. U. Ultrasound Med Biol, 31(1):93-8, 2005. 0301-5629 (Print) Comparative Study Journal Article Research Support, Non-U.S. Gov't
bibtex
bibtex
@Article{MeyerWiethe_2005_1019,
author = {Meyer-Wiethe, K. and Cangur, H. and Seidel, G. U.},
journal = {Ultrasound Med Biol},
note = {0301-5629 (Print) Comparative Study Journal Article Research Support, Non-U.S. Gov't},
number = {1},
pages = {93-8},
title = {Comparison of different mathematical models to analyze diminution kinetics of ultrasound contrast enhancement in a flow phantom},
volume = {31},
year = {2005},
keywords = {Contrast, Media/*pharmacokinetics, Half-Life, Humans, Logistic, Models, Microbubbles, Microcirculation/ultrasonography, *Models, Cardiovascular, Phantoms, Imaging, Regional, Blood, Flow, Ultrasonography/*methods},
title_with_no_special_chars = {Comparison of different mathematical models to analyze diminution kinetics of ultrasound contrast enhancement in a flow phantom}
}Relation of family history of premature coronary heart disease and metabolic risk factors to risk of coronary arterial calcium in asymptomatic subjects. Michos, E. D., Nasir, K., Rumberger, J. A., Vasamreddy, C., Braunstein, J. B., Budoff, M. J., & Blumenthal, R. S. Am J Cardiol, 95(5):655-7, 2005.
bibtex
bibtex
@Article{Michos_2005_3796,
author = {Michos, E. D. and Nasir, K. and Rumberger, J. A. and Vasamreddy, C. and Braunstein, J. B. and Budoff, M. J. and Blumenthal, R. S.},
journal = {Am J Cardiol},
number = {5},
pages = {655-7},
title = {Relation of family history of premature coronary heart disease and metabolic risk factors to risk of coronary arterial calcium in asymptomatic subjects},
volume = {95},
year = {2005},
keywords = {Calcinosis/epidemiology/*genetics, Calcium/metabolism, Coronary, Arteriosclerosis/epidemiology/*genetics/*metabolism, Coronary, Disease/*genetics/*metabolism, Coronary, Vessels/pathology, Female, Humans, Hyperlipidemias/complications/epidemiology, Hypertension/complications/epidemiology, Logistic, Models, Male, Middle, Aged, Obesity/complications/epidemiology, Prevalence, Risk, Factors, Tomography, X-Ray, Computed},
title_with_no_special_chars = {Relation of family history of premature coronary heart disease and metabolic risk factors to risk of coronary arterial calcium in asymptomatic subjects}
}A hybrid framework for 3D medical image segmentation. Chen, T. & Metaxas, D. Medical Image Analysis, 9(6):547-565, 2005.
bibtex
bibtex
@Article{Chen_2005_5427,
author = {Chen, T. and Metaxas, D.},
journal = {Medical Image Analysis},
number = {6},
pages = {547-565},
title = {A hybrid framework for {3D} medical image segmentation},
volume = {9},
year = {2005},
keywords = {Segmentation, Deformable, models, Markov, random, fields, Gibbs, prior, models, Insight, ToolKit},
title_with_no_special_chars = {A hybrid framework for 3D medical image segmentation}
}Towards a novel class of predictive microbial growth models. Van Impe, J., F., Poschet, F., Geeraerd, A., H., & Vereecken, K., M. International journal of food microbiology, 100(1-3):97-105, 4, 2005.
abstract bibtex
abstract bibtex
Food safety and quality are influenced by the presence (and possible proliferation) of pathogenic and spoilage microorganisms during the life cycle of the product (i.e., from the raw ingredients at the start of the production process until the moment of consumption). In order to simulate and predict microbial evolution in foods, mathematical models are developed in the field of predictive microbiology. In general, microbial growth is a self-limiting process, principally due to either (i) the exhaustion of one of the essential nutrients, and/or (ii) the accumulation of toxic products that inhibit growth. Nowadays, most mathematical models used in predictive microbiology do not explicitly incorporate this basic microbial knowledge. In this paper, a novel class of microbial growth models is proposed. In contrast with the currently used logistic type models, e.g., the model of Baranyi and Roberts [Baranyi, J., Roberts, T.A., 1994. A dynamic approach to predicting bacterial growth in food. International Journal of Food Microbiology 23, 277-294], the novel model class explicitly incorporates nutrient exhaustion and/or metabolic waste product effects. As such, this novel model prototype constitutes an elementary building block to be extended in a natural way towards, e.g., microbial interactions in co-cultures (mediated by metabolic products) and microbial growth in structured foods (influenced by, e.g., local substrate concentrations). While under certain conditions the mathematical equivalence with classical logistic type models is clear and results in equal fitting capacities and parameter estimation quality (see Poschet et al. [Poschet, F., Vereecken, K.M., Geeraerd, A.H., Nicolai, B.M., Van Impe, J.F., 2004. Analysis of a novel class of predictive microbial growth models and application to co-culture growth. International Journal of Food Microbiology, this issue] for a more elaborated analysis in this respect), the biological interpretability and extendability represent the main added value.
@article{
title = {Towards a novel class of predictive microbial growth models.},
type = {article},
year = {2005},
identifiers = {[object Object]},
keywords = {Bacteria,Bacteria: growth & development,Bacteria: metabolism,Coculture Techniques,Consumer Product Safety,Food Microbiology,Hydrogen-Ion Concentration,Logistic Models,Models, Biological,Models, Theoretical,Predictive Value of Tests,Temperature,Time Factors},
pages = {97-105},
volume = {100},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/15854696},
month = {4},
day = {15},
id = {4819b5a2-8df1-3e62-9348-4fb5f9a90ddc},
created = {2015-06-19T12:52:56.000Z},
accessed = {2015-06-02},
file_attached = {false},
profile_id = {a0759483-03fa-3e0b-88ee-8f55266b3657},
group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
last_modified = {2015-06-19T12:53:05.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {Food safety and quality are influenced by the presence (and possible proliferation) of pathogenic and spoilage microorganisms during the life cycle of the product (i.e., from the raw ingredients at the start of the production process until the moment of consumption). In order to simulate and predict microbial evolution in foods, mathematical models are developed in the field of predictive microbiology. In general, microbial growth is a self-limiting process, principally due to either (i) the exhaustion of one of the essential nutrients, and/or (ii) the accumulation of toxic products that inhibit growth. Nowadays, most mathematical models used in predictive microbiology do not explicitly incorporate this basic microbial knowledge. In this paper, a novel class of microbial growth models is proposed. In contrast with the currently used logistic type models, e.g., the model of Baranyi and Roberts [Baranyi, J., Roberts, T.A., 1994. A dynamic approach to predicting bacterial growth in food. International Journal of Food Microbiology 23, 277-294], the novel model class explicitly incorporates nutrient exhaustion and/or metabolic waste product effects. As such, this novel model prototype constitutes an elementary building block to be extended in a natural way towards, e.g., microbial interactions in co-cultures (mediated by metabolic products) and microbial growth in structured foods (influenced by, e.g., local substrate concentrations). While under certain conditions the mathematical equivalence with classical logistic type models is clear and results in equal fitting capacities and parameter estimation quality (see Poschet et al. [Poschet, F., Vereecken, K.M., Geeraerd, A.H., Nicolai, B.M., Van Impe, J.F., 2004. Analysis of a novel class of predictive microbial growth models and application to co-culture growth. International Journal of Food Microbiology, this issue] for a more elaborated analysis in this respect), the biological interpretability and extendability represent the main added value.},
bibtype = {article},
author = {Van Impe, J F and Poschet, F and Geeraerd, A H and Vereecken, K M},
journal = {International journal of food microbiology},
number = {1-3}
}Synergy, redundancy, and independence in population codes. Schneidman, E., Bialek, W., & Berry, M. J The Journal of neuroscience : the official journal of the Society for Neuroscience, 25(21):5195--206, 2005.
Paper doi abstract bibtex
Paper doi abstract bibtex Decoding the activity of a population of neurons is a fundamental problem in neuroscience. A key aspect of this problem is determining whether correlations in the activity, i.e., noise correlations, are important. If they are important, then the decoding problem is high dimensional: decoding algorithms must take the correlational structure in the activity into account. If they are not important, or if they play a minor role, then the decoding problem can be reduced to lower dimension and thus made more tractable. The issue of whether correlations are important has been a subject of heated debate. The debate centers around the validity of the measures used to address it. Here, we evaluate three of the most commonly used ones: synergy, DeltaI(shuffled), and DeltaI. We show that synergy and DeltaI(shuffled) are confounded measures: they can be zero when correlations are clearly important for decoding and positive when they are not. In contrast, DeltaI is not confounded. It is zero only when correlations are not important for decoding and positive only when they are; that is, it is zero only when one can decode exactly as well using a decoder that ignores correlations as one can using a decoder that does not, and it is positive only when one cannot decode as well. Finally, we show that DeltaI has an information theoretic interpretation; it is an upper bound on the information lost when correlations are ignored.
@article{Schneidman2005,
abstract = {Decoding the activity of a population of neurons is a fundamental problem in neuroscience. A key aspect of this problem is determining whether correlations in the activity, i.e., noise correlations, are important. If they are important, then the decoding problem is high dimensional: decoding algorithms must take the correlational structure in the activity into account. If they are not important, or if they play a minor role, then the decoding problem can be reduced to lower dimension and thus made more tractable. The issue of whether correlations are important has been a subject of heated debate. The debate centers around the validity of the measures used to address it. Here, we evaluate three of the most commonly used ones: synergy, DeltaI(shuffled), and DeltaI. We show that synergy and DeltaI(shuffled) are confounded measures: they can be zero when correlations are clearly important for decoding and positive when they are not. In contrast, DeltaI is not confounded. It is zero only when correlations are not important for decoding and positive only when they are; that is, it is zero only when one can decode exactly as well using a decoder that ignores correlations as one can using a decoder that does not, and it is positive only when one cannot decode as well. Finally, we show that DeltaI has an information theoretic interpretation; it is an upper bound on the information lost when correlations are ignored.},
author = {Schneidman, Elad and Bialek, William and Berry, Michael J},
doi = {10.1523/JNEUROSCI.5319-04.2005},
file = {:Users/brekels/Documents/Mendeley Desktop/Synergy, redundancy, and independence in population codes - Schneidman, Bialek, Berry.pdf:pdf},
isbn = {1529-2401 (Electronic)},
issn = {1529-2401},
journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
keywords = {Action Potentials,Animals,Humans,Models,Neurological,Neurons,Neurons: physiology,Statistics as Topic},
number = {21},
pages = {5195--206},
pmid = {15917459},
title = {{Synergy, redundancy, and independence in population codes}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15917459},
volume = {25},
year = {2005}
}2004 (3)
The role of early visual cortex in visual integration: a neural model of recurrent interaction. Deco, G. & Lee, T. 20(4):1089-100, 2004.
abstract bibtex
abstract bibtex
This paper presents a model on the potential functional roles of the early visual cortex in the primate visual system. Our hypothesis is that early visual areas, such as V1, are important for continual interaction among various higher order visual areas during visual processing. The interaction is mediated by recurrent connections between higher order visual areas and V1, manifested in the long-latency context-sensitive activities often observed in neurophysiological experiments, and is responsible for the re-integration of information analysed by the higher visual areas. Specifically, we considered the case of integrating ‘what‘ and ‘where‘ information from the ventral and dorsal streams. We found that such a cortical architecture provides simple solutions and fresh insights into the problems of attentional routing and visual search. The computational viability of this architecture was tested by simulating a large-scale neural dynamical network.
@article{
title = {The role of early visual cortex in visual integration: a neural model of recurrent interaction},
type = {article},
year = {2004},
keywords = {Attention,Attention: physiology,Models,Neurological,Photic Stimulation,Photic Stimulation: methods,Reaction Time,Reaction Time: physiology,Visual Cortex,Visual Cortex: physiology,Visual Fields,Visual Fields: physiology},
pages = {1089-100},
volume = {20},
id = {4917f8f2-313f-3da0-bea4-534b13727982},
created = {2017-09-01T15:54:30.864Z},
file_attached = {false},
profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
last_modified = {2017-09-01T15:54:30.965Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {false},
hidden = {false},
abstract = {This paper presents a model on the potential functional roles of the early visual cortex in the primate visual system. Our hypothesis is that early visual areas, such as V1, are important for continual interaction among various higher order visual areas during visual processing. The interaction is mediated by recurrent connections between higher order visual areas and V1, manifested in the long-latency context-sensitive activities often observed in neurophysiological experiments, and is responsible for the re-integration of information analysed by the higher visual areas. Specifically, we considered the case of integrating ‘what‘ and ‘where‘ information from the ventral and dorsal streams. We found that such a cortical architecture provides simple solutions and fresh insights into the problems of attentional routing and visual search. The computational viability of this architecture was tested by simulating a large-scale neural dynamical network.},
bibtype = {article},
author = {Deco, Gustavo and Lee, Tai},
number = {4}
}Global hot spots of biological invasions: Evaluating options for ballast-water management. Drake, J., M. & Lodge, D., M. Proceedings of the Royal Society B: Biological Sciences, 271(1539):575-580, 2004.
abstract bibtex
abstract bibtex
Biological invasions from ballast water are a severe environmental threat and exceedingly costly to society. We identify global hot spots of invasion based on worldwide patterns of ship traffic. We then estimate the rate of port-to-port invasion using gravity models for spatial interactions, and we identify bottlenecks to the regional exchange of species using the Ford-Fulkerson algorithm for network flows. Finally, using stochastic simulations of different strategies for controlling ballast-water introductions, we find that reducing the per-ship-visit chance of causing invasion is more effective in reducing the rate of biotic homogenization than eliminating key ports that are the epicentres for global spread.
@article{
title = {Global hot spots of biological invasions: Evaluating options for ballast-water management},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {Ballast water,Biological invasion,Biotic homogenization,Ford-Fulkerson algorithm},
pages = {575-580},
volume = {271},
id = {df79e515-42e1-33af-b22a-98cf5916d694},
created = {2018-09-13T13:16:05.602Z},
file_attached = {true},
profile_id = {9aa84141-6744-3000-aa2d-8b83b70f0402},
group_id = {3addd0f7-d578-34d3-be80-24022cc062a1},
last_modified = {2018-09-13T13:17:43.200Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
folder_uuids = {46d73cb0-1cc4-42db-86d0-93a26fce7f83},
private_publication = {false},
abstract = {Biological invasions from ballast water are a severe environmental threat and exceedingly costly to society. We identify global hot spots of invasion based on worldwide patterns of ship traffic. We then estimate the rate of port-to-port invasion using gravity models for spatial interactions, and we identify bottlenecks to the regional exchange of species using the Ford-Fulkerson algorithm for network flows. Finally, using stochastic simulations of different strategies for controlling ballast-water introductions, we find that reducing the per-ship-visit chance of causing invasion is more effective in reducing the rate of biotic homogenization than eliminating key ports that are the epicentres for global spread.},
bibtype = {article},
author = {Drake, John M. and Lodge, David M.},
journal = {Proceedings of the Royal Society B: Biological Sciences},
number = {1539}
}Dynamic Bayesian Networks modelling the dependability of systems with degradations and exogenous constraints. Weber, P., Jouffe, L., Munteanu, P., Weber, P., Jouffe, L., Munteanu, P., & Bayesian, D. In 11th IFAC Symposium on Information Control Problems in Manufacturing, 2004.
Website abstract bibtex
Website abstract bibtex The work reported here presents an original method to model dependability of systems, taking into account degradations and failure modes governed by exogenous constraints. The component degradation dynamics is considered as a semi-Markov process. Environmental behaviour introduces switching models conditioned by exogenous constraints. Dynamic Bayesian Networks (DBN) are employed to formalise such complex dynamic processes through a compact representation. DBN allow simulating these processes, taking into account events due to the environmental behaviour. A hydraulic system is used to illustrate the reliability estimations obtained by the proposed modelling method.
@inproceedings{
title = {Dynamic Bayesian Networks modelling the dependability of systems with degradations and exogenous constraints},
type = {inproceedings},
year = {2004},
keywords = {dynamic bayesian network,hidden markov,markov switching model,models,reliability evaluation},
websites = {https://hal.archives-ouvertes.fr/hal-00131316/document},
city = {Salvador-Bahia},
id = {6538bf10-00e2-37b9-94c4-184f8e87d09b},
created = {2015-04-23T15:46:50.000Z},
file_attached = {false},
profile_id = {95e10851-cdf3-31de-9f82-1ab629e601b0},
group_id = {f4f27d7f-2273-33eb-bbb9-78e3e17cc268},
last_modified = {2017-03-14T09:42:43.424Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
private_publication = {false},
abstract = {The work reported here presents an original method to model dependability of systems, taking into account degradations and failure modes governed by exogenous constraints. The component degradation dynamics is considered as a semi-Markov process. Environmental behaviour introduces switching models conditioned by exogenous constraints. Dynamic Bayesian Networks (DBN) are employed to formalise such complex dynamic processes through a compact representation. DBN allow simulating these processes, taking into account events due to the environmental behaviour. A hydraulic system is used to illustrate the reliability estimations obtained by the proposed modelling method.},
bibtype = {inproceedings},
author = {Weber, Philippe and Jouffe, Lionel and Munteanu, Paul and Weber, Philippe and Jouffe, Lionel and Munteanu, Paul and Bayesian, Dynamic},
booktitle = {11th IFAC Symposium on Information Control Problems in Manufacturing}
}2003 (1)
Grandmothers and the Evolution of Human Longevity. Hawkes, K. American journal of human biology, 15(3):380-400, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex ABSTRACT Great apes, our closest living relatives, live longer and mature later than most other mammals and modern humans are even later-maturing and potentially longer-lived. Evolutionary life-history theory seeks to explain cross-species differences in these variables and the covariation between them. That provides the foundation for a hypothesis that a novel role for grandmothers underlies the shift from an ape-like ancestral pattern to one more like our own in the first widely successful members of genus Homo. This hypothesis links four distinctive features of human life histories: 1) our potential longevity, 2) our late maturity, 3) our midlife menopause, and 4) our early weaning with next offspring produced before the previous infant can feed itself. I discuss the problem, then, using modern humans and chimpanzees to represent, respectively, genus Homo and australopithecines, I focus on two corollaries of this grandmother hypothesis: 1) that ancestral age-specific fertility declines persisted in our genus, while 2) senescence in other aspects of physiological performance slowed down. The data are scanty but they illustrate similarities in age-specific fertility decline and differences in somatic durability that are consist- ent with the hypothesis that increased longevity in our genus is a legacy of the ‘‘reproductive’’ role of ancestral grandmothers
@article{
title = {Grandmothers and the Evolution of Human Longevity},
type = {article},
year = {2003},
identifiers = {[object Object]},
keywords = {*Evolution,*Family,*Longevity,Aging,Animals,Biological,Humans,Models,Pan troglodytes},
pages = {380-400},
volume = {15},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12704714},
edition = {2003/04/22},
id = {48b60b26-ce0d-3210-90d4-f3cd1e798e69},
created = {2017-06-19T13:41:50.765Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:41:50.891Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
language = {eng},
notes = {<m:note> <m:bold>From Duplicate 1 ( </m:bold> <m:bold> </m:bold><m:bold><m:italic>Grandmothers and the evolution of human longevity</m:italic></m:bold><m:bold> </m:bold> <m:bold> - Hawkes, K )<m:linebreak/> </m:bold> <m:linebreak/>Hawkes, Kristen<m:linebreak/>Review<m:linebreak/>United States<m:linebreak/>American journal of human biology : the official journal of the Human Biology Council<m:linebreak/>Am J Hum Biol. 2003 May-Jun;15(3):380-400.<m:linebreak/> <m:linebreak/> </m:note>},
abstract = {ABSTRACT Great apes, our closest living relatives, live longer and mature later than most other mammals and modern humans are even later-maturing and potentially longer-lived. Evolutionary life-history theory seeks to explain cross-species differences in these variables and the covariation between them. That provides the foundation for a hypothesis that a novel role for grandmothers underlies the shift from an ape-like ancestral pattern to one more like our own in the first widely successful members of genus Homo. This hypothesis links four distinctive features of human life histories: 1) our potential longevity, 2) our late maturity, 3) our midlife menopause, and 4) our early weaning with next offspring produced before the previous infant can feed itself. I discuss the problem, then, using modern humans and chimpanzees to represent, respectively, genus Homo and australopithecines, I focus on two corollaries of this grandmother hypothesis: 1) that ancestral age-specific fertility declines persisted in our genus, while 2) senescence in other aspects of physiological performance slowed down. The data are scanty but they illustrate similarities in age-specific fertility decline and differences in somatic durability that are consist- ent with the hypothesis that increased longevity in our genus is a legacy of the ‘‘reproductive’’ role of ancestral grandmothers},
bibtype = {article},
author = {Hawkes, Kristen},
journal = {American journal of human biology},
number = {3}
}2002 (9)
Middle temporal visual area microstimulation influences veridical judgments of motion direction. Nichols, M. & Newsome, W. 22(21):9530-9540, 2002.
Paper abstract bibtex
Paper abstract bibtex Microstimulation of direction columns in the middle temporal visual area (MT, or V5) provides a powerful tool for probing the relationship between cortical physiology and visual motion perception. In the current study we obtained "veridical" reports of perceived motion from rhesus monkeys by permitting a continuous range of possible responses that mapped isomorphically onto a continuous range of possible motion directions. In contrast to previous studies, therefore, the animals were freed from experimenter-imposed "categories" that typify forced choice tasks. We report three new findings: (1) MT neurons with widely disparate preferred directions can cooperate to shape direction estimates, inconsistent with a pure "winner-take-all" read-out algorithm and consistent with a distributed coding scheme like vector averaging, whereas neurons with nearly opposite preferred directions seem to compete in a manner consistent with the winner-take-all hypothesis, (2) microstimulation can influence direction estimates even when paired with the most powerful motion stimuli available, and (3) microstimulation effects can be elicited when a manual response (instead of our standard oculomotor response) is used to communicate the perceptual report.
@article{
title = {Middle temporal visual area microstimulation influences veridical judgments of motion direction},
type = {article},
year = {2002},
keywords = {Algorithms,Animals,Brain Mapping,Electric Stimulation/methods,Fixation, Ocular/physiology,Judgment/physiology,Macaca mulatta,Microelectrodes,Models, Neurological,Motion Perception/physiology,Neurons/physiology,Photic Stimulation/methods,Reproducibility of Results,Saccades/physiology,Temporal Lobe/physiology,Visual Cortex/physiology},
pages = {9530-9540},
volume = {22},
id = {997a2ff5-1369-36ff-8481-66f744bb339a},
created = {2017-09-01T15:54:30.239Z},
file_attached = {true},
profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
last_modified = {2017-09-01T15:54:30.352Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {false},
hidden = {false},
language = {eng},
abstract = {Microstimulation of direction columns in the middle temporal visual area (MT, or V5) provides a powerful tool for probing the relationship between cortical physiology and visual motion perception. In the current study we obtained "veridical" reports of perceived motion from rhesus monkeys by permitting a continuous range of possible responses that mapped isomorphically onto a continuous range of possible motion directions. In contrast to previous studies, therefore, the animals were freed from experimenter-imposed "categories" that typify forced choice tasks. We report three new findings: (1) MT neurons with widely disparate preferred directions can cooperate to shape direction estimates, inconsistent with a pure "winner-take-all" read-out algorithm and consistent with a distributed coding scheme like vector averaging, whereas neurons with nearly opposite preferred directions seem to compete in a manner consistent with the winner-take-all hypothesis, (2) microstimulation can influence direction estimates even when paired with the most powerful motion stimuli available, and (3) microstimulation effects can be elicited when a manual response (instead of our standard oculomotor response) is used to communicate the perceptual report.},
bibtype = {article},
author = {Nichols, M. and Newsome, William},
number = {21}
}Vulnerable atherosclerotic plaque: Emerging challenge for animal models. Rekhter, M. Curr.Opin.Cardiol., 17(6):626-632, 2002. DA - 20021205 NOT IN FILE
bibtex
bibtex
@Article{Rekhter_2002_1390,
author = {Rekhter, M.},
journal = {Curr.Opin.Cardiol.},
note = {DA - 20021205 NOT IN FILE},
number = {6},
pages = {626-632},
title = {Vulnerable atherosclerotic plaque: {E}merging challenge for animal models},
volume = {17},
year = {2002},
keywords = {Animals, Collagen, Coronary, Arteriosclerosis, Coronary, Thrombosis, Disease, Models, Animal, etiology, Models, Cardiovascular, pathology, therapy, Thrombosis},
title_with_no_special_chars = {Vulnerable atherosclerotic plaque Emerging challenge for animal models}
}Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies. Morris, A., P., Whittaker, J., C., & Balding, D., J. Am J Hum Genet, 70(3):686-707., 2002.
Paper abstract bibtex
Paper abstract bibtex We present a Bayesian, Markov-chain Monte Carlo method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. The method explicitly models the genealogy underlying a sample of case chromosomes in the vicinity of a putative disease locus, in contrast with the assumption of a star-shaped tree made by many existing multipoint methods. Within this modeling framework, we can allow for missing marker information and for uncertainty about the true underlying genealogy and the makeup of ancestral marker haplotypes. A crucial advantage of our method is the incorporation of the shattered coalescent model for genealogies, allowing for multiple founding mutations at the disease locus and for sporadic cases of disease. Output from the method includes approximate posterior distributions of the location of the disease locus and population-marker haplotype proportions. In addition, output from the algorithm is used to construct a cladogram to represent genetic heterogeneity at the disease locus, highlighting clusters of case chromosomes sharing the same mutation. We present detailed simulations to provide evidence of improvements over existing methodology. Furthermore, inferences about the location of the disease locus are shown to remain robust to modeling assumptions.
@article{
title = {Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies},
type = {article},
year = {2002},
identifiers = {[object Object]},
keywords = {*Pedigree,Algorithms,Alleles,Bayes Theorem,Bias (Epidemiology),Case-Control Studies,Chromosome Mapping/*methods/statistics & numerical,Computer Simulation,Cystic Fibrosis Transmembrane Conductance Regulato,Cystic Fibrosis/*genetics,Female,Genetic Heterogeneity,Genetic Markers/genetics,Haplotypes/genetics,Human,Linkage Disequilibrium/genetics,Male,Markov Chains,Models, Genetic,Monte Carlo Method,Mutation/genetics,Phylogeny,Probability,Recombination, Genetic/genetics,Sequence Deletion,Support, Non-U.S. Gov't},
pages = {686-707.},
volume = {70},
id = {b7168238-9085-3a82-81a6-a75268e0c428},
created = {2017-06-19T13:42:46.478Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:42:46.621Z},
tags = {02/04/26},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
abstract = {We present a Bayesian, Markov-chain Monte Carlo method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. The method explicitly models the genealogy underlying a sample of case chromosomes in the vicinity of a putative disease locus, in contrast with the assumption of a star-shaped tree made by many existing multipoint methods. Within this modeling framework, we can allow for missing marker information and for uncertainty about the true underlying genealogy and the makeup of ancestral marker haplotypes. A crucial advantage of our method is the incorporation of the shattered coalescent model for genealogies, allowing for multiple founding mutations at the disease locus and for sporadic cases of disease. Output from the method includes approximate posterior distributions of the location of the disease locus and population-marker haplotype proportions. In addition, output from the algorithm is used to construct a cladogram to represent genetic heterogeneity at the disease locus, highlighting clusters of case chromosomes sharing the same mutation. We present detailed simulations to provide evidence of improvements over existing methodology. Furthermore, inferences about the location of the disease locus are shown to remain robust to modeling assumptions.},
bibtype = {article},
author = {Morris, A P and Whittaker, J C and Balding, D J},
journal = {Am J Hum Genet},
number = {3}
}Spatial applicability of emission factors for modeling mobile emissions. Niemeier, D., a. Environmental science & technology, 36(4):736-41, 2, 2002.
Paper Website abstract bibtex
Paper Website abstract bibtex Driving cycles are used to create mobile emission factors. Emission factors are, in turn, used to estimate mobile source inventories, provide standards for new vehicle emissions testing, and facilitate comparisons of laboratory experiments. This study examines the spatial representativeness of the driving cycles underlying California's CO, THC, and NOx emission rates that are applied when estimating regional mobile emissions inventories. Sixteen randomly selected vehicles were tested on a laboratory dynamometer using driving cycles representative of driving in different cities. A total of 214 tests, with repetitions, representing six driving cycles, were conducted on the 16 vehicles. We used a random effects analysis of variance to statistically examine the differences in the resulting emission rates. The study results suggest that California mobile source pollutant inventories prepared using emission rates based on the standard drive cycle may be off by as much as 30% for regions where traffic congestion and roadway networks differ significantly from those of Los Angeles.
@article{
title = {Spatial applicability of emission factors for modeling mobile emissions.},
type = {article},
year = {2002},
identifiers = {[object Object]},
keywords = {Air Pollutants,Air Pollutants: analysis,Automobile Driving,California,Cities,Models, Theoretical,Reference Values,Reproducibility of Results,Vehicle Emissions},
pages = {736-41},
volume = {36},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/11878391},
month = {2},
day = {15},
id = {ffd6f07a-dde7-3eee-b078-675e2186513d},
created = {2014-05-31T04:14:24.000Z},
file_attached = {true},
profile_id = {9edae5ec-3a23-3830-8934-2c27bef6ccbe},
group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
last_modified = {2014-11-19T06:02:41.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {Driving cycles are used to create mobile emission factors. Emission factors are, in turn, used to estimate mobile source inventories, provide standards for new vehicle emissions testing, and facilitate comparisons of laboratory experiments. This study examines the spatial representativeness of the driving cycles underlying California's CO, THC, and NOx emission rates that are applied when estimating regional mobile emissions inventories. Sixteen randomly selected vehicles were tested on a laboratory dynamometer using driving cycles representative of driving in different cities. A total of 214 tests, with repetitions, representing six driving cycles, were conducted on the 16 vehicles. We used a random effects analysis of variance to statistically examine the differences in the resulting emission rates. The study results suggest that California mobile source pollutant inventories prepared using emission rates based on the standard drive cycle may be off by as much as 30% for regions where traffic congestion and roadway networks differ significantly from those of Los Angeles.},
bibtype = {article},
author = {Niemeier, D a},
journal = {Environmental science & technology},
number = {4}
}Activity-dependent regulation of HCN pacemaker channels by cyclic AMP: signaling through dynamic allosteric coupling. Wang, J., Chen, S., Nolan, M., F., & Siegelbaum, S., a. Neuron, 36(3):451-61, 10, 2002.
Paper Website abstract bibtex
Paper Website abstract bibtex Signal transduction in neurons is a dynamic process, generally thought to be driven by transient changes in the concentration of second messengers. Here we describe a novel regulatory mechanism in which the dynamics of signaling through cyclic AMP are mediated by activity-dependent changes in the affinity of the hyperpolarization-activated, cation nonselective (HCN) channels for cAMP, rather than by changes in cAMP concentration. Due to the allosteric coupling of channel opening and ligand binding, changes in cellular electrical activity that alter the opening of the HCN channels modify the binding of static, basal levels of cAMP. These changes in ligand binding produce long-lasting changes in channel function which can contribute to the regulation of rhythmic firing patterns.
@article{
title = {Activity-dependent regulation of HCN pacemaker channels by cyclic AMP: signaling through dynamic allosteric coupling.},
type = {article},
year = {2002},
identifiers = {[object Object]},
keywords = {Action Potentials,Action Potentials: drug effects,Action Potentials: physiology,Allosteric Regulation,Allosteric Regulation: drug effects,Allosteric Regulation: physiology,Animals,Central Nervous System,Central Nervous System: metabolism,Cerebral Cortex,Cerebral Cortex: metabolism,Cyclic AMP,Cyclic AMP: metabolism,Cyclic AMP: pharmacology,Dose-Response Relationship,Drug,Electric Stimulation,Female,Ion Channels,Ion Channels: drug effects,Ion Channels: metabolism,Kinetics,Models,Muscle Proteins,Muscle Proteins: drug effects,Muscle Proteins: metabolism,Neural Pathways,Neural Pathways: metabolism,Neurological,Neurons,Neurons: drug effects,Neurons: metabolism,Oocytes,Reaction Time,Reaction Time: drug effects,Reaction Time: physiology,Signal Transduction,Signal Transduction: drug effects,Signal Transduction: physiology,Synaptic Transmission,Synaptic Transmission: drug effects,Synaptic Transmission: physiology,Thalamus,Thalamus: metabolism,Xenopus laevis},
pages = {451-61},
volume = {36},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/12408847},
month = {10},
day = {24},
id = {4ef89909-f8bc-37f5-ace7-73124dabac80},
created = {2012-06-14T17:02:50.000Z},
file_attached = {true},
profile_id = {b662c5f6-8d1c-39ee-8a62-3ff04dae55cf},
last_modified = {2017-03-09T18:36:24.602Z},
read = {true},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
folder_uuids = {65a9638b-8c1a-4479-b941-46ea2e673403},
private_publication = {false},
abstract = {Signal transduction in neurons is a dynamic process, generally thought to be driven by transient changes in the concentration of second messengers. Here we describe a novel regulatory mechanism in which the dynamics of signaling through cyclic AMP are mediated by activity-dependent changes in the affinity of the hyperpolarization-activated, cation nonselective (HCN) channels for cAMP, rather than by changes in cAMP concentration. Due to the allosteric coupling of channel opening and ligand binding, changes in cellular electrical activity that alter the opening of the HCN channels modify the binding of static, basal levels of cAMP. These changes in ligand binding produce long-lasting changes in channel function which can contribute to the regulation of rhythmic firing patterns.},
bibtype = {article},
author = {Wang, Jing and Chen, Shan and Nolan, Matthew F and Siegelbaum, Steven a},
journal = {Neuron},
number = {3}
}Genomic analysis of uncultured marine viral communities. Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F., & Rohwer, F. Proceedings of the National Academy of Sciences of the United States of America, 99(22):14250--14255, October, 2002.
doi abstract bibtex
doi abstract bibtex
Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.
@article{breitbart_genomic_2002,
title = {Genomic analysis of uncultured marine viral communities},
volume = {99},
issn = {0027-8424},
doi = {10.1073/pnas.202488399},
abstract = {Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65\% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3\% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.},
language = {eng},
number = {22},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
author = {Breitbart, Mya and Salamon, Peter and Andresen, Bjarne and Mahaffy, Joseph M. and Segall, Anca M. and Mead, David and Azam, Farooq and Rohwer, Forest},
month = oct,
year = {2002},
pmid = {12384570},
pmcid = {PMC137870},
keywords = {Bacteriophages, Base Sequence, DNA Viruses, DNA, Viral, Genetic Variation, Models, Genetic, Molecular Sequence Data, Phycodnaviridae, Seawater},
pages = {14250--14255}
}Human mutation--blame (mostly) men. Ellegren, H. Nat Genet, 31(1):9-10., 2002.
Paper bibtex
Paper bibtex @article{
title = {Human mutation--blame (mostly) men},
type = {article},
year = {2002},
identifiers = {[object Object]},
keywords = {*Mutation,Animal,Comparative Study,DNA/genetics,Evolution,Female,Genetic,Human,Male,Models,Molecular,Polymorphism (Genetics),Primates/genetics,RNA-Binding Proteins/genetics,X Chromosome/*genetics,Y Chromosome/*genetics},
pages = {9-10.},
volume = {31},
id = {61983c7d-2056-316b-bd71-9cf44d9c9a9e},
created = {2017-06-19T13:42:10.378Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:42:10.525Z},
tags = {02/06/17},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>eng<m:linebreak/>News</m:note>},
bibtype = {article},
author = {Ellegren, H},
journal = {Nat Genet},
number = {1}
}Intrinsic and extrinsic contributions to stochasticity in gene expression. Swain, P., S., Elowitz, M., B., & Siggia, E., D. Proceedings of the National Academy of Sciences of the United States of America, 99(20):12795-12800, 2002.
Paper abstract bibtex
Paper abstract bibtex Gene expression is a stochastic, or "noisy," process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates "intrinsic" noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent "extrinsic" noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than approximately 2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable-a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.
@article{
title = {Intrinsic and extrinsic contributions to stochasticity in gene expression.},
type = {article},
year = {2002},
identifiers = {[object Object]},
keywords = {Biophysical Phenomena,Biophysics,Escherichia coli,Escherichia coli: metabolism,Gene Expression Regulation,Genetic,Messenger,Messenger: metabolism,Models,Protein Biosynthesis,RNA,Theoretical,Time Factors,Transcription},
pages = {12795-12800},
volume = {99},
id = {009fc879-22c6-3763-bc9b-659156a1c497},
created = {2015-08-20T10:31:21.000Z},
file_attached = {true},
profile_id = {1593dc7b-4550-3536-a5a4-21ffd4cbffb8},
group_id = {9cd45c01-6b67-3572-a936-df749337a5f1},
last_modified = {2015-08-20T10:42:27.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Swain2002},
abstract = {Gene expression is a stochastic, or "noisy," process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates "intrinsic" noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent "extrinsic" noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than approximately 2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable-a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.},
bibtype = {article},
author = {Swain, Peter S and Elowitz, Michael B and Siggia, Eric D},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {20}
}Evolutionary and statistical properties of three genetic distances. Kalinowski, S., T. Mol Ecol, 11(8):1263-1273, 2002.
Paper Website abstract bibtex
Paper Website abstract bibtex Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.
@article{
title = {Evolutionary and statistical properties of three genetic distances},
type = {article},
year = {2002},
identifiers = {[object Object]},
keywords = {*Evolution, Molecular,*Genetics, Population,Computer Simulation,Models, Genetic,Mutation},
pages = {1263-1273},
volume = {11},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12144649},
edition = {2002/07/30},
id = {45ffbee5-04e5-36be-85f2-5ddcbdfff387},
created = {2017-06-19T13:42:46.622Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:42:46.787Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
language = {eng},
notes = {<m:note>Kalinowski, Steven T<m:linebreak/>Review<m:linebreak/>England<m:linebreak/>Molecular ecology<m:linebreak/>1520<m:linebreak/>Mol Ecol. 2002 Aug;11(8):1263-73.</m:note>},
abstract = {Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.},
bibtype = {article},
author = {Kalinowski, S T},
journal = {Mol Ecol},
number = {8}
}2001 (6)
After BRCA1 and BRCA2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer. Cui, J., Antoniou, A., C., Dite, G., S., Southey, M., C., Venter, D., J., Easton, D., F., Giles, G., G., McCredie, M., R., & Hopper, J., L. Am J Hum Genet, 68(2):420-31., 2001.
Paper abstract bibtex
Paper abstract bibtex Mutations in BRCA1 and BRCA2 that cause a dominantly inherited high risk of female breast cancer seem to explain only a small proportion of the aggregation of the disease. To study the possible additional genetic components, we conducted single-locus and two-locus segregation analyses, with and without a polygenic background, using three-generation families ascertained through 858 women with breast cancer diagnosed at age <40 years, ascertained through population cancer registries in Melbourne and Sydney, Australia. Extensive testing for deleterious mutations in BRCA1 and BRCA2, to date, has identified 34 carriers. Our analysis suggested that, after other possible unmeasured familial factors are adjusted for and the known BRCA1 and BRCA2 mutation carriers are excluded, there appears to be a residual dominantly inherited risk of female breast cancer in addition to that derived from mutations in BRCA1 and BRCA2. This study also suggests that there is a substantial recessively inherited risk of early-onset breast cancer. According to the best-fitting model, after excluding known carriers of mutations in BRCA1 and BRCA2, about 1/250 (95% confidence interval [CI] 1/500 to 1/125) women have a recessive risk of 86% (95% CI 69%-100%) by age 50 years and of almost 100% by age 60 years. Possible reasons that our study has implicated a novel strong recessive effect include our inclusion of data on lineal aunts and grandmothers, study of families ascertained through women with early-onset breast cancer, allowance for multiple familial factors in the analysis, and removal of families for whom the cause (i.e., BRCA1 or BRCA2) is known. Our findings may have implications for attempts to identify new breast cancer-susceptibility genes.
@article{
title = {After BRCA1 and BRCA2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer},
type = {article},
year = {2001},
identifiers = {[object Object]},
keywords = {Age Factors,Age of Onset,Australia,BRCA1 Protein/*genetics,BRCA2 Protein,Breast Neoplasms/*genetics,Cohort Studies,Family Health,Female,Heterozygote,Human,Male,Models, Genetic,Molecular Sequence Data,Mutation,Neoplasm Proteins/*genetics,Pedigree,Probability,Risk Factors,Statistics,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.,Transcription Factors/*genetics},
pages = {420-31.},
volume = {68},
id = {23f12ce0-3889-312a-be6e-926c320ad4f9},
created = {2017-06-19T13:45:18.919Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:45:19.048Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
abstract = {Mutations in BRCA1 and BRCA2 that cause a dominantly inherited high risk of female breast cancer seem to explain only a small proportion of the aggregation of the disease. To study the possible additional genetic components, we conducted single-locus and two-locus segregation analyses, with and without a polygenic background, using three-generation families ascertained through 858 women with breast cancer diagnosed at age <40 years, ascertained through population cancer registries in Melbourne and Sydney, Australia. Extensive testing for deleterious mutations in BRCA1 and BRCA2, to date, has identified 34 carriers. Our analysis suggested that, after other possible unmeasured familial factors are adjusted for and the known BRCA1 and BRCA2 mutation carriers are excluded, there appears to be a residual dominantly inherited risk of female breast cancer in addition to that derived from mutations in BRCA1 and BRCA2. This study also suggests that there is a substantial recessively inherited risk of early-onset breast cancer. According to the best-fitting model, after excluding known carriers of mutations in BRCA1 and BRCA2, about 1/250 (95% confidence interval [CI] 1/500 to 1/125) women have a recessive risk of 86% (95% CI 69%-100%) by age 50 years and of almost 100% by age 60 years. Possible reasons that our study has implicated a novel strong recessive effect include our inclusion of data on lineal aunts and grandmothers, study of families ascertained through women with early-onset breast cancer, allowance for multiple familial factors in the analysis, and removal of families for whom the cause (i.e., BRCA1 or BRCA2) is known. Our findings may have implications for attempts to identify new breast cancer-susceptibility genes.},
bibtype = {article},
author = {Cui, J and Antoniou, A C and Dite, G S and Southey, M C and Venter, D J and Easton, D F and Giles, G G and McCredie, M R and Hopper, J L},
journal = {Am J Hum Genet},
number = {2}
}Replication studies in longevity: puzzling findings in Danish centenarians at the 3'APOB-VNTR locus. Varcasia, O., Garasto, S., Rizza, T., Andersen-Ranberg, K., Jeune, B., Bathum, L., Andreev, K., Tan, Q., Yashin, A., I., Bonafe, M., Franceschi, C., & De Benedictis, G. Ann Hum Genet, 65(Pt 4):371-376, 2001.
Website abstract bibtex
Website abstract bibtex In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20-64-year-old subjects. However, when Danish and Italian data were compared, a significant difference (p = 0.0004) was found between the frequencies of Small alleles in youths, which disappeared in centenarians (p = 0.290). Furthermore, the demographic-genetic approach revealed in Danes a significant gene-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history.
@article{
title = {Replication studies in longevity: puzzling findings in Danish centenarians at the 3'APOB-VNTR locus},
type = {article},
year = {2001},
identifiers = {[object Object]},
keywords = {Adult,Aged,Aged, 80 and over,Alleles,Apolipoproteins B/*genetics,Comparative Study,DNA/analysis/genetics,Demography,Denmark,Female,Gene Frequency/genetics,Genotype,Humans,Italy,Longevity/*genetics,Male,Middle Aged,Minisatellite Repeats/*genetics,Models, Genetic,Polymerase Chain Reaction,Research Support, Non-U.S. Gov't,Risk,Sex Characteristics},
pages = {371-376},
volume = {65},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11592926},
id = {30365bd9-8031-3f7e-8ef2-9d02c1ab8dba},
created = {2017-06-19T13:45:42.031Z},
file_attached = {false},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:45:42.142Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0003-4800<m:linebreak/>Journal Article</m:note>},
abstract = {In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20-64-year-old subjects. However, when Danish and Italian data were compared, a significant difference (p = 0.0004) was found between the frequencies of Small alleles in youths, which disappeared in centenarians (p = 0.290). Furthermore, the demographic-genetic approach revealed in Danes a significant gene-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history.},
bibtype = {article},
author = {Varcasia, O and Garasto, S and Rizza, T and Andersen-Ranberg, K and Jeune, B and Bathum, L and Andreev, K and Tan, Q and Yashin, A I and Bonafe, M and Franceschi, C and De Benedictis, G},
journal = {Ann Hum Genet},
number = {Pt 4}
}A prospective evaluation of lipoprotein-associated phospholipase A(2) levels and the risk of future cardiovascular events in women. Blake, G. J., Dada, N., Fox, J. C., Manson, J. E., & Ridker, P. M. J Am Coll Cardiol, 38(5):1302-6, 2001. Hl43851/hl/nhlbi Hl58755/hl/nhlbi Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States
bibtex
bibtex
@Article{Blake_2001_1509,
author = {Blake, G. J. and Dada, N. and Fox, J. C. and Manson, J. E. and Ridker, P. M.},
journal = {J Am Coll Cardiol},
note = {Hl43851/hl/nhlbi Hl58755/hl/nhlbi Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States},
number = {5},
pages = {1302-6},
title = {A prospective evaluation of lipoprotein-associated phospholipase A(2) levels and the risk of future cardiovascular events in women},
volume = {38},
year = {2001},
keywords = {Aged, Biological, Markers/*blood, C-Reactive, Protein/metabolism, Case-Control, Studies, Cerebrovascular, Accident/epidemiology/*etiology, Coronary, Disease/epidemiology/*etiology, Estrogen, Replacement, Therapy, Female, Humans, Hypertension/complications, Inflammation, Logistic, Models, Middle, Aged, Multivariate, Analysis, Myocardial, Infarction/epidemiology/*etiology, Obesity/complications, Phospholipases, A/*blood/immunology, Predictive, Value, of, Tests, Prospective, Studies, Questionnaires, Risk, Factors, Single-Blind, Method, Smoking, *Women's, Health},
title_with_no_special_chars = {A prospective evaluation of lipoproteinassociated phospholipase A2 levels and the risk of future cardiovascular events in women}
}Protecting Against Bad Air. Luzzatto, L. & Notaro, R. Science, 293(July):442-443, 2001.
Paper bibtex
Paper bibtex @article{
title = {Protecting Against Bad Air},
type = {article},
year = {2001},
identifiers = {[object Object]},
keywords = {*Agriculture,*Glucosephosphate Dehydrogenase Deficiency/epidemi,*Variation (Genetics),Animal,Child,Erythrocytes/enzymology/parasitology,Evolution,Falciparum/*enzymology/epidemiology/*gene,Genetic,Glucosephosphate Dehydrogenase/blood/*genetics/met,Haplotypes,Human,Immunity,Malaria,Microsatellite Repeats,Models,Natural/genetics,Plasmodium falciparum/physiology,Polymorphism,Polymorphism (Genetics),Prevalence,Restriction Fragment Length,Selection (Genetics)},
pages = {442-443},
volume = {293},
id = {e244ac6a-cafa-3de1-81ae-e83092bdc695},
created = {2017-06-19T13:42:01.571Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:42:01.713Z},
tags = {03/03/18},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note> <m:bold>From Duplicate 1 ( </m:bold> <m:bold> </m:bold><m:bold><m:italic>Malaria. Protecting against bad air</m:italic></m:bold><m:bold> </m:bold> <m:bold> - Luzzatto, L; Notaro, R )<m:linebreak/> </m:bold> <m:linebreak/>eng<m:linebreak/>Comment<m:linebreak/>Journal Article<m:linebreak/> <m:linebreak/> </m:note>},
bibtype = {article},
author = {Luzzatto, Lucio and Notaro, Rosario},
journal = {Science},
number = {July}
}Objects and attention: The state of the art. Scholl, B. J. Cognition, 80(1-2):1-46, 2001.
abstract bibtex
abstract bibtex
What are the units of attention? In addition to standard models holding that attention can select spatial regions and visual features, recent work suggests that in some cases attention can directly select discrete objects. This paper reviews the state of the art with regard to such 'object-based' attention, and explores how objects of attention relate to locations, reference frames, perceptual groups, surfaces, parts, and features. Also discussed are the dynamic aspects of objecthood, including the question of how attended objects are individuated in time, and the possibility of attending to simple dynamic motions and events. The final sections of this review generalize these issues beyond vision science, to other modalities and fields such as auditory objects of attention and the infant's 'object concept'.
@Article{Scholl2001b,
author = {B. J. Scholl},
journal = {Cognition},
title = {Objects and attention: {T}he state of the art.},
year = {2001},
number = {1-2},
pages = {1-46},
volume = {80},
abstract = {What are the units of attention? In addition to standard models holding
that attention can select spatial regions and visual features, recent
work suggests that in some cases attention can directly select discrete
objects. This paper reviews the state of the art with regard to such
'object-based' attention, and explores how objects of attention relate
to locations, reference frames, perceptual groups, surfaces, parts,
and features. Also discussed are the dynamic aspects of objecthood,
including the question of how attended objects are individuated in
time, and the possibility of attending to simple dynamic motions
and events. The final sections of this review generalize these issues
beyond vision science, to other modalities and fields such as auditory
objects of attention and the infant's 'object concept'.},
keywords = {80 and over, Adenoviridae, Adolescent, Adult, Aged, Analysis of Variance, Animals, Attention, Auditory Perception, Biopsy, Bone Nails, Bone Neoplasms, Bone Screws, Bone Transplantation, Breast Neoplasms, Carcinoma, Child, Child Development, Cognition, Cohort Studies, Comparative Study, Concept Formation, Constriction, Esophageal Neoplasms, Female, Femoral Neck Fractures, Femoral Neoplasms, Femur Head, Femur Neck, Fibula, Follow-Up Studies, Fracture Fixation, Fractures, Gene Expression, Gene Transfer Techniques, Green Fluorescent Proteins, Hepatitis, Homologous, Humans, Inbred Strains, Infant, Injections, Internal, Intramedullary, Intravenous, Judgment, Knee Joint, Liver, Luminescent Proteins, Male, Meta-Analysis, Middle Aged, Models, Motion, Motion Perception, Needle, Neoplasms, Non-P.H.S., Non-U.S. Gov't, P.H.S., Perceptual Distortion, Portal Vein, Preschool, Problem Solving, Psychological, Radiation-Induced, Rats, Research Support, Retrospective Studies, Second Primary, Self Concept, Sensitivity and Specificity, Social Perception, Space Perception, Spontaneous, Squamous Cell, Students, Time Factors, Tomography, Transplantation, Treatment Outcome, U.S. Gov't, Visual Perception, X-Ray Computed, 11245838},
}How amoeboids self-organize into a fruiting body: multicellular coordination in Dictyostelium discoideum. Marée, A., F., M. & Hogeweg, P. Proceedings of the National Academy of Sciences of the United States of America, 98(7):3879-83, 3, 2001.
Paper Website abstract bibtex
Paper Website abstract bibtex When individual amoebae of the cellular slime mold Dictyostelium discoideum are starving, they aggregate to form a multicellular migrating slug, which moves toward a region suitable for culmination. The culmination of the morphogenesis involves complex cell movements that transform a mound of cells into a globule of spores on a slender stalk. The movement has been likened to a "reverse fountain," whereby prestalk cells in the upper part form a stalk that moves downwards and anchors to the substratum, while prespore cells in the lower part move upwards to form the spore head. So far, however, no satisfactory explanation has been produced for this process. Using a computer simulation that we developed, we now demonstrate that the processes that are essential during the earlier stages of the morphogenesis are in fact sufficient to produce the dynamics of the culmination stage. These processes are cAMP signaling, differential adhesion, cell differentiation, and production of extracellular matrix. Our model clarifies the processes that generate the observed cell movements. More specifically, we show that periodic upward movements, caused by chemotactic motion, are essential for successful culmination, because the pressure waves they induce squeeze the stalk downwards through the cell mass. The mechanisms revealed by our model have a number of self-organizing and self-correcting properties and can account for many previously unconnected and unexplained experimental observations.
@article{
title = {How amoeboids self-organize into a fruiting body: multicellular coordination in Dictyostelium discoideum.},
type = {article},
year = {2001},
identifiers = {[object Object]},
keywords = {Animals,Biological,Cell Differentiation,Cell Differentiation: physiology,Cell Movement,Cell Movement: physiology,Cyclic AMP,Cyclic AMP: physiology,Dictyostelium,Dictyostelium: growth & development,Dictyostelium: physiology,Models},
pages = {3879-83},
volume = {98},
websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=31146&tool=pmcentrez&rendertype=abstract},
month = {3},
day = {27},
id = {cd87c653-e9b1-3e1a-85f7-72898d9c4afd},
created = {2016-02-10T15:06:25.000Z},
file_attached = {true},
profile_id = {397d75f1-832d-36e0-bbe6-b6878f88c402},
group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
last_modified = {2017-03-14T10:42:46.538Z},
read = {true},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Maree2001},
folder_uuids = {8010415f-2a72-427e-8a93-e658ed2fb621},
private_publication = {false},
abstract = {When individual amoebae of the cellular slime mold Dictyostelium discoideum are starving, they aggregate to form a multicellular migrating slug, which moves toward a region suitable for culmination. The culmination of the morphogenesis involves complex cell movements that transform a mound of cells into a globule of spores on a slender stalk. The movement has been likened to a "reverse fountain," whereby prestalk cells in the upper part form a stalk that moves downwards and anchors to the substratum, while prespore cells in the lower part move upwards to form the spore head. So far, however, no satisfactory explanation has been produced for this process. Using a computer simulation that we developed, we now demonstrate that the processes that are essential during the earlier stages of the morphogenesis are in fact sufficient to produce the dynamics of the culmination stage. These processes are cAMP signaling, differential adhesion, cell differentiation, and production of extracellular matrix. Our model clarifies the processes that generate the observed cell movements. More specifically, we show that periodic upward movements, caused by chemotactic motion, are essential for successful culmination, because the pressure waves they induce squeeze the stalk downwards through the cell mass. The mechanisms revealed by our model have a number of self-organizing and self-correcting properties and can account for many previously unconnected and unexplained experimental observations.},
bibtype = {article},
author = {Marée, Athanasius F M and Hogeweg, P},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {7}
}2000 (3)
Single-particle electron cryo-microscopy: towards atomic resolution. van Heel, M., Gowen, B., Matadeen, R., Orlova, E., V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M., & Patwardhan, a. Quarterly reviews of biophysics, 33(4):307-69, 11, 2000.
Paper Website bibtex
Paper Website bibtex @article{
title = {Single-particle electron cryo-microscopy: towards atomic resolution.},
type = {article},
year = {2000},
identifiers = {[object Object]},
keywords = {Animals,Computers,Cryoelectron Microscopy,Cryoelectron Microscopy: instrumentation,Cryoelectron Microscopy: methods,Escherichia coli,Escherichia coli: chemistry,Hemoglobins,Hemoglobins: chemistry,Image Processing, Computer-Assisted,Models, Theoretical,Software},
pages = {307-69},
volume = {33},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/11233408},
month = {11},
id = {1ea4b56b-251a-34f0-92ba-2542e4d21394},
created = {2011-07-28T18:39:52.000Z},
file_attached = {true},
profile_id = {219e8e76-b8c8-3aa5-898d-2153cb61efd4},
group_id = {cd79d359-3d3b-38cd-822c-b775fd5f31ce},
last_modified = {2017-03-14T11:02:08.776Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {VanHeel2000},
private_publication = {false},
bibtype = {article},
author = {van Heel, M and Gowen, B and Matadeen, R and Orlova, E V and Finn, R and Pape, T and Cohen, D and Stark, H and Schmidt, R and Schatz, M and Patwardhan, a},
journal = {Quarterly reviews of biophysics},
number = {4}
}Bivalent sequential binding model of a Bacillus thuringiensis toxin to gypsy moth aminopeptidase N receptor. Jenkins, J., L., Lee, M., K., Valaitis, a., P., Curtiss, a., & Dean, D., H. The Journal of biological chemistry, 275(19):14423-31, 5, 2000.
Paper abstract bibtex
Paper abstract bibtex Specificity for target insects of Bacillus thuringiensis insecticidal Cry toxins is largely determined by toxin affinity for insect midgut receptors. The mode of binding for one such toxin-receptor complex was investigated by extensive toxin mutagenesis, followed by real-time receptor binding analysis using an optical biosensor (BIAcore). Wild-type Cry1Ac, a three-domain, lepidopteran-specific toxin, bound purified gypsy moth (Lymantria dispar) aminopeptidase N (APN) biphasically. Site 1 displayed fast association and dissociation kinetics, while site 2 possessed slower kinetics, yet tighter affinity. We empirically determined that two Cry1Ac surface regions are involved in in vivo toxicity and APN binding. Mutations within domain III affected binding rates to APN site 1, whereas mutations in domain II affected binding rates to APN site 2. Furthermore, domain III contact is completely inhibited in the presence of N-acetylgalactosamine, indicating loss of domain III binding eliminates all APN binding. Based upon these observations, the following model is proposed. A cavity in lectin-like domain III initiates docking through recognition of an N-acetylgalactosamine moiety on L. dispar APN. Following primary docking, a higher affinity domain II binding mechanism occurs, which is critical for insecticidal activity.
@article{
title = {Bivalent sequential binding model of a Bacillus thuringiensis toxin to gypsy moth aminopeptidase N receptor.},
type = {article},
year = {2000},
identifiers = {[object Object]},
keywords = {Animals,Antigens, CD13,Antigens, CD13: metabolism,Bacillus thuringiensis,Bacillus thuringiensis: metabolism,Bacterial Proteins,Bacterial Proteins: metabolism,Bacterial Toxins,Binding Sites,Computer Simulation,Endotoxins,Endotoxins: metabolism,Hemolysin Proteins,Kinetics,Membrane Proteins,Membrane Proteins: metabolism,Models, Molecular,Moths,Moths: metabolism,Protein Binding},
pages = {14423-31},
volume = {275},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/10799525},
month = {5},
day = {12},
id = {2f09550a-9a54-33e5-ad47-bc71528b2485},
created = {2012-02-08T16:01:18.000Z},
file_attached = {true},
profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
last_modified = {2012-02-08T16:17:26.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
abstract = {Specificity for target insects of Bacillus thuringiensis insecticidal Cry toxins is largely determined by toxin affinity for insect midgut receptors. The mode of binding for one such toxin-receptor complex was investigated by extensive toxin mutagenesis, followed by real-time receptor binding analysis using an optical biosensor (BIAcore). Wild-type Cry1Ac, a three-domain, lepidopteran-specific toxin, bound purified gypsy moth (Lymantria dispar) aminopeptidase N (APN) biphasically. Site 1 displayed fast association and dissociation kinetics, while site 2 possessed slower kinetics, yet tighter affinity. We empirically determined that two Cry1Ac surface regions are involved in in vivo toxicity and APN binding. Mutations within domain III affected binding rates to APN site 1, whereas mutations in domain II affected binding rates to APN site 2. Furthermore, domain III contact is completely inhibited in the presence of N-acetylgalactosamine, indicating loss of domain III binding eliminates all APN binding. Based upon these observations, the following model is proposed. A cavity in lectin-like domain III initiates docking through recognition of an N-acetylgalactosamine moiety on L. dispar APN. Following primary docking, a higher affinity domain II binding mechanism occurs, which is critical for insecticidal activity.},
bibtype = {article},
author = {Jenkins, J L and Lee, M K and Valaitis, a P and Curtiss, a and Dean, D H},
journal = {The Journal of biological chemistry},
number = {19}
}Why are the majority of hereditary cases of early-onset breast cancer sporadic? A simulation study. Cui, J. & Hopper, J., L. Cancer Epidemiol Biomarkers Prev, 9(8):805-12., 2000.
Paper abstract bibtex
Paper abstract bibtex Population-based studies, including those of Ashkenazi Jews, have observed that at least 50% of women with early-onset breast cancer who carry a germ line mutation in BRCA1 or BRCA2 do not report a family history of the disease. That is, the majority of "hereditary" cases are "sporadic." Furthermore, the great majority of "familial breast cancers" are not hereditary. We conducted a simulation study to evaluate the probability that a woman with early-onset breast cancer is a mutation carrier, given the number of affected relatives, for a range of plausible values of allele frequency (0.001-0.01), and increased risk in mutation carriers (5-20, equivalent to cumulative risks to age 70 of 25-70%, respectively, for Australian women). Families consisted of a case proband and her mother, sisters, and maternal and paternal grandmothers, and aunts. The numbers of sisters and aunts were generated according to Poisson distributions, and ages were assigned according to a Weibull distribution. The simulated distributions of family history and of the prevalence of mutation carriers among case probands were in general similar to those observed in population-based studies, although there was a suggestion of heterogeneity of breast cancer risk in mutation carriers. As is being observed empirically in population-based samples, a family history of breast cancer was not a strong predictor of mutation status; each affected female relative increased the risk of being a mutation carrier by only 2- to 3-fold. The probability of being a mutation carrier was generally low, except in families with extreme histories of breast cancer.
@article{
title = {Why are the majority of hereditary cases of early-onset breast cancer sporadic? A simulation study},
type = {article},
year = {2000},
identifiers = {[object Object]},
keywords = {Adult,Age Distribution,Age of Onset,Aged,Australia/epidemiology,Breast Neoplasms/*epidemiology/ethnology/*genetics,Computer Simulation,Family Health,Female,Gene Frequency,Genes, BRCA1,Great Britain/epidemiology,Human,Jews/statistics & numerical data,Middle Age,Models, Genetic,Mutation,Pedigree,Prevalence,Singapore/epidemiology,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.,Washington/epidemiology},
pages = {805-12.},
volume = {9},
id = {373ef46c-3714-3339-8c8d-5b9047cf28e7},
created = {2017-06-19T13:44:21.419Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:44:21.571Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
abstract = {Population-based studies, including those of Ashkenazi Jews, have observed that at least 50% of women with early-onset breast cancer who carry a germ line mutation in BRCA1 or BRCA2 do not report a family history of the disease. That is, the majority of "hereditary" cases are "sporadic." Furthermore, the great majority of "familial breast cancers" are not hereditary. We conducted a simulation study to evaluate the probability that a woman with early-onset breast cancer is a mutation carrier, given the number of affected relatives, for a range of plausible values of allele frequency (0.001-0.01), and increased risk in mutation carriers (5-20, equivalent to cumulative risks to age 70 of 25-70%, respectively, for Australian women). Families consisted of a case proband and her mother, sisters, and maternal and paternal grandmothers, and aunts. The numbers of sisters and aunts were generated according to Poisson distributions, and ages were assigned according to a Weibull distribution. The simulated distributions of family history and of the prevalence of mutation carriers among case probands were in general similar to those observed in population-based studies, although there was a suggestion of heterogeneity of breast cancer risk in mutation carriers. As is being observed empirically in population-based samples, a family history of breast cancer was not a strong predictor of mutation status; each affected female relative increased the risk of being a mutation carrier by only 2- to 3-fold. The probability of being a mutation carrier was generally low, except in families with extreme histories of breast cancer.},
bibtype = {article},
author = {Cui, J and Hopper, J L},
journal = {Cancer Epidemiol Biomarkers Prev},
number = {8}
}1999 (4)
Measuring and developing suturing technique with a virtual reality surgical simulator. O'Toole, R V, Playter, R R, Krummel, T M, Blank, W C, Cornelius, N H, Roberts, W R, Bell, W J, & Raibert, M Journal of the American College of Surgeons, 189(1):114--127, July, 1999.
abstract bibtex
abstract bibtex
BACKGROUND We have developed an interactive virtual reality (VR) surgical simulator for the training and assessment of suturing technique. The surgical simulator is comprised of surgical tools with force feedback, a 3-dimensional graphics visual display of the simulated surgical field, physics-based computer simulations of the tissues and tools, and software to measure and evaluate the trainee's performance. STUDY DESIGN This study uses the simulator to measure and compare the skills of 8 experienced vascular surgeons versus 12 medical students when performing a virtual reality suturing task. Eight parameters of the suturing task were measured: total tissue damage, accuracy of needle puncture, peak tissue tearing force, time to complete the task, damage to the surface of the tissue, angular error in needle technique, total distance traveled by the tool tip, and a measure of overall error. Three test conditions (dominant hand, nondominant hand, and 3-dimensional needle guide) were tested. Statistical significance was defined as a univariate two-sided p value \textless or = 0.05. RESULTS The surgeons' average performance was significantly better than the students' average performance for three of the measured parameters (total tissue damage, time to complete the task, and total distance traveled by the tool tip) for each of the test conditions. For the test condition most similar to surgery (using the dominant hand to suture) one additional parameter was also significantly different (the measure of overall error). The medical students showed improvements for 6 of the 7 parameters for which the users received feedback during the training process. The surgeons also had significant improvement for 4 of the 7 parameters. The students had a larger improvement than the surgeons for 6 of the parameters, but these differences were not statistically significant. CONCLUSIONS Data indicate differences between surgeon and nonsurgeon performance and in improvement in performance with training. One possible explanation for the superior performance of the surgeons is that their suturing skills applied well to the simulated suturing task. Additional research is required to confirm or deny the similarity between actual and simulated surgical tasks and the relevance of virtual reality surgical simulation to surgical skill assessment and training.
@article{otoole_measuring_1999,
title = {Measuring and developing suturing technique with a virtual reality surgical simulator},
volume = {189},
issn = {1072-7515},
abstract = {BACKGROUND
We have developed an interactive virtual reality (VR) surgical simulator for the training and assessment of suturing technique. The surgical simulator is comprised of surgical tools with force feedback, a 3-dimensional graphics visual display of the simulated surgical field, physics-based computer simulations of the tissues and tools, and software to measure and evaluate the trainee's performance.
STUDY DESIGN
This study uses the simulator to measure and compare the skills of 8 experienced vascular surgeons versus 12 medical students when performing a virtual reality suturing task. Eight parameters of the suturing task were measured: total tissue damage, accuracy of needle puncture, peak tissue tearing force, time to complete the task, damage to the surface of the tissue, angular error in needle technique, total distance traveled by the tool tip, and a measure of overall error. Three test conditions (dominant hand, nondominant hand, and 3-dimensional needle guide) were tested. Statistical significance was defined as a univariate two-sided p value {\textless} or = 0.05.
RESULTS
The surgeons' average performance was significantly better than the students' average performance for three of the measured parameters (total tissue damage, time to complete the task, and total distance traveled by the tool tip) for each of the test conditions. For the test condition most similar to surgery (using the dominant hand to suture) one additional parameter was also significantly different (the measure of overall error). The medical students showed improvements for 6 of the 7 parameters for which the users received feedback during the training process. The surgeons also had significant improvement for 4 of the 7 parameters. The students had a larger improvement than the surgeons for 6 of the parameters, but these differences were not statistically significant.
CONCLUSIONS
Data indicate differences between surgeon and nonsurgeon performance and in improvement in performance with training. One possible explanation for the superior performance of the surgeons is that their suturing skills applied well to the simulated suturing task. Additional research is required to confirm or deny the similarity between actual and simulated surgical tasks and the relevance of virtual reality surgical simulation to surgical skill assessment and training.},
number = {1},
journal = {Journal of the American College of Surgeons},
author = {O'Toole, R V and Playter, R R and Krummel, T M and Blank, W C and Cornelius, N H and Roberts, W R and Bell, W J and Raibert, M},
month = jul,
year = {1999},
pmid = {10401747},
keywords = {Computer Simulation, Computer-Assisted Instruction, Educational Measurement, General Surgery, Humans, Models, Educational, Suture Techniques, User-Computer Interface, Vascular Surgical Procedures},
pages = {114--127}
}The conceptual structure of research utilization. Estabrooks, C., A. 1999.
bibtex
bibtex
@article{
title = {The conceptual structure of research utilization},
type = {article},
year = {1999},
identifiers = {[object Object]},
id = {e8334dc3-a5a9-376c-ad94-9ea7843d072d},
created = {2016-12-15T22:52:55.000Z},
file_attached = {false},
profile_id = {369acd69-1fe7-313d-821e-cb7bbe1ddab2},
last_modified = {2017-03-25T14:39:59.517Z},
read = {false},
starred = {false},
authored = {true},
confirmed = {false},
hidden = {false},
private_publication = {false},
bibtype = {article},
author = {Estabrooks, C A}
}EMAN: semiautomated software for high-resolution single-particle reconstructions. Ludtke, S., J., Baldwin, P., R., & Chiu, W. J Struct Biol, 128(1):82-97, 12, 1999.
Paper Website abstract bibtex
Paper Website abstract bibtex We present EMAN (Electron Micrograph ANalysis), a software package
for performing semiautomated single-particle reconstructions from
transmission electron micrographs. The goal of this project is to
provide software capable of performing single-particle reconstructions
beyond 10 A as such high-resolution data become available. A complete
single-particle reconstruction algorithm is implemented. Options
are available to generate an initial model for particles with no
symmetry, a single axis of rotational symmetry, or icosahedral symmetry.
Model refinement is an iterative process, which utilizes classification
by model-based projection matching. CTF (contrast transfer function)
parameters are determined using a new paradigm in which data from
multiple micrographs are fit simultaneously. Amplitude and phase
CTF correction is then performed automatically as part of the refinement
loop. A graphical user interface is provided, so even those with
little image processing experience will be able to begin performing
reconstructions. Advanced users can directly use the lower level
shell commands and even expand the package utilizing EMAN's extensive
image-processing library. The package was written from scratch in
C++ and is provided free of charge on our Web site. We present an
overview of the package as well as several conformance tests with
simulated data.
@article{
title = {EMAN: semiautomated software for high-resolution single-particle reconstructions.},
type = {article},
year = {1999},
identifiers = {[object Object]},
keywords = {Algorithms; Bluetongue virus; Capsid; Cryoelectron,Computer-Assisted; Internet; Models,Molecular; Programming Languages; Protein Structu,Secondary; Software},
pages = {82-97},
volume = {128},
websites = {http://dx.doi.org/10.1006/jsbi.1999.4174},
month = {12},
institution = {Verna and Marrs McLean Department of Biochemistry, National Center for Macromolecular Imaging, Houston, Texas 77030, USA.},
id = {f30335b8-3359-333e-8eac-1621828469c9},
created = {2011-07-28T18:39:52.000Z},
file_attached = {true},
profile_id = {219e8e76-b8c8-3aa5-898d-2153cb61efd4},
group_id = {cd79d359-3d3b-38cd-822c-b775fd5f31ce},
last_modified = {2017-03-14T11:02:08.776Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Ludtke.etal:99:EMAN:},
source_type = {article},
private_publication = {false},
abstract = {We present EMAN (Electron Micrograph ANalysis), a software package
for performing semiautomated single-particle reconstructions from
transmission electron micrographs. The goal of this project is to
provide software capable of performing single-particle reconstructions
beyond 10 A as such high-resolution data become available. A complete
single-particle reconstruction algorithm is implemented. Options
are available to generate an initial model for particles with no
symmetry, a single axis of rotational symmetry, or icosahedral symmetry.
Model refinement is an iterative process, which utilizes classification
by model-based projection matching. CTF (contrast transfer function)
parameters are determined using a new paradigm in which data from
multiple micrographs are fit simultaneously. Amplitude and phase
CTF correction is then performed automatically as part of the refinement
loop. A graphical user interface is provided, so even those with
little image processing experience will be able to begin performing
reconstructions. Advanced users can directly use the lower level
shell commands and even expand the package utilizing EMAN's extensive
image-processing library. The package was written from scratch in
C++ and is provided free of charge on our Web site. We present an
overview of the package as well as several conformance tests with
simulated data.},
bibtype = {article},
author = {Ludtke, S J and Baldwin, P R and Chiu, W},
journal = {J Struct Biol},
number = {1}
}Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism?. Gould, S., J. & Lloyd, E., A. Proc Natl Acad Sci U S A, 96(21):11904-9., 1999.
Paper abstract bibtex
Paper abstract bibtex Two major clarifications have greatly abetted the understanding and fruitful expansion of the theory of natural selection in recent years: the acknowledgment that interactors, not replicators, constitute the causal unit of selection; and the recognition that interactors are Darwinian individuals, and that such individuals exist with potency at several levels of organization (genes, organisms, demes, and species in particular), thus engendering a rich hierarchical theory of selection in contrast with Darwin's own emphasis on the organismic level. But a piece of the argument has been missing, and individuals at levels distinct from organisms have been denied potency (although granted existence within the undeniable logic of the theory), because they do not achieve individuality with the same devices used by organisms and therefore seem weak by comparison. We show here that different features define Darwinian individuality across scales of size and time. In particular, species-individuals may develop few emergent features as direct adaptations. The interactor approach works with emergent fitnesses, not with emergent features; and species, as a consequence of their different mechanism for achieving individuality (reproductive exclusivity among subparts, that is, among organisms), express many effects from other levels. Organisms, by contrast, suppress upwardly cascading effects, because the organismic style of individuality (by functional integration of subparts) does not permit much competition or differential reproduction of parts from within. Species do not suppress the operation of lower levels; such effects therefore become available as exaptations conferring emergent fitness-a primary source of the different strength that species achieve as effective Darwinian individuals in evolution.
@article{
title = {Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism?},
type = {article},
year = {1999},
identifiers = {[object Object]},
keywords = {*Evolution,*Selection (Genetics),Animal,DNA Replication,Human,Models, Genetic,Variation (Genetics)},
pages = {11904-9.},
volume = {96},
id = {a48d23a0-771a-36b0-968c-60bbb311287c},
created = {2017-06-19T13:45:32.688Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:45:32.806Z},
tags = {02/12/04},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>eng<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
abstract = {Two major clarifications have greatly abetted the understanding and fruitful expansion of the theory of natural selection in recent years: the acknowledgment that interactors, not replicators, constitute the causal unit of selection; and the recognition that interactors are Darwinian individuals, and that such individuals exist with potency at several levels of organization (genes, organisms, demes, and species in particular), thus engendering a rich hierarchical theory of selection in contrast with Darwin's own emphasis on the organismic level. But a piece of the argument has been missing, and individuals at levels distinct from organisms have been denied potency (although granted existence within the undeniable logic of the theory), because they do not achieve individuality with the same devices used by organisms and therefore seem weak by comparison. We show here that different features define Darwinian individuality across scales of size and time. In particular, species-individuals may develop few emergent features as direct adaptations. The interactor approach works with emergent fitnesses, not with emergent features; and species, as a consequence of their different mechanism for achieving individuality (reproductive exclusivity among subparts, that is, among organisms), express many effects from other levels. Organisms, by contrast, suppress upwardly cascading effects, because the organismic style of individuality (by functional integration of subparts) does not permit much competition or differential reproduction of parts from within. Species do not suppress the operation of lower levels; such effects therefore become available as exaptations conferring emergent fitness-a primary source of the different strength that species achieve as effective Darwinian individuals in evolution.},
bibtype = {article},
author = {Gould, S J and Lloyd, E A},
journal = {Proc Natl Acad Sci U S A},
number = {21}
}1998 (2)
How heritable is individual susceptibility to death? The results of an analysis of survival data on Danish, Swedish and Finnish twins. Iachine, I., A., Holm, N., V., Harris, J., R., Begun, A., Z., Iachina, M., K., Laitinen, M., Kaprio, J., & Yashin, A., I. Twin Res, 1(4):196-205, 1998.
Website abstract bibtex
Website abstract bibtex Molecular epidemiological studies confirm a substantial contribution of individual genes to variability in susceptibility to disease and death for humans. To evaluate the contribution of all genes to susceptibility and to estimate individual survival characteristics, survival data on related individuals (eg twins or other relatives) are needed. Correlated gamma-frailty models of bivariate survival are used in a joint analysis of survival data on more than 31,000 pairs of Danish, Swedish and Finnish male and female twins using the maximum likelihood method. Additive decomposition of frailty into genetic and environmental components is used to estimate heritability in frailty. The estimate of the standard deviation of frailty from the pooled data is about 1.5. The hypothesis that variance in frailty and correlations of frailty for twins are similar in the data from all three countries is accepted. The estimate of narrow-sense heritability in frailty is about 0.5. The age trajectories of individual hazards are evaluated for all three populations of twins and both sexes. The results of our analysis confirm the presence of genetic influences on individual frailty and longevity. They also suggest that the mechanism of these genetic influences may be similar for the three Scandinavian countries. Furthermore, results indicate that the increase in individual hazard with age is more rapid than predicted by traditional demographic life tables.
@article{
title = {How heritable is individual susceptibility to death? The results of an analysis of survival data on Danish, Swedish and Finnish twins},
type = {article},
year = {1998},
identifiers = {[object Object]},
keywords = {*Death,*Genetic Predisposition to Disease,Adult,Age Factors,Aged,Aged, 80 and over,Denmark,Disease Susceptibility,Environment,Epidemiology, Molecular,Female,Finland,Forecasting,Health,Humans,Life Tables,Likelihood Functions,Longevity/genetics,Male,Middle Aged,Models, Genetic,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.,Sex Factors,Survival Analysis,Sweden,Twins/*genetics},
pages = {196-205},
volume = {1},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10100811},
id = {161c25f0-f407-3983-ac34-656acbfb7169},
created = {2017-06-19T13:42:57.913Z},
file_attached = {false},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:42:58.237Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>1369-0523<m:linebreak/>Journal Article<m:linebreak/>Twin Study</m:note>},
abstract = {Molecular epidemiological studies confirm a substantial contribution of individual genes to variability in susceptibility to disease and death for humans. To evaluate the contribution of all genes to susceptibility and to estimate individual survival characteristics, survival data on related individuals (eg twins or other relatives) are needed. Correlated gamma-frailty models of bivariate survival are used in a joint analysis of survival data on more than 31,000 pairs of Danish, Swedish and Finnish male and female twins using the maximum likelihood method. Additive decomposition of frailty into genetic and environmental components is used to estimate heritability in frailty. The estimate of the standard deviation of frailty from the pooled data is about 1.5. The hypothesis that variance in frailty and correlations of frailty for twins are similar in the data from all three countries is accepted. The estimate of narrow-sense heritability in frailty is about 0.5. The age trajectories of individual hazards are evaluated for all three populations of twins and both sexes. The results of our analysis confirm the presence of genetic influences on individual frailty and longevity. They also suggest that the mechanism of these genetic influences may be similar for the three Scandinavian countries. Furthermore, results indicate that the increase in individual hazard with age is more rapid than predicted by traditional demographic life tables.},
bibtype = {article},
author = {Iachine, I A and Holm, N V and Harris, J R and Begun, A Z and Iachina, M K and Laitinen, M and Kaprio, J and Yashin, A I},
journal = {Twin Res},
number = {4}
}On-line identification of hysteretic systems. Chassiakos, A., G., Masri, S., F., Smyth, A., W., & Caughey, T., K. Journal of Applied Mechanics, 65(1):194-203, 1998.
abstract bibtex
abstract bibtex
Using adaptive estimation approaches, a method is presented for the on-line identification of hysteretic systems under arbitrary dynamic environments. The availability of such an identification approach is crucial for the on-line control and monitoring of nonlinear structural systems to be actively controlled. In spite of the challenges encountered in the identification of the hereditary nature of th restoring force of such nonlinear systems, it is shown through the use of simulation studies and experimental measurements that the proposed approach can yield reliable estimates of the hysteretic restoring force under a very wide range of excitation levels and response ranges.
@article{
title = {On-line identification of hysteretic systems},
type = {article},
year = {1998},
identifiers = {[object Object]},
keywords = {models,random vibration},
pages = {194-203},
volume = {65},
id = {f9bdf1de-9ef4-3a7f-9230-1a94021801df},
created = {2017-05-12T08:30:48.204Z},
file_attached = {false},
profile_id = {dd7220fd-7458-3c83-a8de-576e82421d0e},
group_id = {fb736a4d-bfc6-38f5-9312-b6487188b71f},
last_modified = {2017-05-16T06:48:44.580Z},
read = {true},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Chassiakos1998},
source_type = {article},
abstract = {Using adaptive estimation approaches, a method is presented for the on-line identification of hysteretic systems under arbitrary dynamic environments. The availability of such an identification approach is crucial for the on-line control and monitoring of nonlinear structural systems to be actively controlled. In spite of the challenges encountered in the identification of the hereditary nature of th restoring force of such nonlinear systems, it is shown through the use of simulation studies and experimental measurements that the proposed approach can yield reliable estimates of the hysteretic restoring force under a very wide range of excitation levels and response ranges.},
bibtype = {article},
author = {Chassiakos, A G and Masri, S F and Smyth, A W and Caughey, T K},
journal = {Journal of Applied Mechanics},
number = {1}
}1997 (1)
Formalisation for decision support in anaesthesiology. Renardel de Lavalette, G., Groenboom, R., Rotterdam, E, van Harmelen , F, ten Teije , A, & de Geus , F. Artificial Intelligence in Medicine, 11(3):189–214, Elsevier, 11, 1997.
abstract bibtex
abstract bibtex
This paper reports on research for decision support for anaesthesiologists at the University Hospital in Groningen, the Netherlands. Based on CAROLA, an existing automated operation documentation system, we designed a support environment that will assist in real-time diagnosis. The core of the work presented here consists of a knowledge base (containing anaesthesiological knowledge) and a diagnosis system. The knowledge base is specified in the logic-based formal specification language AFSL. This leads to a powerful and precise treatment of knowledge structuring and data abstraction.
@article{b24000c856414830948c326f9708ff73,
title = "Formalisation for decision support in anaesthesiology",
abstract = "This paper reports on research for decision support for anaesthesiologists at the University Hospital in Groningen, the Netherlands. Based on CAROLA, an existing automated operation documentation system, we designed a support environment that will assist in real-time diagnosis. The core of the work presented here consists of a knowledge base (containing anaesthesiological knowledge) and a diagnosis system. The knowledge base is specified in the logic-based formal specification language AFSL. This leads to a powerful and precise treatment of knowledge structuring and data abstraction.",
keywords = "Anesthesiology, Artificial Intelligence, Body Surface Area, Body Temperature, Decision Support Techniques, Hematocrit, Humans, Models, Theoretical, Journal Article",
author = "{Renardel de Lavalette}, {G R} and R. Groenboom and E Rotterdam and {van Harmelen}, F and {ten Teije}, A and {de Geus}, F.",
year = "1997",
month = "11",
volume = "11",
pages = "189--214",
journal = "Artificial Intelligence in Medicine",
issn = "0933-3657",
publisher = "Elsevier",
number = "3",
}1996 (2)
The genetical archaeology of the human genome. von Haeseler, A., Sajantila, A., & Paabo, S. Nat Genet, 14(2):135-140, 1996.
abstract bibtex
abstract bibtex
Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.
@article{
title = {The genetical archaeology of the human genome},
type = {article},
year = {1996},
identifiers = {[object Object]},
keywords = {*Gene Pool,*Genome, Human,DNA, Mitochondrial/genetics,Evolution, Molecular,Female,Human,Male,Models, Genetic,Phylogeny,Support, Non-U.S. Gov't,Variation (Genetics)/*genetics},
pages = {135-140},
volume = {14},
id = {da42c725-f648-32fa-a720-c48d07c5c47c},
created = {2017-06-19T13:46:05.495Z},
file_attached = {false},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:46:05.676Z},
tags = {03/09/17},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
abstract = {Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.},
bibtype = {article},
author = {von Haeseler, A and Sajantila, A and Paabo, S},
journal = {Nat Genet},
number = {2}
}Analysis of Hox gene expression in the chick limb bud. Nelson, C., E., Morgan, B., a., Burke, a., C., Laufer, E., DiMambro, E., Murtaugh, L., C., Gonzales, E., Tessarollo, L., Parada, L., F., & Tabin, C. Development (Cambridge, England), 122(5):1449-66, 5, 1996.
Paper Website abstract bibtex
Paper Website abstract bibtex The vertebrate Hox genes have been shown to be important for patterning the primary and secondary axes of the developing vertebrate embryo. The function of these genes along the primary axis of the embryo has been generally interpreted in the context of positional specification and homeotic transformation of axial structures. The way in which these genes are expressed and function during the development of the secondary axes, particularly the limb, is less clear. In order to provide a reference for understanding the role of the Hox genes in limb patterning, we isolated clones of 23 Hox genes expressed during limb development, characterized their expression patterns and analyzed their regulation by the signalling centers which pattern the limb. The expression patterns of the Abd-B-related Hoxa and Hoxd genes have previously been partially characterized; however, our study reveals that these genes are expressed in patterns more dynamic and complex than generally appreciated, only transiently approximating simple, concentric, nested domains. Detailed analysis of these patterns suggests that the expression of each of the Hoxa and Hoxd genes is regulated in up to three independent phases. Each of these phases appears to be associated with the specification and patterning of one of the proximodistal segments of the limb (upper arm, lower arm and hand). Interestingly, in the last of these phases, the expression of the Hoxd genes violates the general rule of spatial and temporal colinearity of Hox gene expression with gene order along the chromosome. In contrast to the Abd-B-related Hoxa and Hoxd genes, which are expressed in both the fore and hind limbs, different sets of Hoxc genes are expressed in the two limbs. There is a correlation between the relative position of these genes along the chromosome and the axial level of the limb bud in which they are expressed. The more 3' genes are expressed in the fore limb bud while the 5' genes are expressed in the hind limb bud; intermediate genes are transcribed in both limbs. However, there is no clear correlation between the relative position of the genes along the chromosome and their expression domains within the limb. With the exception of Hoxc-11, which is transcribed in a posterior portion of the hind limb, Hoxc gene expression is restricted to the anterior/proximal portion of the limb bud. Importantly, comparison of the distributions of Hoxc-6 RNA and protein products reveals posttranscriptional regulation of this gene, suggesting that caution must be exercised in interpreting the functional significance of the RNA distribution of any of the vertebrate Hox genes. To understand the genesis of the complex patterns of Hox gene expression in the limb bud, we examined the propagation of Hox gene expression relative to cell proliferation. We find that shifts in Hox gene expression cannot be attributed to passive expansion due to cell proliferation. Rather, phase-specific Hox gene expression patterns appear to result from a context-dependent response of the limb mesoderm to Sonic hedgehog. Sonic hedgehog (the patterning signal from the Zone of Polarizing Activity) is known to be able to activate Hoxd gene expression in the limb. Although we find that Sonic hedgehog is capable of initiating and polarizing Hoxd gene expression during both of the latter two phases of Hox gene expression, the specific patterns induced are not determined by the signal, but depend upon the temporal context of the mesoderm receiving the signal. Misexpression of Sonic hedgehog also reveals that Hoxb-9, which is normally excluded from the posterior mesenchyme of the leg, is negatively regulated by Sonic hedgehog and that Hoxc-11, which is expressed in the posterior portion of the leg, is not affected by Sonic hedgehog and hence is not required to pattern the skeletal elements of the lower leg.
@article{
title = {Analysis of Hox gene expression in the chick limb bud.},
type = {article},
year = {1996},
identifiers = {[object Object]},
keywords = {Amino Acid Sequence,Animals,Base Sequence,Cell Movement,Chick Embryo,Extremities,Extremities: embryology,Gene Expression Regulation, Developmental,Gene Library,Genes, Homeobox,Hedgehog Proteins,Immunohistochemistry,In Situ Hybridization,Models, Genetic,Molecular Sequence Data,Morphogenesis,Muscles,Muscles: cytology,Muscles: embryology,Polymerase Chain Reaction,Proteins,Proteins: metabolism,Time Factors,Tissue Distribution,Trans-Activators,Transcription, Genetic},
pages = {1449-66},
volume = {122},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/8625833},
month = {5},
id = {9e81f849-717e-3abe-be53-e44f82a2f3f6},
created = {2016-04-08T12:19:40.000Z},
file_attached = {true},
profile_id = {994bc413-6766-31df-917a-32165aa30f6c},
group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
last_modified = {2017-03-14T10:42:46.538Z},
read = {true},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Nelson1996},
folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
private_publication = {false},
abstract = {The vertebrate Hox genes have been shown to be important for patterning the primary and secondary axes of the developing vertebrate embryo. The function of these genes along the primary axis of the embryo has been generally interpreted in the context of positional specification and homeotic transformation of axial structures. The way in which these genes are expressed and function during the development of the secondary axes, particularly the limb, is less clear. In order to provide a reference for understanding the role of the Hox genes in limb patterning, we isolated clones of 23 Hox genes expressed during limb development, characterized their expression patterns and analyzed their regulation by the signalling centers which pattern the limb. The expression patterns of the Abd-B-related Hoxa and Hoxd genes have previously been partially characterized; however, our study reveals that these genes are expressed in patterns more dynamic and complex than generally appreciated, only transiently approximating simple, concentric, nested domains. Detailed analysis of these patterns suggests that the expression of each of the Hoxa and Hoxd genes is regulated in up to three independent phases. Each of these phases appears to be associated with the specification and patterning of one of the proximodistal segments of the limb (upper arm, lower arm and hand). Interestingly, in the last of these phases, the expression of the Hoxd genes violates the general rule of spatial and temporal colinearity of Hox gene expression with gene order along the chromosome. In contrast to the Abd-B-related Hoxa and Hoxd genes, which are expressed in both the fore and hind limbs, different sets of Hoxc genes are expressed in the two limbs. There is a correlation between the relative position of these genes along the chromosome and the axial level of the limb bud in which they are expressed. The more 3' genes are expressed in the fore limb bud while the 5' genes are expressed in the hind limb bud; intermediate genes are transcribed in both limbs. However, there is no clear correlation between the relative position of the genes along the chromosome and their expression domains within the limb. With the exception of Hoxc-11, which is transcribed in a posterior portion of the hind limb, Hoxc gene expression is restricted to the anterior/proximal portion of the limb bud. Importantly, comparison of the distributions of Hoxc-6 RNA and protein products reveals posttranscriptional regulation of this gene, suggesting that caution must be exercised in interpreting the functional significance of the RNA distribution of any of the vertebrate Hox genes. To understand the genesis of the complex patterns of Hox gene expression in the limb bud, we examined the propagation of Hox gene expression relative to cell proliferation. We find that shifts in Hox gene expression cannot be attributed to passive expansion due to cell proliferation. Rather, phase-specific Hox gene expression patterns appear to result from a context-dependent response of the limb mesoderm to Sonic hedgehog. Sonic hedgehog (the patterning signal from the Zone of Polarizing Activity) is known to be able to activate Hoxd gene expression in the limb. Although we find that Sonic hedgehog is capable of initiating and polarizing Hoxd gene expression during both of the latter two phases of Hox gene expression, the specific patterns induced are not determined by the signal, but depend upon the temporal context of the mesoderm receiving the signal. Misexpression of Sonic hedgehog also reveals that Hoxb-9, which is normally excluded from the posterior mesenchyme of the leg, is negatively regulated by Sonic hedgehog and that Hoxc-11, which is expressed in the posterior portion of the leg, is not affected by Sonic hedgehog and hence is not required to pattern the skeletal elements of the lower leg.},
bibtype = {article},
author = {Nelson, C E and Morgan, B a and Burke, a C and Laufer, E and DiMambro, E and Murtaugh, L C and Gonzales, E and Tessarollo, L and Parada, L F and Tabin, C},
journal = {Development (Cambridge, England)},
number = {5}
}1995 (1)
An investigation into the role of phenotypic plasticity in evolution. Behera, N & Nanjundiah, V Journal of theoretical biology, 172(3):225--234, February, 1995.
doi abstract bibtex
doi abstract bibtex
Phenotypic plasticity can modify evolutionary pathways and accelerate the course of evolution. This was brought out in a quantitative model by Hinton & Nowlan (1987, Complex Systems 1, 497-502). The present work confirms and extends their results. We consider a population of genetically haploid individuals of fixed size. Genotypes are represented by one-dimensional arrays (strings) of genes. Each gene can be in one of three allelic states, designated 1, 0 and X. 1 and 0 stand for fixed states, that is for states with predetermined effects on the phenotype. X stands for a plastic state: the phenotypic effect of an X can be equivalent to that of a 1 or a 0, the actual choice being realized by a process of random coin-tossing. Our model, in contrast to that of Hinton and Nowlan, assumes a relatively smooth dependence of fitness on distance from a pre-assigned target genotype. From the fitness values, the number of individuals reaching reproductive maturity is determined. Reproduction involves random mating and a single recombinational event, with one of the two progeny genotypes becoming, in turn, a possible parental genotype for the next generation. We find that it is because of the special assumptions in the Hinton and Nowlan model that phenotypic plasticity invariably accelerates evolution. The relationship is not as straightforward with realistic fitness schemes. Instead, the general result is that plasticity, up to a certain optimal level, slows down the rate of evolutionary change but improves the level of adaptation finally reached.
@article{behera_investigation_1995,
title = {An investigation into the role of phenotypic plasticity in evolution},
volume = {172},
issn = {0022-5193},
doi = {10.1006/jtbi.1995.0019},
abstract = {Phenotypic plasticity can modify evolutionary pathways and accelerate the course of evolution. This was brought out in a quantitative model by Hinton \& Nowlan (1987, Complex Systems 1, 497-502). The present work confirms and extends their results. We consider a population of genetically haploid individuals of fixed size. Genotypes are represented by one-dimensional arrays (strings) of genes. Each gene can be in one of three allelic states, designated 1, 0 and X. 1 and 0 stand for fixed states, that is for states with predetermined effects on the phenotype. X stands for a plastic state: the phenotypic effect of an X can be equivalent to that of a 1 or a 0, the actual choice being realized by a process of random coin-tossing. Our model, in contrast to that of Hinton and Nowlan, assumes a relatively smooth dependence of fitness on distance from a pre-assigned target genotype. From the fitness values, the number of individuals reaching reproductive maturity is determined. Reproduction involves random mating and a single recombinational event, with one of the two progeny genotypes becoming, in turn, a possible parental genotype for the next generation. We find that it is because of the special assumptions in the Hinton and Nowlan model that phenotypic plasticity invariably accelerates evolution. The relationship is not as straightforward with realistic fitness schemes. Instead, the general result is that plasticity, up to a certain optimal level, slows down the rate of evolutionary change but improves the level of adaptation finally reached.},
language = {eng},
number = {3},
journal = {Journal of theoretical biology},
author = {Behera, N and Nanjundiah, V},
month = feb,
year = {1995},
pmid = {7715194},
keywords = {Adaptation, Physiological, Animals, Biological Evolution, Genetic Variation, Genotype, Models, Biological, Phenotype, Reproduction},
pages = {225--234}
}1989 (1)
Observations of the J = 1-0 CO lines in the Mars atmosphere - Radiodetection of C-13O and monitoring of C-12O. Lellouch, E., Gerin, M., Combes, F., Atreya, S., & Encrenaz, T. ıcarus, 77:414--438, February, 1989.
doi bibtex
doi bibtex
@article{lellouch_observations_1989,
title = {Observations of the {J} = 1-0 {CO} lines in the {Mars} atmosphere - {Radiodetection} of {C}-13O and monitoring of {C}-12O},
volume = {77},
doi = {10.1016/0019-1035(89)90097-3},
journal = {ıcarus},
author = {Lellouch, E. and Gerin, M. and Combes, F. and Atreya, S. and Encrenaz, T.},
month = feb,
year = {1989},
keywords = {ANALYSIS, ATMOSPHERE, Abundance, CALCULATIONS, Calibrating, Carbon monoxide, Doppler Effect, EARTH-BASED OBSERVATIONS, ISOTOPIC RATIOS, Line Spectra, MARS, MIXING, MODELS, Mars Atmosphere, Millimeter Waves, RADIO METHODS, Receivers, Schottky Diodes, Spectra, TECHNIQUES, TEMPERATURE, THERMAL PROPERTIES, Temperature Inversions, ℡ESCOPE METHODS},
pages = {414--438}
}1988 (1)
Primate motor cortex and free arm movements to visual targets in three-dimensional space. I. Relations between single cell discharge and direction of movement. Schwartz, A., Kettner, R., & Georgopoulos, A. 8(8):2913-2927, 1988.
Paper abstract bibtex
Paper abstract bibtex We describe the relations between the neuronal activity in primate motor cortex and the direction of arm movement in three-dimensional (3-D) space. The electrical signs of discharge of 568 cells were recorded while monkeys made movements of equal amplitude from the same starting position to 8 visual targets in a reaction time task. The layout of the targets in 3-D space was such that the direction of the movement ranged over the whole 3-D directional continuum in approximately equal angular intervals. We found that the discharge rate of 475/568 (83.6%) cells varied in an orderly fashion with the direction of movement: discharge rate was highest with movements in a certain direction (the cell's "preferred direction") and decreased progressively with movements in other directions, as a function of the cosine of the angle formed by the direction of the movement and the cell's preferred direction. The preferred directions of different cells were distributed throughout 3-D space. These findings generalize to 3-D space previous results obtained in 2-D space (Georgopoulos et al., 1982) and suggest that the motor cortex is a nodal point in the construction of patterns of output signals specifying the direction of arm movement in extrapersonal space.
@article{
title = {Primate motor cortex and free arm movements to visual targets in three-dimensional space. I. Relations between single cell discharge and direction of movement},
type = {article},
year = {1988},
keywords = {Animals,Arm,Carpus, Animal,Electromyography,Macaca mulatta/physiology,Macaca/physiology,Male,Models, Neurological,Motor Cortex/cytology/physiology,Movement,Neurons/physiology,Psychomotor Performance/physiology,Reaction Time,Regression Analysis},
pages = {2913-2927},
volume = {8},
id = {4a8e9b14-6f4d-34a2-a9f8-cb190a906c6c},
created = {2017-09-01T15:54:32.099Z},
file_attached = {true},
profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
last_modified = {2017-09-01T15:54:32.217Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {false},
hidden = {false},
language = {eng},
abstract = {We describe the relations between the neuronal activity in primate motor cortex and the direction of arm movement in three-dimensional (3-D) space. The electrical signs of discharge of 568 cells were recorded while monkeys made movements of equal amplitude from the same starting position to 8 visual targets in a reaction time task. The layout of the targets in 3-D space was such that the direction of the movement ranged over the whole 3-D directional continuum in approximately equal angular intervals. We found that the discharge rate of 475/568 (83.6%) cells varied in an orderly fashion with the direction of movement: discharge rate was highest with movements in a certain direction (the cell's "preferred direction") and decreased progressively with movements in other directions, as a function of the cosine of the angle formed by the direction of the movement and the cell's preferred direction. The preferred directions of different cells were distributed throughout 3-D space. These findings generalize to 3-D space previous results obtained in 2-D space (Georgopoulos et al., 1982) and suggest that the motor cortex is a nodal point in the construction of patterns of output signals specifying the direction of arm movement in extrapersonal space.},
bibtype = {article},
author = {Schwartz, A. and Kettner, R. and Georgopoulos, A.},
number = {8}
}1985 (1)
The coordination of arm movements: an experimentally confirmed mathematical model. Flash, T. & Hogan, N. Journal of Neuroscience, 5(7):1688--1703, 1985.
abstract bibtex
abstract bibtex
This paper presents studies of the coordination of voluntary human arm movements. A mathematical model is formulated which is shown to predict both the qualitative features and the quantitative details observed experimentally in planar, multijoint arm movements. Coordination is modeled mathematically by defining an objective function, a measure of performance for any possible movement. The unique trajectory which yields the best performance is determined using dynamic optimization theory. In the work presented here, the objective function is the square of the magnitude of jerk (rate of change of acceleration) of the hand integrated over the entire movement. This is equivalent to assuming that a major goal of motor coordination is the production of the smoothest possible movement of the hand. Experimental observations of human subjects performing voluntary unconstrained movements in a horizontal plane are presented. They confirm the following predictions of the mathematical model: unconstrained point-to-point motions are approximately straight with bell-shaped tangential velocity profiles; curved motions (through an intermediate point or around an obstacle) have portions of low curvature joined by portions of high curvature; at points of high curvature, the tangential velocity is reduced; the durations of the low-curvature portions are approximately equal. The theoretical analysis is based solely on the kinematics of movement independent of the dynamics of the musculoskeletal system and is successful only when formulated in terms of the motion of the hand in extracorporal space. The implications with respect to movement organization are discussed.
@Article{Flash1985,
Title = {The coordination of arm movements: an experimentally confirmed mathematical model},
Author = {Flash, T. and Hogan, N.},
Journal = {Journal of Neuroscience},
Year = {1985},
Number = {7},
Pages = {1688--1703},
Volume = {5},
Abstract = {This paper presents studies of the coordination of voluntary human arm movements. A mathematical model is formulated which is shown to predict both the qualitative features and the quantitative details observed experimentally in planar, multijoint arm movements. Coordination is modeled mathematically by defining an objective function, a measure of performance for any possible movement. The unique trajectory which yields the best performance is determined using dynamic optimization theory. In the work presented here, the objective function is the square of the magnitude of jerk (rate of change of acceleration) of the hand integrated over the entire movement. This is equivalent to assuming that a major goal of motor coordination is the production of the smoothest possible movement of the hand. Experimental observations of human subjects performing voluntary unconstrained movements in a horizontal plane are presented. They confirm the following predictions of the mathematical model: unconstrained point-to-point motions are approximately straight with bell-shaped tangential velocity profiles; curved motions (through an intermediate point or around an obstacle) have portions of low curvature joined by portions of high curvature; at points of high curvature, the tangential velocity is reduced; the durations of the low-curvature portions are approximately equal. The theoretical analysis is based solely on the kinematics of movement independent of the dynamics of the musculoskeletal system and is successful only when formulated in terms of the motion of the hand in extracorporal space. The implications with respect to movement organization are discussed.},
Owner = {jf2lin},
Timestamp = {2016.07.25}
}1978 (1)
A model for the statistical fluctuations of protein numbers in a microbial population. Berg, O., G. Journal of theoretical biology, 71(4):587-603, 1978.
Paper abstract bibtex
Paper abstract bibtex Abstract A model is presented for the distribution of protein molecules between the cells in a microbial population during steady-state growth. A general expression is derived under the sole assumption that each protein molecule has equal probability of joining either ... \n
@article{
title = {A model for the statistical fluctuations of protein numbers in a microbial population.},
type = {article},
year = {1978},
identifiers = {[object Object]},
keywords = {Bacterial Proteins,Bacterial Proteins: metabolism,Biological,Cell Count,Genes,Genetic,Mitosis,Models,Protein Biosynthesis,Regulator,Transcription,beta-Galactosidase,beta-Galactosidase: metabolism},
pages = {587-603},
volume = {71},
id = {bf82197e-46c9-3ca5-ad78-f87104ef3f27},
created = {2015-08-20T10:31:21.000Z},
file_attached = {true},
profile_id = {1593dc7b-4550-3536-a5a4-21ffd4cbffb8},
group_id = {9cd45c01-6b67-3572-a936-df749337a5f1},
last_modified = {2015-08-20T10:42:24.000Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Berg1978},
abstract = {Abstract A model is presented for the distribution of protein molecules between the cells in a microbial population during steady-state growth. A general expression is derived under the sole assumption that each protein molecule has equal probability of joining either ... \n},
bibtype = {article},
author = {Berg, O G},
journal = {Journal of theoretical biology},
number = {4}
}21-24 Sept. 2003 (1)
Active shape models with invariant optimal features (IOF-ASM) application to cardiac MRI segmentation. Ordas, S., Boisrobert, L., Huguet, M., & Frangi, A. Computers in Cardiology, 2003, 21-24 Sept. 2003.
doi bibtex
doi bibtex
@Article{Ordas_2124Sept2003_3683,
author = {Ordas, S. and Boisrobert, L. and Huguet, M. and Frangi, A.F.},
journal = {Computers in Cardiology, 2003},
pages = {633-636},
title = {Active shape models with invariant optimal features (IOF-ASM) application to cardiac MRI segmentation},
year = {21-24 Sept. 2003},
issn = {0276-6547},
keywords = {biomedical, MRI, cardiology, image, segmentation, medical, image, processing, active, shape, models, cardiac, MRI, segmentation, differential, Cartesian, invariant, features, endocardial, contours, heart, epicardium, heart, ventricles, invariant, optimal, features, nonlinear, appearance, model},
doi = {10.1109/CIC.2003.1291235},
title_with_no_special_chars = {Active shape models with invariant optimal features IOFASM application to cardiac MRI segmentation}
}