Keyword: models
2021 (1)
Applications of Physiologically Based Biopharmaceutics Modeling (PBBM) to Support Drug Product Quality: A Workshop Summary Report. Mitra, A., Suarez-Sharp, S., Pepin, X. J. H., Flanagan, T., Zhao, Y., Kotzagiorgis, E., Parrott, N., Sharan, S., Tistaert, C., Heimbach, T., Zolnik, B., Sjogren, E., Wu, F., Anand, O., Kakar, S., Li, M., Veerasingham, S., Kijima, S., Lima Santos, G. M., Ning, B., Raines, K., Rullo, G., Mandula, H., Delvadia, P., Dressman, J., Dickinson, P. A., & Babiskin, A. J Pharm Sci, 110(2):594–609, February, 2021.
doi abstract bibtex
doi abstract bibtex
This report summarizes the proceedings for Day 3 of the workshop titled "Current State and Future Expectations of Translational Modeling Strategies toSupportDrug Product Development, Manufacturing Changes and Controls". From a drug product quality perspective, patient-centric product development necessitates the development of clinically relevant drug product specifications (CRDPS). In this regard, Physiologically Based Biopharmaceutics modeling (PBBM) is a viable tool to establish links between in-vitro to in-vivo data, and support with establishing CRDPS. The theme of day 3 was practical applications of PBBM to support drug product quality. In this manuscript, case studies from US FDA, EMA and pharmaceutical industry on applications of PBBM in drug product quality are summarized which include 1) regulatory agency's perspectives on establishing the safe space and achieving study waivers, 2) model-informed risk assessment on the effects of acid reducing agents, bridging of dissolution methods, food effect, and formulation selection, and 3) understanding clinical formulation performance. Breakout session discussions focused on four topics - 1) terminologies related to physiologically based modeling in support of drug product quality, 2) regulatory harmonization on evidentiary standards, 3) CRDPS approaches and 4) bridging between biorelevant and quality control (QC) dissolution methods.
@article{mitra_applications_2021,
title = {Applications of {Physiologically} {Based} {Biopharmaceutics} {Modeling} ({PBBM}) to {Support} {Drug} {Product} {Quality}: {A} {Workshop} {Summary} {Report}},
volume = {110},
issn = {1520-6017 (Electronic) 0022-3549 (Linking)},
doi = {10.1016/j.xphs.2020.10.059},
abstract = {This report summarizes the proceedings for Day 3 of the workshop titled "Current State and Future Expectations of Translational Modeling Strategies toSupportDrug Product Development, Manufacturing Changes and Controls". From a drug product quality perspective, patient-centric product development necessitates the development of clinically relevant drug product specifications (CRDPS). In this regard, Physiologically Based Biopharmaceutics modeling (PBBM) is a viable tool to establish links between in-vitro to in-vivo data, and support with establishing CRDPS. The theme of day 3 was practical applications of PBBM to support drug product quality. In this manuscript, case studies from US FDA, EMA and pharmaceutical industry on applications of PBBM in drug product quality are summarized which include 1) regulatory agency's perspectives on establishing the safe space and achieving study waivers, 2) model-informed risk assessment on the effects of acid reducing agents, bridging of dissolution methods, food effect, and formulation selection, and 3) understanding clinical formulation performance. Breakout session discussions focused on four topics - 1) terminologies related to physiologically based modeling in support of drug product quality, 2) regulatory harmonization on evidentiary standards, 3) CRDPS approaches and 4) bridging between biorelevant and quality control (QC) dissolution methods.},
number = {2},
journal = {J Pharm Sci},
author = {Mitra, A. and Suarez-Sharp, S. and Pepin, X. J. H. and Flanagan, T. and Zhao, Y. and Kotzagiorgis, E. and Parrott, N. and Sharan, S. and Tistaert, C. and Heimbach, T. and Zolnik, B. and Sjogren, E. and Wu, F. and Anand, O. and Kakar, S. and Li, M. and Veerasingham, S. and Kijima, S. and Lima Santos, G. M. and Ning, B. and Raines, K. and Rullo, G. and Mandula, H. and Delvadia, P. and Dressman, J. and Dickinson, P. A. and Babiskin, A.},
month = feb,
year = {2021},
keywords = {*Biopharmaceutics, *Pharmaceutical Preparations, *dissolution, *physiologically based biopharmaceutics modeling (PBBM), *physiologically based pharmacokinetics modeling (PBPK), *product quality, *safe space, *virtual bioequivalence (VBE), Humans, Models, Biological, Research Report, Solubility},
pages = {594--609},
}2018 (1)
Estimating summary statistics for electronic health record laboratory data for use in high-throughput phenotyping algorithms. Albers, D. J., Elhadad, N., Claassen, J., Perotte, R., Goldstein, A., & Hripcsak, G. Journal of Biomedical Informatics, 78:87–101, 2018.
doi abstract bibtex
doi abstract bibtex
We study the question of how to represent or summarize raw laboratory data taken from an electronic health record (EHR) using parametric model selection to reduce or cope with biases induced through clinical care. It has been previously demonstrated that the health care process (Hripcsak and Albers, 2012, 2013), as defined by measurement context (Hripcsak and Albers, 2013; Albers et al., 2012) and measurement patterns (Albers and Hripcsak, 2010, 2012), can influence how EHR data are distributed statistically (Kohane and Weber, 2013; Pivovarov et al., 2014). We construct an algorithm, PopKLD, which is based on information criterion model selection (Burnham and Anderson, 2002; Claeskens and Hjort, 2008), is intended to reduce and cope with health care process biases and to produce an intuitively understandable continuous summary. The PopKLD algorithm can be automated and is designed to be applicable in high-throughput settings; for example, the output of the PopKLD algorithm can be used as input for phenotyping algorithms. Moreover, we develop the PopKLD-CAT algorithm that transforms the continuous PopKLD summary into a categorical summary useful for applications that require categorical data such as topic modeling. We evaluate our methodology in two ways. First, we apply the method to laboratory data collected in two different health care contexts, primary versus intensive care. We show that the PopKLD preserves known physiologic features in the data that are lost when summarizing the data using more common laboratory data summaries such as mean and standard deviation. Second, for three disease-laboratory measurement pairs, we perform a phenotyping task: we use the PopKLD and PopKLD-CAT algorithms to define high and low values of the laboratory variable that are used for defining a disease state. We then compare the relationship between the PopKLD-CAT summary disease predictions and the same predictions using empirically estimated mean and standard deviation to a gold standard generated by clinical review of patient records. We find that the PopKLD laboratory data summary is substantially better at predicting disease state. The PopKLD or PopKLD-CAT algorithms are not meant to be used as phenotyping algorithms, but we use the phenotyping task to show what information can be gained when using a more informative laboratory data summary. In the process of evaluation our method we show that the different clinical contexts and laboratory measurements necessitate different statistical summaries. Similarly, leveraging the principle of maximum entropy we argue that while some laboratory data only have sufficient information to estimate a mean and standard deviation, other laboratory data captured in an EHR contain substantially more information than can be captured in higher-parameter models.
@article{albers_estimating_2018,
title = {Estimating summary statistics for electronic health record laboratory data for use in high-throughput phenotyping algorithms},
volume = {78},
issn = {1532-0480},
doi = {10.1016/j.jbi.2018.01.004},
abstract = {We study the question of how to represent or summarize raw laboratory data taken from an electronic health record (EHR) using parametric model selection to reduce or cope with biases induced through clinical care. It has been previously demonstrated that the health care process (Hripcsak and Albers, 2012, 2013), as defined by measurement context (Hripcsak and Albers, 2013; Albers et al., 2012) and measurement patterns (Albers and Hripcsak, 2010, 2012), can influence how EHR data are distributed statistically (Kohane and Weber, 2013; Pivovarov et al., 2014). We construct an algorithm, PopKLD, which is based on information criterion model selection (Burnham and Anderson, 2002; Claeskens and Hjort, 2008), is intended to reduce and cope with health care process biases and to produce an intuitively understandable continuous summary. The PopKLD algorithm can be automated and is designed to be applicable in high-throughput settings; for example, the output of the PopKLD algorithm can be used as input for phenotyping algorithms. Moreover, we develop the PopKLD-CAT algorithm that transforms the continuous PopKLD summary into a categorical summary useful for applications that require categorical data such as topic modeling. We evaluate our methodology in two ways. First, we apply the method to laboratory data collected in two different health care contexts, primary versus intensive care. We show that the PopKLD preserves known physiologic features in the data that are lost when summarizing the data using more common laboratory data summaries such as mean and standard deviation. Second, for three disease-laboratory measurement pairs, we perform a phenotyping task: we use the PopKLD and PopKLD-CAT algorithms to define high and low values of the laboratory variable that are used for defining a disease state. We then compare the relationship between the PopKLD-CAT summary disease predictions and the same predictions using empirically estimated mean and standard deviation to a gold standard generated by clinical review of patient records. We find that the PopKLD laboratory data summary is substantially better at predicting disease state. The PopKLD or PopKLD-CAT algorithms are not meant to be used as phenotyping algorithms, but we use the phenotyping task to show what information can be gained when using a more informative laboratory data summary. In the process of evaluation our method we show that the different clinical contexts and laboratory measurements necessitate different statistical summaries. Similarly, leveraging the principle of maximum entropy we argue that while some laboratory data only have sufficient information to estimate a mean and standard deviation, other laboratory data captured in an EHR contain substantially more information than can be captured in higher-parameter models.},
language = {eng},
journal = {Journal of Biomedical Informatics},
author = {Albers, D. J. and Elhadad, N. and Claassen, J. and Perotte, R. and Goldstein, A. and Hripcsak, G.},
year = {2018},
pmid = {29369797},
pmcid = {PMC5856130},
keywords = {Algorithms, Clinical Laboratory Techniques, Data Mining, Electronic Health Records, Electronic health record, High-Throughput Screening Assays, Humans, Kullback-Leibler divergence, Laboratory tests, Models, Statistical, Phenotype, Summary statistic, phenotyping},
pages = {87--101},
}2016 (3)
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. Wen, D., Yu, Y., Hahn, M., W., & Nakhleh, L. Molecular ecology, 25(11):2361-2372, 6, 2016.
abstract bibtex
abstract bibtex
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.
@article{
title = {Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.},
type = {article},
year = {2016},
identifiers = {[object Object]},
keywords = {Animals,Culicidae,Evolution, Molecular,Genome, Insect,Hybridization, Genetic,Models, Genetic,Phylogeny,genetics},
pages = {2361-2372},
volume = {25},
month = {6},
id = {4969f961-914c-3873-8586-ae1ca0c7c0e9},
created = {2017-09-07T16:35:51.015Z},
file_attached = {false},
profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
group_id = {49665d18-5720-3154-b3f7-40652b55b7b9},
last_modified = {2017-09-15T13:46:36.898Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {Wen2016},
source_type = {Journal Article},
language = {eng},
country = {England},
patent_owner = {NLM},
folder_uuids = {213ba69b-866b-4785-8816-8fc333e9477c},
private_publication = {false},
abstract = {The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.},
bibtype = {article},
author = {Wen, Dingqiao and Yu, Yun and Hahn, Matthew W and Nakhleh, Luay},
journal = {Molecular ecology},
number = {11}
}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}
}The robustness of interdependent networks under the interplay between cascading failures and virus propagation. Zhao, D., Wang, Z., Xiao, G., Gao, B., & Wang, L. EPL (Europhysics Letters), 115(5):58004, September, 2016. 00001
![The robustness of interdependent networks under the interplay between cascading failures and virus propagation [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex
Paper doi abstract bibtex Cascading failures and epidemic dynamics, as two successful application realms of network science, are usually investigated separately. How do they affect each other is still an open, interesting problem. In this letter, we couple both processes and put them into the framework of interdependent networks, where each network only supports one dynamical process. Of particular interest, they spontaneously form a feedback loop: virus propagation triggers cascading failures of systems while cascading failures suppress virus propagation (i.e., the interplay between cascading failures and virus propagation, also named CF-VP model). Under this novel model, the interdependent networks will collapse completely if virus transmissibility exceeds a crucial threshold. In addition, only when the network sustaining the epidemic dynamics has a larger average degree, will the interdependent networks become more vulnerable, which is opposite to the observation of traditional cascading models in interdependent networks. To protect interdependent networks we also propose control measures based on the identification capability: a stronger identification capability leads to more robust interdependent networks.
@article{zhao_robustness_2016,
title = {The robustness of interdependent networks under the interplay between cascading failures and virus propagation},
volume = {115},
issn = {0295-5075, 1286-4854},
url = {http://stacks.iop.org/0295-5075/115/i=5/a=58004?key=crossref.1c56bc87a364fbc6ef754c4bd737bf1b},
doi = {10.1209/0295-5075/115/58004},
abstract = {Cascading failures and epidemic dynamics, as two successful application realms of network science, are usually investigated separately. How do they affect each other is still an open, interesting problem. In this letter, we couple both processes and put them into the framework of interdependent networks, where each network only supports one dynamical process. Of particular interest, they spontaneously form a feedback loop: virus propagation triggers cascading failures of systems while cascading failures suppress virus propagation (i.e., the interplay between cascading failures and virus propagation, also named CF-VP model). Under this novel model, the interdependent networks will collapse completely if virus transmissibility exceeds a crucial threshold. In addition, only when the network sustaining the epidemic dynamics has a larger average degree, will the interdependent networks become more vulnerable, which is opposite to the observation of traditional cascading models in interdependent networks. To protect interdependent networks we also propose control measures based on the identification capability: a stronger identification capability leads to more robust interdependent networks.},
number = {5},
urldate = {2016-12-17},
journal = {EPL (Europhysics Letters)},
author = {Zhao, Dawei and Wang, Zhen and Xiao, Gaoxi and Gao, Bo and Wang, Lianhai},
month = sep,
year = {2016},
note = {00001},
keywords = {collapse, models, reboot, health-epidemics-pandemics, systemic-risks},
pages = {58004},
file = {Zhao et al. - 2016 - The robustness of interdependent networks under th.pdf:C\:\\Users\\rsrs\\Documents\\Zotero Database\\storage\\GW6CEIB5\\Zhao et al. - 2016 - The robustness of interdependent networks under th.pdf:application/pdf}
}2015 (1)
Bayesian kernel machine regression for estimating the health effects of multi-pollutant mixtures. Bobb, J. F., Valeri, L., Claus Henn, B., Christiani, D. C., Wright, R. O., Mazumdar, M., Godleski, J. J., & Coull, B. A. Biostatistics (Oxford, England), 16(3):493–508, September, 2015. Publisher: Biostatistics
Paper doi abstract bibtex
Paper doi abstract bibtex Because humans are invariably exposed to complex chemical mixtures, estimating the health effects of multi-pollutant exposures is of critical concern in environmental epidemiology, and to regulatory agencies such as the U.S. Environmental Protection Agency. However, most health effects studies focus on single agents or consider simple two-way interaction models, in part because we lack the statistical methodology to more realistically capture the complexity of mixed exposures. We introduce Bayesian kernel machine regression (BKMR) as a new approach to study mixtures, in which the health outcome is regressed on a flexible function of the mixture (e.g. air pollution or toxic waste) components that is specified using a kernel function. In high-dimensional settings, a novel hierarchical variable selection approach is incorporated to identify important mixture components and account for the correlated structure of the mixture. Simulation studies demonstrate the success of BKMR in estimating the exposure-response function and in identifying the individual components of the mixture responsible for health effects. We demonstrate the features of the method through epidemiology and toxicology applications.
@article{bobb_bayesian_2015,
title = {Bayesian kernel machine regression for estimating the health effects of multi-pollutant mixtures},
volume = {16},
issn = {1468-4357},
url = {https://pubmed.ncbi.nlm.nih.gov/25532525/},
doi = {10.1093/BIOSTATISTICS/KXU058},
abstract = {Because humans are invariably exposed to complex chemical mixtures, estimating the health effects of multi-pollutant exposures is of critical concern in environmental epidemiology, and to regulatory agencies such as the U.S. Environmental Protection Agency. However, most health effects studies focus on single agents or consider simple two-way interaction models, in part because we lack the statistical methodology to more realistically capture the complexity of mixed exposures. We introduce Bayesian kernel machine regression (BKMR) as a new approach to study mixtures, in which the health outcome is regressed on a flexible function of the mixture (e.g. air pollution or toxic waste) components that is specified using a kernel function. In high-dimensional settings, a novel hierarchical variable selection approach is incorporated to identify important mixture components and account for the correlated structure of the mixture. Simulation studies demonstrate the success of BKMR in estimating the exposure-response function and in identifying the individual components of the mixture responsible for health effects. We demonstrate the features of the method through epidemiology and toxicology applications.},
number = {3},
urldate = {2021-12-16},
journal = {Biostatistics (Oxford, England)},
author = {Bobb, Jennifer F. and Valeri, Linda and Claus Henn, Birgit and Christiani, David C. and Wright, Robert O. and Mazumdar, Maitreyi and Godleski, John J. and Coull, Brent A.},
month = sep,
year = {2015},
pmid = {25532525},
note = {Publisher: Biostatistics},
keywords = {Animals, Bangladesh, Bayes Theorem*, Biostatistics, Brent A Coull, Child, Developmental Disabilities / etiology, Dogs, Environmental Health / statistics \& numerical data, Environmental Pollutants / adverse effects*, Extramural, Female, Hemodynamics / drug effects, Humans, Infant, Jennifer F Bobb, Linda Valeri, MEDLINE, Machine Learning, Metals / adverse effects, Models, N.I.H., NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Neurodevelopmental Disorders / etiology, Non-P.H.S., Normal Distribution, PMC5963470, Pregnancy, Preschool, PubMed Abstract, Regression Analysis, Research Support, Statistical, U.S. Gov't, doi:10.1093/biostatistics/kxu058, pmid:25532525},
pages = {493--508},
}2014 (3)
Dynamic nuclear polarization NMR enables the analysis of Sn-Beta zeolite prepared with natural abundance ¹¹⁹Sn precursors. Gunther, W. R, Michaelis, V. K, Caporini, M. A, Griffin, R. G, & Román-Leshkov, Y. Journal of the American Chemical Society, 136(17):6219–6222, April, 2014. Publisher: American Chemical Society ISBN: 1520-5126 (Electronic)${\}$r0002-7863 (Linking)
Paper doi abstract bibtex
Paper doi abstract bibtex The catalytic activity of tin-containing zeolites, such as Sn-Beta, is critically dependent on the successful incorporation of the tin metal center into the zeolite framework. However, synchrotron-based techniques or solid-state nuclear magnetic resonance (ssNMR) of samples enriched with (119)Sn isotopes are the only reliable methods to verify framework incorporation. This work demonstrates, for the first time, the use of dynamic nuclear polarization (DNP) NMR for characterizing zeolites containing ~2 wt % of natural abundance Sn without the need for (119)Sn isotopic enrichment. The biradicals TOTAPOL, bTbK, bCTbK, and SPIROPOL functioned effectively as polarizing sources, and the solvent enabled proper transfer of spin polarization from the radical's unpaired electrons to the target nuclei. Using bCTbK led to an enhancement ($ε$) of 75, allowing the characterization of natural-abundance (119)Sn-Beta with excellent signal-to-noise ratios in \textless24 h. Without DNP, no (119)Sn resonances were detected after 10 days of continuous analysis.
@article{Gunther2014a,
title = {Dynamic nuclear polarization {NMR} enables the analysis of {Sn}-{Beta} zeolite prepared with natural abundance ¹¹⁹{Sn} precursors.},
volume = {136},
issn = {1520-5126},
url = {http://dx.doi.org/10.1021/ja502113d},
doi = {10.1021/ja502113d},
abstract = {The catalytic activity of tin-containing zeolites, such as Sn-Beta, is critically dependent on the successful incorporation of the tin metal center into the zeolite framework. However, synchrotron-based techniques or solid-state nuclear magnetic resonance (ssNMR) of samples enriched with (119)Sn isotopes are the only reliable methods to verify framework incorporation. This work demonstrates, for the first time, the use of dynamic nuclear polarization (DNP) NMR for characterizing zeolites containing {\textasciitilde}2 wt \% of natural abundance Sn without the need for (119)Sn isotopic enrichment. The biradicals TOTAPOL, bTbK, bCTbK, and SPIROPOL functioned effectively as polarizing sources, and the solvent enabled proper transfer of spin polarization from the radical's unpaired electrons to the target nuclei. Using bCTbK led to an enhancement (\$ε\$) of 75, allowing the characterization of natural-abundance (119)Sn-Beta with excellent signal-to-noise ratios in {\textless}24 h. Without DNP, no (119)Sn resonances were detected after 10 days of continuous analysis.},
number = {17},
journal = {Journal of the American Chemical Society},
author = {Gunther, William R and Michaelis, Vladimir K and Caporini, Marc A and Griffin, Robert G and Román-Leshkov, Yuriy},
month = apr,
year = {2014},
pmid = {24697321},
note = {Publisher: American Chemical Society
ISBN: 1520-5126 (Electronic)\${\textbackslash}\$r0002-7863 (Linking)},
keywords = {Magnetic Resonance Spectroscopy, Magnetic Resonance Spectroscopy: methods, Models, Molecular, Tin, Tin: analysis, Zeolites, Zeolites: chemistry},
pages = {6219--6222},
}The World 5 model; Peak metals, minerals, energy, wealth, food and population; urgent policy considerations for a sustainable society. Sverdrup, H. U., Koca, D., & Ragnarsdóttir, K. V. In Equity within planetary boundaries, pages 265–265, 2014.
![The World 5 model; Peak metals, minerals, energy, wealth, food and population; urgent policy considerations for a sustainable society [pdf]](https://bibbase.org/img/filetypes/pdf.svg "pdf")
Paper abstract bibtex
Paper abstract bibtex In this paper we show that several metals, elements and energy resources are about to run into scarcity within the next decades, and most elements within some centuries. A new global systems model was assembled to analyse this scarcity as a continuation of the model used in the Limits-to-Growth World3 model. We show that this scarcity will lead to “peak wealth”, “peak population”, “peak costs”, “peak junk”, “peak problems” and possibly “peak civilization”, unless some urgent measures are systematically taken throughout the world. Scarcity implies that materials that underpin modern society will largely be unavailable for global mass production of goods. The material volumes that can be supplied from fossil reserves will be reduced with respect to today and all materials will go up sharply in price. The future resource supply is thus unsustainable as long as resource use continues as today. The creation of money from conversion of resources and work, as well as the current extensive borrowing from the future, cause concerns that peak oil and peak materials may lead to “peak wealth” and the end of the golden age we currently have for developed nations. Our policy recommendations are that overnments must take this issue seriously and immediately start preparing for legislations that can close material cycles, optimize energy use and minimize all types of irreversible material losses as soon as possible. Forceful programs promoting extensive recycling are needed as well as special care in closing loops and reducing irreversible losses. Research efforts in this field needs to be based on systems thinking and a concerted effort is needed globally
@inproceedings{sverdrup_world_2014,
title = {The {World} 5 model; {Peak} metals, minerals, energy, wealth, food and population; urgent policy considerations for a sustainable society},
url = {http://www.peakoilindia.org/wp-content/uploads/2013/10/The-World-5-model.pdf},
abstract = {In this paper we show that several metals, elements and energy resources are about to run into scarcity within the next decades, and most elements within some centuries. A new global systems model was assembled to analyse this scarcity as a continuation of the model used in the Limits-to-Growth World3 model. We show that this scarcity will lead to “peak wealth”, “peak population”, “peak costs”, “peak junk”, “peak problems” and possibly “peak civilization”, unless some urgent measures are systematically taken throughout the world. Scarcity implies that materials that underpin modern society will largely be unavailable for global mass production of goods. The material volumes that can be supplied from fossil reserves will be reduced with respect to today and all materials will go up sharply in price. The future resource supply is thus unsustainable as long as resource use continues as today. The creation of money from conversion of resources and work, as well as the current extensive borrowing from the future, cause concerns that peak oil and peak materials may lead to “peak wealth” and the end of the golden age we currently have for developed nations. Our policy recommendations are that overnments must take this issue seriously and immediately start preparing for legislations that can close material cycles, optimize energy use and minimize all types of irreversible material losses as soon as possible. Forceful programs promoting extensive recycling are needed as well as special care in closing loops and reducing irreversible losses. Research efforts in this field needs to be based on systems thinking and a concerted effort is needed globally},
urldate = {2015-03-25},
booktitle = {Equity within planetary boundaries},
author = {Sverdrup, Harald Ulrik and Koca, Deniz and Ragnarsdóttir, Kristín Vala},
year = {2014},
keywords = {collapse, models, limits-to-growth},
pages = {265--265},
file = {Sverdrup et al. - 2014 - The World 5 model\; Peak metals, minerals, energy, .pdf:C\:\\Users\\rsrs\\Documents\\Zotero Database\\storage\\NKJIUDJW\\Sverdrup et al. - 2014 - The World 5 model\; Peak metals, minerals, energy, .pdf:application/pdf}
}Points of significance: Nonparametric tests. Krzywinski, M. & Altman, N. Nature methods, 11(5):467–8, May, 2014.
Paper doi bibtex
Paper doi bibtex @article{Krzywinski2014,
title = {Points of significance: {Nonparametric} tests.},
volume = {11},
issn = {1548-7105},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24820360},
doi = {10.1038/nmeth.2937},
number = {5},
journal = {Nature methods},
author = {Krzywinski, Martin and Altman, Naomi},
month = may,
year = {2014},
pmid = {24820360},
keywords = {\#nosource, Blood Pressure, Data Interpretation, Humans, Models, Nonparametric, Reference Values, Research Design, Sample Size, Sensitivity and Specificity, Statistical, Statistics},
pages = {467--8},
}2013 (4)
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.
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.},
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year = {2013},
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pages = {4309-14},
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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},
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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}
}Information Retrieval Models: Foundations and Relationships. Roelleke, T. Morgan & Claypool, 2013.
doi abstract bibtex
doi abstract bibtex
Information Retrieval (IR) models are a core component of IR research and IR systems. The past decade brought a consolidation of the family of IR models, which by 2000 consisted of relatively isolated views on TF-IDF (Term-Frequency times Inverse-Document-Frequency) as the weighting scheme in the vector-space model (VSM), the probabilistic relevance framework (PRF), the binary independence retrieval (BIR) model, BM25 (Best-Match Version 25, the main instantiation of the PRF/BIR), and language modelling (LM). Also, the early 2000s saw the arrival of divergence from randomness (DFR). Regarding intuition and simplicity, though LM is clear from a probabilistic point of view, several people stated: "It is easy to understand TF-IDF and BM25. For LM, however, we understand the math, but we do not fully understand why it works." This book takes a horizontal approach gathering the foundations of TF-IDF, PRF, BIR, Poisson, BM25, LM, probabilistic inference networks (PIN's), and divergence-based models. The aim is to create a consolidated and balanced view on the main models. A particular focus of this book is on the "relationships between models." This includes an overview over the main frameworks (PRF, logical IR, VSM, generalized VSM) and a pairing of TF-IDF with other models. It becomes evident that TF-IDF and LM measure the same, namely the dependence (overlap) between document and query. The Poisson probability helps to establish probabilistic, non-heuristic roots for TF-IDF, and the Poisson parameter, average term frequency, is a binding link between several retrieval models and model parameters. Table of Contents: List of Figures / Preface / Acknowledgments / Introduction / Foundations of IR Models / Relationships Between IR Models / Summary & Research Outlook / Bibliography / Author's Biography / Index
@book{Roelleke2013,
title = {Information {Retrieval} {Models}: {Foundations} and {Relationships}},
abstract = {Information Retrieval (IR) models are a core component of IR research and IR systems. The past decade brought a consolidation of the family of IR models, which by 2000 consisted of relatively isolated views on TF-IDF (Term-Frequency times Inverse-Document-Frequency) as the weighting scheme in the vector-space model (VSM), the probabilistic relevance framework (PRF), the binary independence retrieval (BIR) model, BM25 (Best-Match Version 25, the main instantiation of the PRF/BIR), and language modelling (LM). Also, the early 2000s saw the arrival of divergence from randomness (DFR). Regarding intuition and simplicity, though LM is clear from a probabilistic point of view, several people stated: "It is easy to understand TF-IDF and BM25. For LM, however, we understand the math, but we do not fully understand why it works." This book takes a horizontal approach gathering the foundations of TF-IDF, PRF, BIR, Poisson, BM25, LM, probabilistic inference networks (PIN's), and divergence-based models. The aim is to create a consolidated and balanced view on the main models. A particular focus of this book is on the "relationships between models." This includes an overview over the main frameworks (PRF, logical IR, VSM, generalized VSM) and a pairing of TF-IDF with other models. It becomes evident that TF-IDF and LM measure the same, namely the dependence (overlap) between document and query. The Poisson probability helps to establish probabilistic, non-heuristic roots for TF-IDF, and the Poisson parameter, average term frequency, is a binding link between several retrieval models and model parameters. Table of Contents: List of Figures / Preface / Acknowledgments / Introduction / Foundations of IR Models / Relationships Between IR Models / Summary \& Research Outlook / Bibliography / Author's Biography / Index},
publisher = {Morgan \& Claypool},
author = {Roelleke, Thomas},
year = {2013},
doi = {10.2200/S00494ED1V01Y201304ICR027},
keywords = {information retrieval, models},
}Architecture and function of plant light-harvesting complexes II. Pan, X., Liu, Z., Li, M., & Chang, W. 23(4):515–525, 2013.
Paper doi abstract bibtex
Paper doi abstract bibtex The antenna system associated with plant photosystem II (PSII) comprises a series of light-harvesting complexes II (LHCIIs) which are supramolecular assemblies of chlorophylls, carotenoids, lipids and integral membrane proteins. These complexes not only function in capturing and transmitting light energy, but also have pivotal roles in photoprotection under high-light conditions through a mechanism known as non-photochemical quenching process. Among them, the most abundant major species (majLHCII) is located at the periphery of PSII and forms homo/hetero-trimers. Besides, three minor species, named CP29, CP26 and CP24, are adjacent to the PSII core, exist in monomeric form and bridge the majLHCII trimers with the core complex. Structural studies on majLHCII and CP29 have revealed the overall architecture of plant LHC family, the binding sites of pigment molecules and the distribution pattern of chromophores in three-dimensional space. The high-resolution structural data of LHCIIs serve as fundamental bases for an improved understanding on the mechanisms of light harvesting, energy transfer and photoprotection processes in plants.
@article{pan_architecture_2013,
title = {Architecture and function of plant light-harvesting complexes {II}},
volume = {23},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23623335},
doi = {10.1016/j.sbi.2013.04.004},
abstract = {The antenna system associated with plant photosystem II (PSII) comprises a series of light-harvesting complexes II (LHCIIs) which are supramolecular assemblies of chlorophylls, carotenoids, lipids and integral membrane proteins. These complexes not only function in capturing and transmitting light energy, but also have pivotal roles in photoprotection under high-light conditions through a mechanism known as non-photochemical quenching process. Among them, the most abundant major species (majLHCII) is located at the periphery of PSII and forms homo/hetero-trimers. Besides, three minor species, named CP29, CP26 and CP24, are adjacent to the PSII core, exist in monomeric form and bridge the majLHCII trimers with the core complex. Structural studies on majLHCII and CP29 have revealed the overall architecture of plant LHC family, the binding sites of pigment molecules and the distribution pattern of chromophores in three-dimensional space. The high-resolution structural data of LHCIIs serve as fundamental bases for an improved understanding on the mechanisms of light harvesting, energy transfer and photoprotection processes in plants.},
language = {eng},
number = {4},
author = {Pan, Xiaowei and Liu, Zhenfeng and Li, Mei and Chang, Wenrui},
year = {2013},
pmid = {23623335},
keywords = {Binding Sites, Chlorophyll, Chlorophyll/metabolism, Light, Light-Harvesting Protein Complexes, Light-Harvesting Protein Complexes/*metabolism/*ul, Models, Molecular, Photosystem II Protein Complex, Photosystem II Protein Complex/*metabolism/*ultras, Plants/metabolism, Protein Structure, Tertiary, light, plants},
pages = {515--525},
}2012 (9)
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},
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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}
}The recovery paradigm - a model of hope and change for alcohol and drug addiction. Best, D. W. & Lubman, D. I. Australian Family Physician, 41(8):593–597, August, 2012.
abstract bibtex
abstract bibtex
BACKGROUND: Alcohol and drug disorders remain major health and social problems in Australia, contributing enormously to the global burden of disease and the everyday practice of primary care. A recent growth in recovery research and recovery focused policies are starting to have an impact in Australia, with implications for how we attempt to resolve these problems. OBJECTIVE: In this article we discuss recent international findings in recovery research, and explore their implications for primary care. DISCUSSION: Research indicates that over half of dependent substance users will eventually achieve stable recovery. Key predictors of recovery are active engagement in the community and immersion in peer support groups and activities. Recovery requires a twin track approach: enabling and supporting individual recovery journeys, while creating environmental conditions that enable and support a 'social contagion' of recovery, in which recovery is transmitted through supportive social networks and dedicated recovery groups, such as mutual aid.
@article{best_recovery_2012,
title = {The recovery paradigm - a model of hope and change for alcohol and drug addiction},
volume = {41},
issn = {0300-8495},
abstract = {BACKGROUND: Alcohol and drug disorders remain major health and social problems in Australia, contributing enormously to the global burden of disease and the everyday practice of primary care. A recent growth in recovery research and recovery focused policies are starting to have an impact in Australia, with implications for how we attempt to resolve these problems.
OBJECTIVE: In this article we discuss recent international findings in recovery research, and explore their implications for primary care.
DISCUSSION: Research indicates that over half of dependent substance users will eventually achieve stable recovery. Key predictors of recovery are active engagement in the community and immersion in peer support groups and activities. Recovery requires a twin track approach: enabling and supporting individual recovery journeys, while creating environmental conditions that enable and support a 'social contagion' of recovery, in which recovery is transmitted through supportive social networks and dedicated recovery groups, such as mutual aid.},
language = {eng},
number = {8},
journal = {Australian Family Physician},
author = {Best, David W. and Lubman, Dan I.},
month = aug,
year = {2012},
pmid = {23145400},
keywords = {Adaptation, Psychological, Alcoholism, General Practice, Humans, Models, Theoretical, Self-Help Groups, Social Support, Substance-Related Disorders},
pages = {593--597},
}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}
}Frontiers in molecular dynamics simulations of DNA. Pérez, A., Luque, F J., & Orozco, M. Accounts of chemical research, 45(2):196–205, February, 2012.
Paper doi abstract bibtex
Paper doi abstract bibtex It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global thermodynamic and kinetic picture of the binding landscape of DNA will become available in a few years. MD will become a crucial tool in areas such as biomolecular engineering and synthetic biology. MD has also been shown to be an excellent source of parameters for mesoscopic models of DNA flexibility. Such models can be refined through atomistic MD simulations on small duplexes and then applied to the study of entire chromosomes. Recent evidence suggests that MD-derived elastic models can successfully predict the position of regulatory regions in DNA and can help advance our understanding of nucleosome positioning and chromatin plasticity. If these results are confirmed, MD simulations can become the ultimate tool to decipher a physical code that can contribute to gene regulation. We are entering the golden age of MD simulations of DNA. Undoubtedly, the expectations are high, but the challenges are also enormous. These include the need for more accurate potential energy functionals and for longer and more complex simulations in more realistic systems. The joint research effort of several groups will be crucial for adapting the technique to the requirements of the coming decade.
@article{perez_frontiers_2012,
title = {Frontiers in molecular dynamics simulations of {DNA}.},
volume = {45},
issn = {1520-4898},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21830782},
doi = {10.1021/ar2001217},
abstract = {It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global thermodynamic and kinetic picture of the binding landscape of DNA will become available in a few years. MD will become a crucial tool in areas such as biomolecular engineering and synthetic biology. MD has also been shown to be an excellent source of parameters for mesoscopic models of DNA flexibility. Such models can be refined through atomistic MD simulations on small duplexes and then applied to the study of entire chromosomes. Recent evidence suggests that MD-derived elastic models can successfully predict the position of regulatory regions in DNA and can help advance our understanding of nucleosome positioning and chromatin plasticity. If these results are confirmed, MD simulations can become the ultimate tool to decipher a physical code that can contribute to gene regulation. We are entering the golden age of MD simulations of DNA. Undoubtedly, the expectations are high, but the challenges are also enormous. These include the need for more accurate potential energy functionals and for longer and more complex simulations in more realistic systems. The joint research effort of several groups will be crucial for adapting the technique to the requirements of the coming decade.},
number = {2},
journal = {Accounts of chemical research},
author = {Pérez, Alberto and Luque, F Javier and Orozco, Modesto},
month = feb,
year = {2012},
pmid = {21830782},
keywords = {\#nosource, DNA, DNA: chemistry, DNA: metabolism, Models, Molecular, Molecular Dynamics Simulation, Nucleic Acid Conformation, Protein Conformation, Proteins, Proteins: chemistry, Proteins: metabolism, Thermodynamics, X-Ray Diffraction},
pages = {196--205},
}Optimized end-stacking provides specificity of n -Methyl mesoporphyrin IX for human telomeric g-quadruplex DNA. Nicoludis, J. M, Miller, S. T., Jeffrey, P. D, Barrett, S. P, Rablen, P. R, Lawton, T. J, & Yatsunyk, L. a Journal of the American Chemical Society, 134(50):20446–20456, December, 2012.
Paper doi abstract bibtex
Paper doi abstract bibtex N-methyl mesoporphyrin IX (NMM) is exceptionally selective for G-quadruplexes (GQ) relative to duplex DNA and, as such, has found a wide range of applications in biology and chemistry. In addition, NMM is selective for parallel vs. antiparallel GQ folds, as was recently demonstrated in our laboratory. Here, we present the X-ray crystal structure of a complex between NMM and human telomeric DNA dAGGG(TTAGGG)3, Tel22, determined in two space groups, P21212 and P6, at 1.65 and 2.15 Å resolution, respectively. The former is the highest resolution structure of the human telomeric GQ DNA reported to date. The biological unit contains a Tel22 dimer of 5'-5' stacked parallel-stranded quadruplexes capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. NMM is capable of adjusting its macrocycle geometry to closely match that of the terminal G-tetrad required for efficient π-π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. Based on the biochemical data, binding of NMM to Tel22 does not rely on relatively non-specific electrostatic interactions, which characterize most canonical GQ ligands, rather it is hydrophobic in nature. The structural features observed in the NMM-Tel22 complex described here will serve as guidelines for developing new quadruplex ligands that have excellent affinity and precisely defined selectivity.
@article{Nicoludis2012,
title = {Optimized end-stacking provides specificity of n -{Methyl} mesoporphyrin {IX} for human telomeric g-quadruplex {DNA}},
volume = {134},
issn = {0002-7863},
url = {http://pubs.acs.org/doi/abs/10.1021/ja3088746 http://www.ncbi.nlm.nih.gov/pubmed/23181361 http://pubs.acs.org/doi/10.1021/ja3088746},
doi = {10.1021/ja3088746},
abstract = {N-methyl mesoporphyrin IX (NMM) is exceptionally selective for G-quadruplexes (GQ) relative to duplex DNA and, as such, has found a wide range of applications in biology and chemistry. In addition, NMM is selective for parallel vs. antiparallel GQ folds, as was recently demonstrated in our laboratory. Here, we present the X-ray crystal structure of a complex between NMM and human telomeric DNA dAGGG(TTAGGG)3, Tel22, determined in two space groups, P21212 and P6, at 1.65 and 2.15 Å resolution, respectively. The former is the highest resolution structure of the human telomeric GQ DNA reported to date. The biological unit contains a Tel22 dimer of 5'-5' stacked parallel-stranded quadruplexes capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. NMM is capable of adjusting its macrocycle geometry to closely match that of the terminal G-tetrad required for efficient π-π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. Based on the biochemical data, binding of NMM to Tel22 does not rely on relatively non-specific electrostatic interactions, which characterize most canonical GQ ligands, rather it is hydrophobic in nature. The structural features observed in the NMM-Tel22 complex described here will serve as guidelines for developing new quadruplex ligands that have excellent affinity and precisely defined selectivity.},
number = {50},
journal = {Journal of the American Chemical Society},
author = {Nicoludis, John M and Miller, Stephen Thomas and Jeffrey, Philip D and Barrett, Steven P and Rablen, Paul R and Lawton, Thomas J and Yatsunyk, Liliya a},
month = dec,
year = {2012},
pmid = {23181361},
keywords = {\#nosource, Circular Dichroism, Crystallography, Fluorescence Resonance Energy Transfer, G-Quadruplexes, Humans, Mesoporphyrins, Mesoporphyrins: chemistry, Models, Molecular, Principal Component Analysis, Spectrophotometry, Telomere, Ultraviolet, X-Ray},
pages = {20446--20456},
}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},
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last_modified = {2014-12-10T09:11:31.000Z},
read = {false},
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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 pyrene-imidazolium derivative that selectively recognizes G-quadruplex DNA. Kim, H. N., Lee, E., Xu, Z., Kim, H., Lee, H., Lee, J., & Yoon, J. Biomaterials, 33(7):2282–8, March, 2012. Publisher: Elsevier Ltd
Paper doi abstract bibtex
Paper doi abstract bibtex G-quadruplexes, formed of four stranded guanine bases stabilized by monovalent cations, serve important role in cancer cell growth and control gene expression in telomere. Since there are various types of quadruplex structures, rapid and simple screening methods with high selectivity, sensitivity and nontoxicity are required for understanding about the biological roles of quadruplex DNA as well as in designing therapeutics. Herein, we report a pyrene-imidazolium derivative, JY-1, which can with high selectivity recognize G-quadruplex using fluorescence and NMR spectroscopy. This is the first example based on the imidazolium derivative, which can detect the G-quadruplex directly to utilize the excimer/monomer emission change in pyrene fluorophore. The selectivity of strong binding to a specific sequence can allow for quadruplex sensing and the detection method presented here is very simple, using fluorescence and NMR study. Also, the groove binding characteristic of JY-1 to the G-quadruplex has a relatively low nonspecific toxicity and the structure-specific differences in fluorescent character between DNA duplex and G-quadruplex may offer more discovery and application in biological study.
@article{Kim2012,
title = {A pyrene-imidazolium derivative that selectively recognizes {G}-quadruplex {DNA}.},
volume = {33},
issn = {1878-5905},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22196901},
doi = {10.1016/j.biomaterials.2011.11.073},
abstract = {G-quadruplexes, formed of four stranded guanine bases stabilized by monovalent cations, serve important role in cancer cell growth and control gene expression in telomere. Since there are various types of quadruplex structures, rapid and simple screening methods with high selectivity, sensitivity and nontoxicity are required for understanding about the biological roles of quadruplex DNA as well as in designing therapeutics. Herein, we report a pyrene-imidazolium derivative, JY-1, which can with high selectivity recognize G-quadruplex using fluorescence and NMR spectroscopy. This is the first example based on the imidazolium derivative, which can detect the G-quadruplex directly to utilize the excimer/monomer emission change in pyrene fluorophore. The selectivity of strong binding to a specific sequence can allow for quadruplex sensing and the detection method presented here is very simple, using fluorescence and NMR study. Also, the groove binding characteristic of JY-1 to the G-quadruplex has a relatively low nonspecific toxicity and the structure-specific differences in fluorescent character between DNA duplex and G-quadruplex may offer more discovery and application in biological study.},
number = {7},
journal = {Biomaterials},
author = {Kim, Ha Na and Lee, Eun-Hae and Xu, Zhaochao and Kim, Hee-Eun and Lee, Hee-Seung and Lee, Joon-Hwa and Yoon, Juyoung},
month = mar,
year = {2012},
pmid = {22196901},
note = {Publisher: Elsevier Ltd},
keywords = {\#nosource, Circular Dichroism, DNA, DNA: chemistry, Fluorescence, Fluorescence: methods, Fluorescent Dyes, Fluorescent Dyes: chemistry, G-Quadruplexes, Imidazoles, Imidazoles: chemistry, Magnetic Resonance Spectroscopy, Magnetic Resonance Spectroscopy: methods, Models, Molecular, Molecular Structure, Nucleic Acid Conformation, Pyrenes, Pyrenes: chemistry, Spectrometry},
pages = {2282--8},
}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},
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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 (9)
EEG–BOLD correlations during (post-) adolescent brain maturation. Lüchinger, R., Michels, L., Martin, E., & Brandeis, D. NeuroImage, 56(3):1493–1505, June, 2011.
Paper doi abstract bibtex
Paper doi abstract bibtex The transition from adolescence to adulthood is a critical stage in the human lifespan during which the brain still undergoes substantial structural and functional change. The changing frequency composition of the resting state EEG reflects maturation of brain function. This study investigated (post)adolescent brain maturation captured by two independently but simultaneously recorded neuronal signals: EEG and fMRI. Data were collected in a 20 min eyes-open/eyes-closed resting state paradigm. EEG, fMRI-BOLD signal and EEG-BOLD correlations were compared between groups of adults, age 25 (n=18), and adolescents, age 15 (n=18). A typical developmental decrease of low-frequency EEG power was observed even at this late stage of brain maturation. Frequency and condition specific EEG-fMRI correlations proved robust for multiple brain regions. However, no consistent change in the EEG-BOLD correlations was identified that would correspond to the neuronal maturation captured by the EEG. This result indicates that the EEG-BOLD correlation measures a distinct aspect of neurophysiological activity that presumably matures earlier, since it is less sensitive to late maturation than the neuronal activity captured by low-frequency EEG.
@article{luchinger_eegbold_2011,
title = {{EEG}–{BOLD} correlations during (post-) adolescent brain maturation},
volume = {56},
issn = {10538119},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21349336},
doi = {10.1016/j.neuroimage.2011.02.050},
abstract = {The transition from adolescence to adulthood is a critical stage in the human lifespan during which the brain still undergoes substantial structural and functional change. The changing frequency composition of the resting state EEG reflects maturation of brain function. This study investigated (post)adolescent brain maturation captured by two independently but simultaneously recorded neuronal signals: EEG and fMRI. Data were collected in a 20 min eyes-open/eyes-closed resting state paradigm. EEG, fMRI-BOLD signal and EEG-BOLD correlations were compared between groups of adults, age 25 (n=18), and adolescents, age 15 (n=18). A typical developmental decrease of low-frequency EEG power was observed even at this late stage of brain maturation. Frequency and condition specific EEG-fMRI correlations proved robust for multiple brain regions. However, no consistent change in the EEG-BOLD correlations was identified that would correspond to the neuronal maturation captured by the EEG. This result indicates that the EEG-BOLD correlation measures a distinct aspect of neurophysiological activity that presumably matures earlier, since it is less sensitive to late maturation than the neuronal activity captured by low-frequency EEG.},
number = {3},
urldate = {2015-04-10},
journal = {NeuroImage},
author = {Lüchinger, Rafael and Michels, Lars and Martin, Ernst and Brandeis, Daniel},
month = jun,
year = {2011},
pmid = {21349336},
keywords = {Adolescent, Adult, Aging, Aging: physiology, Alpha Rhythm, Alpha Rhythm: physiology, Brain, Brain: growth \& development, Data Interpretation, Delta Rhythm, Delta Rhythm: physiology, Electroencephalography, Female, Humans, Magnetic Resonance Imaging, Male, Models, Nerve Net, Nerve Net: growth \& development, Nerve Net: physiology, Neurological, Oxygen, Oxygen: blood, Photic Stimulation, Regression Analysis, Rest, Rest: physiology, Statistical, Theta Rhythm, Theta Rhythm: physiology, Young Adult},
pages = {1493--1505},
}Macrophage-mediated inflammation in metabolic disease. Chawla, A., Nguyen, K. D, & Goh, Y P S. Nature Reviews. Immunology, 11(11):738–49, November, 2011. Publisher: Nature Publishing Group
Paper doi bibtex
Paper doi bibtex Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders. Dudley, K. J, Li, X., Kobor, M. S, Kippin, T. E, & Bredy, T. W Neuroscience and biobehavioral reviews, 35(7):1544–51, June, 2011. Publisher: Elsevier Ltd
Paper doi abstract bibtex
Paper doi abstract bibtex The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.
@article{dudley_epigenetic_2011,
title = {Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders.},
volume = {35},
issn = {1873-7528},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21251925},
doi = {10.1016/j.neubiorev.2010.12.016},
abstract = {The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.},
number = {7},
urldate = {2012-03-24},
journal = {Neuroscience and biobehavioral reviews},
author = {Dudley, Kevin J and Li, Xiang and Kobor, Michael S and Kippin, Tod E and Bredy, Timothy W},
month = jun,
year = {2011},
pmid = {21251925},
note = {Publisher: Elsevier Ltd},
keywords = {Brain, Brain: growth \& development, Brain: physiology, Disease Susceptibility, Disease Susceptibility: psychology, Epigenesis, Genetic, Epigenesis, Genetic: genetics, Humans, Mental Disorders, Mental Disorders: complications, Mental Disorders: genetics, Mental Disorders: psychology, Models, Genetic, Resilience, Psychological, Stress, Psychological, Stress, Psychological: complications, Stress, Psychological: genetics, Stress, Psychological: psychology},
pages = {1544--51},
}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},
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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}
}Direct and indirect effects in a survival context. Lange, T. & Hansen, J. V. Epidemiology (Cambridge, Mass.), 22(4):575–581, July, 2011.
doi abstract bibtex
doi abstract bibtex
A cornerstone of epidemiologic research is to understand the causal pathways from an exposure to an outcome. Mediation analysis based on counterfactuals is an important tool when addressing such questions. However, none of the existing techniques for formal mediation analysis can be applied to survival data. This is a severe shortcoming, as many epidemiologic questions can be addressed only with censored survival data. A solution has been to use a number of Cox models (with and without the potential mediator), but this approach does not allow a causal interpretation and is not mathematically consistent. In this paper, we propose a simple measure of mediation in a survival setting. The measure is based on counterfactuals, and measures the natural direct and indirect effects. The method allows a causal interpretation of the mediated effect (in terms of additional cases per unit of time) and is mathematically consistent. The technique is illustrated by analyzing socioeconomic status, work environment, and long-term sickness absence. A detailed implementation guide is included in an online eAppendix (http://links.lww.com/EDE/A476).
@article{lange_direct_2011,
title = {Direct and indirect effects in a survival context},
volume = {22},
issn = {1531-5487},
doi = {10.1097/EDE.0b013e31821c680c},
abstract = {A cornerstone of epidemiologic research is to understand the causal pathways from an exposure to an outcome. Mediation analysis based on counterfactuals is an important tool when addressing such questions. However, none of the existing techniques for formal mediation analysis can be applied to survival data. This is a severe shortcoming, as many epidemiologic questions can be addressed only with censored survival data. A solution has been to use a number of Cox models (with and without the potential mediator), but this approach does not allow a causal interpretation and is not mathematically consistent. In this paper, we propose a simple measure of mediation in a survival setting. The measure is based on counterfactuals, and measures the natural direct and indirect effects. The method allows a causal interpretation of the mediated effect (in terms of additional cases per unit of time) and is mathematically consistent. The technique is illustrated by analyzing socioeconomic status, work environment, and long-term sickness absence. A detailed implementation guide is included in an online eAppendix (http://links.lww.com/EDE/A476).},
language = {eng},
number = {4},
journal = {Epidemiology (Cambridge, Mass.)},
author = {Lange, Theis and Hansen, Jørgen V.},
month = jul,
year = {2011},
pmid = {21552129},
keywords = {Adult, Female, Humans, Male, Causality, Models, Statistical, Confidence Intervals, Epidemiologic Methods, Proportional Hazards Models, Sick Leave, Socioeconomic Factors, Survival Analysis, Workplace},
pages = {575--581},
file = {Lange and Hansen - 2011 - Direct and indirect effects in a survival context.pdf:/Users/soumikp/Zotero/storage/NR6634Y3/Lange and Hansen - 2011 - Direct and indirect effects in a survival context.pdf:application/pdf},
}Development of a Transparent Interactive Decision Interrogator to Facilitate the Decision-Making Process in Health Care. Bujkiewicz, S., Jones, H. E., Lai, M. C., Cooper, N. J., Hawkins, N., Squires, H., Abrams, K. R., Spiegelhalter, D. J., & Sutton, A. J. Value in Health, 14(5):768–776, July, 2011.
Paper doi abstract bibtex
Paper doi abstract bibtex Background: Decisions about the use of new technologies in health care are often based on complex economic models. Decision makers frequently make informal judgments about evidence, uncertainty, and the assumptions that underpin these models. Objectives: Transparent interactive decision interrogator (TIDI) facilitates more formal critique of decision models by decision makers such as members of appraisal committees of the National Institute for Health and Clinical Excellence in the UK. By allowing them to run advanced statistical models under different scenarios in real time, TIDI can make the decision process more efficient and transparent, while avoiding limitations on pre-prepared analysis. Methods: TIDI, programmed in Visual Basic for applications within Excel, provides an interface for controlling all components of a decision model developed in the appropriate software (e.g., meta-analysis in WinBUGS and the decision model in R) by linking software packages using RExcel and R2WinBUGS. TIDI’s graphical controls allow the user to modify assumptions and to run the decision model, and results are returned to an Excel spreadsheet. A tool displaying tornado plots helps to evaluate the influence of individual parameters on the model outcomes, and an interactive meta-analysis module allows the user to select any combination of available studies, explore the impact of bias adjustment, and view results using forest plots. We demonstrate TIDI using an example of a decision model in antenatal care. Conclusion: Use of TIDI during the NICE appraisal of tumor necrosis factor-alpha inhibitors (in psoriatic arthritis) successfully demonstrated its ability to facilitate critiques of the decision models by decision makers.
@article{bujkiewicz_development_2011-1,
title = {Development of a {Transparent} {Interactive} {Decision} {Interrogator} to {Facilitate} the {Decision}-{Making} {Process} in {Health} {Care}},
volume = {14},
issn = {10983015},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1098301510000896},
doi = {10.1016/j.jval.2010.12.002},
abstract = {Background: Decisions about the use of new technologies in health care are often based on complex economic models. Decision makers frequently make informal judgments about evidence, uncertainty, and the assumptions that underpin these models. Objectives: Transparent interactive decision interrogator (TIDI) facilitates more formal critique of decision models by decision makers such as members of appraisal committees of the National Institute for Health and Clinical Excellence in the UK. By allowing them to run advanced statistical models under different scenarios in real time, TIDI can make the decision process more efficient and transparent, while avoiding limitations on pre-prepared analysis. Methods: TIDI, programmed in Visual Basic for applications within Excel, provides an interface for controlling all components of a decision model developed in the appropriate software (e.g., meta-analysis in WinBUGS and the decision model in R) by linking software packages using RExcel and R2WinBUGS. TIDI’s graphical controls allow the user to modify assumptions and to run the decision model, and results are returned to an Excel spreadsheet. A tool displaying tornado plots helps to evaluate the influence of individual parameters on the model outcomes, and an interactive meta-analysis module allows the user to select any combination of available studies, explore the impact of bias adjustment, and view results using forest plots. We demonstrate TIDI using an example of a decision model in antenatal care. Conclusion: Use of TIDI during the NICE appraisal of tumor necrosis factor-alpha inhibitors (in psoriatic arthritis) successfully demonstrated its ability to facilitate critiques of the decision models by decision makers.},
language = {en},
number = {5},
urldate = {2019-08-06},
journal = {Value in Health},
author = {Bujkiewicz, Sylwia and Jones, Hayley E. and Lai, Monica C.W. and Cooper, Nicola J. and Hawkins, Neil and Squires, Hazel and Abrams, Keith R. and Spiegelhalter, David J. and Sutton, Alex J.},
month = jul,
year = {2011},
keywords = {Arthritis, Bias, Biomedical, Computer Graphics, Cost-Benefit Analysis, Decision Support Techniques, Drug Costs, Economic, Evidence-Based Medicine, Fetus, Health Services Research, Humans, Immunosuppressive Agents, Models, Outcome and Process Assessment (Health Care), Prenatal Diagnosis, Psoriatic, Rh Isoimmunization, Rh-Hr Blood-Group System, Rho(D) Immune Globulin, Software, Statistical, Technology Assessment, Treatment Outcome, Tumor Necrosis Factor-alpha, Uncertainty, United Kingdom, User-Computer Interface},
pages = {768--776},
file = {Bujkiewicz et al. - 2011 - Development of a Transparent Interactive Decision .pdf:/Users/neil.hawkins/Zotero/storage/SWNTRTZX/Bujkiewicz et al. - 2011 - Development of a Transparent Interactive Decision .pdf:application/pdf},
}Child ADHD severity and positive and negative parenting as predictors of child social functioning: evaluation of three theoretical models. Kaiser, N. M, McBurnett, K., & Pfiffner, L. J Journal of Attention Disorders, 15(3):193–203, April, 2011.
Paper doi abstract bibtex
Paper doi abstract bibtex Prior research has established links between child social functioning and both parenting and child ADHD severity; however, research examining the way that these variables work together is lacking. The current article aims to test three possible models (main effects, mediation, and moderation) by which ADHD severity and positive and negative parenting on the part of both mothers and fathers may work together to predict child social functioning.
@article{kaiser_child_2011,
title = {Child {ADHD} severity and positive and negative parenting as predictors of child social functioning: evaluation of three theoretical models.},
volume = {15},
issn = {1557-1246},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20424006},
doi = {10.1177/1087054709356171},
abstract = {Prior research has established links between child social functioning and both parenting and child ADHD severity; however, research examining the way that these variables work together is lacking. The current article aims to test three possible models (main effects, mediation, and moderation) by which ADHD severity and positive and negative parenting on the part of both mothers and fathers may work together to predict child social functioning.},
number = {3},
urldate = {2012-08-13},
journal = {Journal of Attention Disorders},
author = {Kaiser, Nina M and McBurnett, Keith and Pfiffner, Linda J},
month = apr,
year = {2011},
pmid = {20424006},
keywords = {Aggression, Aggression: psychology, Analysis of Variance, Attention Deficit Disorder with Hyperactivity, Attention Deficit Disorder with Hyperactivity: psy, Child, Female, Humans, Male, Models, Parent-Child Relations, Parenting, Parenting: psychology, Preschool, Psychological, Psychometrics, Questionnaires, Severity of Illness Index, Social Behavior},
pages = {193--203},
}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}
}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".
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pages = {113-34},
volume = {8},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/20502987},
publisher = {Humana Press Inc.},
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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}
}Patient-specific models of deep brain stimulation: influence of field model complexity on neural activation predictions. Chaturvedi, A., Butson, C., Lempka, S., Cooper, S., & McIntyre, C. Brain Stimulation, 3(2):65–67, Elsevier Inc., April, 2010.
Paper doi bibtex
Paper doi bibtex @Article{SCI:Cha2010a,
author = "A. Chaturvedi and C.R. Butson and S.F. Lempka and
S.E. Cooper and C.C. McIntyre",
title = "Patient-specific models of deep brain stimulation:
influence of field model complexity on neural
activation predictions",
journal = "Brain Stimulation",
volume = "3",
number = "2",
pages = "65--67",
year = "2010",
publisher = "Elsevier Inc.",
month = "April",
issn = "1935-861X",
doi = "10.1016/j.brs.2010.01.003",
pmid = "20607090",
keywords = "Action Potentials, Action Potentials: physiology,
Computer Simulation, Deep Brain Stimulation, Deep
Brain Stimulation: instrumentation, Deep Brain
Stimulation: methods, Humans, Male, Middle Aged,
Models, Neurological, Parkinson Disease, Parkinson
Disease: therapy, Subthalamic Nucleus, Subthalamic
Nucleus: physiology",
url = "http://www.sci.utah.edu/publications/Cha2010a/Chaturvedi_BrainStim2010.pdf",
}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},
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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},
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edition = {2010/01/19},
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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}
}Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. Greenwood, J. R, Calkins, D., Sullivan, A. P, & Shelley, J. C Journal of computer-aided molecular design, 24(6-7):591–604, June, 2010.
Paper doi abstract bibtex
Paper doi abstract bibtex Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett-Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pK(T) and pK(a). Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pK(T) values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pK(a) effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.
@article{Greenwood2010,
title = {Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution.},
volume = {24},
issn = {1573-4951},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20354892},
doi = {10.1007/s10822-010-9349-1},
abstract = {Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett-Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pK(T) and pK(a). Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pK(T) values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pK(a) effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.},
number = {6-7},
journal = {Journal of computer-aided molecular design},
author = {Greenwood, Jeremy R and Calkins, David and Sullivan, Arron P and Shelley, John C},
month = jun,
year = {2010},
pmid = {20354892},
keywords = {\#nosource, Chemical, Heterocyclic Compounds, Heterocyclic Compounds: chemistry, Isomerism, Models, Pharmaceutical Preparations, Pharmaceutical Preparations: chemistry, Quantum Theory, Solutions, Solutions: chemistry, Water, Water: chemistry},
pages = {591--604},
}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},
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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}
}2009 (7)
Biomagnification of mercury in selected species from an Arctic marine food web in Svalbard. Jaeger, I., Hop, H., & Gabrielsen, G., W. The Science of the total environment, 407(16):4744-51, Elsevier B.V., 8, 2009.
Website abstract bibtex
Website abstract bibtex Concentrations and biomagnification of total mercury (TotHg) and methyl mercury (MeHg) were studied in selected species from the pelagic food web in Kongsfjorden, Svalbard. Twelve species of zooplankton, fish and seabirds, were sampled representing a gradient of trophic positions in the Svalbard marine food web. TotHg and MeHg were analysed in liver, muscle and/or whole specimens. The present study is the first to provide MeHg levels in seabirds from the Svalbard area. The relative MeHg levels decreased with increasing levels of TotHg in seabird tissues. Stable isotopes of nitrogen (delta(15)N) were used to determine the trophic levels and the rate of biomagnification of mercury in the food web. A linear relationship between mercury levels and trophic position was found for all seabird species combined and their trophic level, but there was no relationship within species. Biomagnification factors were all >1 for both TotHg and MeHg, indicating biomagnification from prey to predator. TotHg levels in the different seabirds were similar to levels detected in the Kongsfjorden area in the 1990s.
@article{
title = {Biomagnification of mercury in selected species from an Arctic marine food web in Svalbard.},
type = {article},
year = {2009},
identifiers = {[object Object]},
keywords = {Animals,Arctic Regions,Birds,Birds: metabolism,Environmental Monitoring,Fishes,Fishes: metabolism,Food Chain,Mercury,Mercury: analysis,Mercury: pharmacokinetics,Methylmercury Compounds,Methylmercury Compounds: analysis,Methylmercury Compounds: pharmacokinetics,Models, Biological,Norway,Water Pollutants, Chemical,Water Pollutants, Chemical: analysis,Water Pollutants, Chemical: pharmacokinetics,Zooplankton,Zooplankton: metabolism},
pages = {4744-51},
volume = {407},
websites = {http://www.ncbi.nlm.nih.gov/pubmed/19454364},
month = {8},
publisher = {Elsevier B.V.},
day = {1},
id = {df3c07b5-1275-3e3a-9f84-d243c4d8997e},
created = {2012-09-27T18:36:49.000Z},
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last_modified = {2017-03-14T12:29:49.371Z},
read = {true},
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confirmed = {true},
hidden = {false},
citation_key = {Jaeger2009},
folder_uuids = {4246fe96-2389-417f-9056-527e16d7e71c},
private_publication = {false},
abstract = {Concentrations and biomagnification of total mercury (TotHg) and methyl mercury (MeHg) were studied in selected species from the pelagic food web in Kongsfjorden, Svalbard. Twelve species of zooplankton, fish and seabirds, were sampled representing a gradient of trophic positions in the Svalbard marine food web. TotHg and MeHg were analysed in liver, muscle and/or whole specimens. The present study is the first to provide MeHg levels in seabirds from the Svalbard area. The relative MeHg levels decreased with increasing levels of TotHg in seabird tissues. Stable isotopes of nitrogen (delta(15)N) were used to determine the trophic levels and the rate of biomagnification of mercury in the food web. A linear relationship between mercury levels and trophic position was found for all seabird species combined and their trophic level, but there was no relationship within species. Biomagnification factors were all >1 for both TotHg and MeHg, indicating biomagnification from prey to predator. TotHg levels in the different seabirds were similar to levels detected in the Kongsfjorden area in the 1990s.},
bibtype = {article},
author = {Jaeger, Iris and Hop, Haakon and Gabrielsen, Geir W},
journal = {The Science of the total environment},
number = {16}
}Receptor-Fc fusion therapeutics, traps, and MIMETIBODY technology. Huang, C. Current opinion in biotechnology, 20(6):692–9, December, 2009.
Paper doi abstract bibtex
Paper doi abstract bibtex Fc fusion proteins are molecules in which the immunoglobulin Fc is fused genetically to a protein of interest, such as an extracellular domain of a receptor, ligand, enzyme, or peptide. Fc fusion proteins have some antibody-like properties such as long serum half-life and easy expression and purification, making them an attractive platform for therapeutic drugs. Five Fc fusion based drugs are on the market presently, and many more are in different stages of clinical trials, demonstrating that Fc fusion proteins have become credible alternatives to monoclonal antibodies as therapeutics. This review summarizes the Fc fusion proteins that have been approved for use in the clinic and those that are currently in clinical trials, as well as the different approaches to design Fc fusion proteins.
@article{huang_receptor-fc_2009,
title = {Receptor-{Fc} fusion therapeutics, traps, and {MIMETIBODY} technology.},
volume = {20},
issn = {1879-0429},
url = {http://dx.doi.org/10.1016/j.copbio.2009.10.010},
doi = {10.1016/j.copbio.2009.10.010},
abstract = {Fc fusion proteins are molecules in which the immunoglobulin Fc is fused genetically to a protein of interest, such as an extracellular domain of a receptor, ligand, enzyme, or peptide. Fc fusion proteins have some antibody-like properties such as long serum half-life and easy expression and purification, making them an attractive platform for therapeutic drugs. Five Fc fusion based drugs are on the market presently, and many more are in different stages of clinical trials, demonstrating that Fc fusion proteins have become credible alternatives to monoclonal antibodies as therapeutics. This review summarizes the Fc fusion proteins that have been approved for use in the clinic and those that are currently in clinical trials, as well as the different approaches to design Fc fusion proteins.},
number = {6},
journal = {Current opinion in biotechnology},
author = {Huang, Chichi},
month = dec,
year = {2009},
keywords = {Animals, Antibodies, Biological, Biopharmaceutics, Biopharmaceutics: methods, Chemistry, Combinatorial Chemistry Techniques, Fc, Fc: chemistry, Humans, Immunoglobulin Fc Fragments, Immunoglobulin Fc Fragments: chemistry, Ligands, Models, Monoclonal, Monoclonal: chemistry, Peptides, Peptides: chemistry, Pharmaceutical, Pharmaceutical: methods, Protein Binding, Protein Engineering, Protein Engineering: methods, Receptors, Recombinant Fusion Proteins, Recombinant Fusion Proteins: chemistry},
pages = {692--9},
}Double-quantum homonuclear NMR correlation spectroscopy of quadrupolar nuclei subjected to magic-angle spinning and high magnetic field. Wang, Q, Hu, B, Lafon, O, Trébosc, J, Deng, F, & Amoureux, J P Journal of magnetic resonance (San Diego, Calif. : 1997), 200(2):251–260, October, 2009.
Paper doi abstract bibtex
Paper doi abstract bibtex We present a new application of the R2(2)(1) symmetry-based dipolar recoupling scheme, for exciting directly double-quantum (2Q) coherences between the central transition of homonuclear half-integer quadrupolar nuclei. With respect to previously published 2Q-recoupling methods (M. Eden, D. Zhou, J. Yu, Chem. Phys. Lett. 431 (2006) 397), the R2(2)(1) sequence is used without pi/2 bracketing pulses and with an original super-cycling. This leads to an improved efficiency (a factor of two for spin-5/2) and to a much higher robustness to radio-frequency field inhomogeneity and resonance offset. The 2Q-coherence excitation performances are demonstrated experimentally by (27)Al NMR experiments on the aluminophosphates berlinite, VPI5, AlPO(4)-14, and AlPO(4)-CJ3. The two-dimensional 2Q-1Q correlation experiments incorporating these recoupling sequences allow the observation of 2Q cross-peaks between central transitions, even at high magnetic field where the difference in offset between octahedral and tetrahedral (27)Al sites exceeds 10 kHz.
@article{Wang2009,
title = {Double-quantum homonuclear {NMR} correlation spectroscopy of quadrupolar nuclei subjected to magic-angle spinning and high magnetic field.},
volume = {200},
issn = {1096-0856},
url = {http://www.sciencedirect.com/science/article/pii/S1090780709001980},
doi = {10.1016/j.jmr.2009.07.009},
abstract = {We present a new application of the R2(2)(1) symmetry-based dipolar recoupling scheme, for exciting directly double-quantum (2Q) coherences between the central transition of homonuclear half-integer quadrupolar nuclei. With respect to previously published 2Q-recoupling methods (M. Eden, D. Zhou, J. Yu, Chem. Phys. Lett. 431 (2006) 397), the R2(2)(1) sequence is used without pi/2 bracketing pulses and with an original super-cycling. This leads to an improved efficiency (a factor of two for spin-5/2) and to a much higher robustness to radio-frequency field inhomogeneity and resonance offset. The 2Q-coherence excitation performances are demonstrated experimentally by (27)Al NMR experiments on the aluminophosphates berlinite, VPI5, AlPO(4)-14, and AlPO(4)-CJ3. The two-dimensional 2Q-1Q correlation experiments incorporating these recoupling sequences allow the observation of 2Q cross-peaks between central transitions, even at high magnetic field where the difference in offset between octahedral and tetrahedral (27)Al sites exceeds 10 kHz.},
number = {2},
journal = {Journal of magnetic resonance (San Diego, Calif. : 1997)},
author = {Wang, Q and Hu, B and Lafon, O and Trébosc, J and Deng, F and Amoureux, J P},
month = oct,
year = {2009},
pmid = {19646906},
keywords = {Algorithms, Aluminum Compounds, Aluminum Compounds: analysis, Biomolecular, Biomolecular: methods, Chemical, Computer Simulation, Electromagnetic Fields, Models, Nuclear Magnetic Resonance, Phosphates, Phosphates: analysis, Sensitivity and Specificity, Spin Labels},
pages = {251--260},
}The European Pollen Database: past efforts and current activities. Fyfe, R. M., de Beaulieu, J. L., Binney, H., Bradshaw, R. H. W., Brewer, S., Le Flao, A., Finsinger, W., Gaillard, M. J., Giesecke, T., Gil-Romera, G., Grimm, E. C., Huntley, B., Kunes, P., Kuhl, N., Leydet, M., Lotter, A. F., Tarasov, P. E., & Tonkov, S. Vegetation History and Archaeobotany, 18(5):417–424, September, 2009.
Paper abstract bibtex
Paper abstract bibtex Pollen stratigraphies are the most spatially extensive data available for the reconstruction of past land-cover change. Detailed knowledge of past land-cover is becoming increasingly important to evaluate the present trends in, and drivers of, vegetation composition. The European Pollen Database (EPD) was established in the late 1980s and developed in the early 1990s to provide a structure for archiving, exchanging, and analysing Quaternary pollen data from Europe. It provides a forum for scientists to meet and engage in collaborative investigations or data analysis. In May 2007 several EPD support groups were developed to assist in the task of maintaining and updating the database. The mapping and data accuracy work group (MADCAP) aims to produce an atlas of past plant distributions as detected by pollen analyses in Europe, in order to meet the growing need for this data from palaeoecologists and the wider scientific community. Due to data handling problems in the past, a significant number of EPD datasets have errors. The initial task of the work group, therefore, was a systematic review of pollen sequences, in order to identify and correct errors. The EPD currently (January 2009) archives 1,032 pollen sequences, of which 668 have age-depth models that allow chronological comparison. Many errors have been identified and corrected, or flagged for users, most notably errors in the pollen count data. The application of spatial analyses to pollen data is related to the number of data points that are available for analysis. We therefore take this opportunity to encourage the submission of pollen analytical results to the EPD or other relevant pollen databases. Only in this way will the scientific community be able to gain a better understanding of past vegetation dynamics.
@article{fyfe_european_2009,
title = {The {European} {Pollen} {Database}: past efforts and current activities},
volume = {18},
issn = {0939-6314},
url = {://000268729300005},
abstract = {Pollen stratigraphies are the most spatially extensive data available for the reconstruction of past land-cover change. Detailed knowledge of past land-cover is becoming increasingly important to evaluate the present trends in, and drivers of, vegetation composition. The European Pollen Database (EPD) was established in the late 1980s and developed in the early 1990s to provide a structure for archiving, exchanging, and analysing Quaternary pollen data from Europe. It provides a forum for scientists to meet and engage in collaborative investigations or data analysis. In May 2007 several EPD support groups were developed to assist in the task of maintaining and updating the database. The mapping and data accuracy work group (MADCAP) aims to produce an atlas of past plant distributions as detected by pollen analyses in Europe, in order to meet the growing need for this data from palaeoecologists and the wider scientific community. Due to data handling problems in the past, a significant number of EPD datasets have errors. The initial task of the work group, therefore, was a systematic review of pollen sequences, in order to identify and correct errors. The EPD currently (January 2009) archives 1,032 pollen sequences, of which 668 have age-depth models that allow chronological comparison. Many errors have been identified and corrected, or flagged for users, most notably errors in the pollen count data. The application of spatial analyses to pollen data is related to the number of data points that are available for analysis. We therefore take this opportunity to encourage the submission of pollen analytical results to the EPD or other relevant pollen databases. Only in this way will the scientific community be able to gain a better understanding of past vegetation dynamics.},
number = {5},
journal = {Vegetation History and Archaeobotany},
author = {Fyfe, R. M. and de Beaulieu, J. L. and Binney, H. and Bradshaw, R. H. W. and Brewer, S. and Le Flao, A. and Finsinger, W. and Gaillard, M. J. and Giesecke, T. and Gil-Romera, G. and Grimm, E. C. and Huntley, B. and Kunes, P. and Kuhl, N. and Leydet, M. and Lotter, A. F. and Tarasov, P. E. and Tonkov, S.},
month = sep,
year = {2009},
keywords = {ABIES, CASTANEA-SATIVA MILL., Data accuracy, Data archive, EPD, European Pollen Database, FAGUS-SYLVATICA, FENNOSCANDIA, FUTURE, LAST GLACIAL PERIOD, MODELS, REFUGIA, SPREAD, VEGETATION},
pages = {417--424},
}In obese rat muscle transport of palmitate is increased and is channeled to triacylglycerol storage despite an increase in mitochondrial palmitate oxidation. Holloway, G P, Benton, C R, Mullen, K L, Yoshida, Y, Snook, L A, Han, X X, Glatz, J F, Luiken, J J, Lally, J, Dyck, D J, & Bonen, A Am J Physiol Endocrinol Metab, 296(4):E738–47, 2009. ISBN: 0193-1849 (Print) 0193-1849 (Linking)
bibtex
bibtex
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}
}Absolute two-photon absorption spectra and two-photon brightness of orange and red fluorescent proteins. Drobizhev, M, Tillo, S, Makarov, N S, Hughes, T E, & Rebane, a The journal of physical chemistry. B, 113(4):855–9, January, 2009.
Paper doi abstract bibtex
Paper doi abstract bibtex Fluorescent proteins with long emission wavelengths are particularly attractive for deep tissue two-photon microscopy. Surprisingly, little is known about their two-photon absorption (2PA) properties. We present absolute 2PA spectra of a number of orange and red fluorescent proteins, including DsRed2, mRFP, TagRFP, and several mFruit proteins, in a wide range of excitation wavelengths (640-1400 nm). To evaluate 2PA cross section (sigma(2)), we use a new method relying only on the optical properties of the intact mature chromophore. In the tuning range of a mode-locked Ti:sapphire laser, 700-1000 nm, TagRFP possesses the highest two-photon cross section, sigma(2) = 315 GM, and brightness, sigma(2)phi = 130 GM, where phi is the fluorescence quantum yield. At longer wavelengths, 1000-1100 nm, tdTomato has the largest values, sigma(2) = 216 GM and sigma(2)phi = 120 GM, per protein chain. Compared to the benchmark EGFP, these proteins present 3-4 times improvement in two-photon brightness.
@article{Drobizhev2009,
title = {Absolute two-photon absorption spectra and two-photon brightness of orange and red fluorescent proteins.},
volume = {113},
issn = {1520-6106},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2656371&tool=pmcentrez&rendertype=abstract},
doi = {10.1021/jp8087379},
abstract = {Fluorescent proteins with long emission wavelengths are particularly attractive for deep tissue two-photon microscopy. Surprisingly, little is known about their two-photon absorption (2PA) properties. We present absolute 2PA spectra of a number of orange and red fluorescent proteins, including DsRed2, mRFP, TagRFP, and several mFruit proteins, in a wide range of excitation wavelengths (640-1400 nm). To evaluate 2PA cross section (sigma(2)), we use a new method relying only on the optical properties of the intact mature chromophore. In the tuning range of a mode-locked Ti:sapphire laser, 700-1000 nm, TagRFP possesses the highest two-photon cross section, sigma(2) = 315 GM, and brightness, sigma(2)phi = 130 GM, where phi is the fluorescence quantum yield. At longer wavelengths, 1000-1100 nm, tdTomato has the largest values, sigma(2) = 216 GM and sigma(2)phi = 120 GM, per protein chain. Compared to the benchmark EGFP, these proteins present 3-4 times improvement in two-photon brightness.},
number = {4},
urldate = {2013-09-06},
journal = {The journal of physical chemistry. B},
author = {Drobizhev, M and Tillo, S and Makarov, N S and Hughes, T E and Rebane, a},
month = jan,
year = {2009},
pmid = {19127988},
keywords = {\#nosource, Color, Luminescent Proteins, Luminescent Proteins: chemistry, Models, Molecular, Molecular Conformation, Photons, Spectrometry, Fluorescence, Spectrophotometry, optogenetics},
pages = {855--9},
}2008 (7)
The discovery of structural form. Kemp, C. & Tenenbaum, J. B Proceedings of the National Academy of Sciences of the United States of America, 105(31):10687–92, August, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex Algorithms for finding structure in data have become increasingly important both as tools for scientific data analysis and as models of human learning, yet they suffer from a critical limitation. Scientists discover qualitatively new forms of structure in observed data: For instance, Linnaeus recognized the hierarchical organization of biological species, and Mendeleev recognized the periodic structure of the chemical elements. Analogous insights play a pivotal role in cognitive development: Children discover that object category labels can be organized into hierarchies, friendship networks are organized into cliques, and comparative relations (e.g., "bigger than" or "better than") respect a transitive order. Standard algorithms, however, can only learn structures of a single form that must be specified in advance: For instance, algorithms for hierarchical clustering create tree structures, whereas algorithms for dimensionality-reduction create low-dimensional spaces. Here, we present a computational model that learns structures of many different forms and that discovers which form is best for a given dataset. The model makes probabilistic inferences over a space of graph grammars representing trees, linear orders, multidimensional spaces, rings, dominance hierarchies, cliques, and other forms and successfully discovers the underlying structure of a variety of physical, biological, and social domains. Our approach brings structure learning methods closer to human abilities and may lead to a deeper computational understanding of cognitive development.
@article{Kemp2008,
title = {The discovery of structural form.},
volume = {105},
issn = {1091-6490},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2492756&tool=pmcentrez&rendertype=abstract},
doi = {10.1073/pnas.0802631105},
abstract = {Algorithms for finding structure in data have become increasingly important both as tools for scientific data analysis and as models of human learning, yet they suffer from a critical limitation. Scientists discover qualitatively new forms of structure in observed data: For instance, Linnaeus recognized the hierarchical organization of biological species, and Mendeleev recognized the periodic structure of the chemical elements. Analogous insights play a pivotal role in cognitive development: Children discover that object category labels can be organized into hierarchies, friendship networks are organized into cliques, and comparative relations (e.g., "bigger than" or "better than") respect a transitive order. Standard algorithms, however, can only learn structures of a single form that must be specified in advance: For instance, algorithms for hierarchical clustering create tree structures, whereas algorithms for dimensionality-reduction create low-dimensional spaces. Here, we present a computational model that learns structures of many different forms and that discovers which form is best for a given dataset. The model makes probabilistic inferences over a space of graph grammars representing trees, linear orders, multidimensional spaces, rings, dominance hierarchies, cliques, and other forms and successfully discovers the underlying structure of a variety of physical, biological, and social domains. Our approach brings structure learning methods closer to human abilities and may lead to a deeper computational understanding of cognitive development.},
number = {31},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
author = {Kemp, Charles and Tenenbaum, Joshua B},
month = aug,
year = {2008},
pmid = {18669663},
keywords = {Algorithms, Data Interpretation, Humans, Learning, Learning: physiology, Models, Research Design, Statistical, Theoretical},
pages = {10687--92},
}Multiscale modeling of nucleic acids: insights into DNA flexibility. Bomble, Y. J & Case, D. a Biopolymers, 89(9):722–31, September, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales.
@article{Bomble2008,
title = {Multiscale modeling of nucleic acids: insights into {DNA} flexibility.},
volume = {89},
issn = {0006-3525},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2561918&tool=pmcentrez&rendertype=abstract},
doi = {10.1002/bip.21000},
abstract = {The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20\% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales.},
number = {9},
journal = {Biopolymers},
author = {Bomble, Yannick J and Case, David a},
month = sep,
year = {2008},
pmid = {18412139},
keywords = {\#nosource, Circular, Circular: chemistry, Computer Simulation, DNA, Models, Molecular, Nucleic Acid Conformation, Trinucleotide Repeats},
pages = {722--31},
}High heritability for a composite index of children's activity level measures. Wood, A. C, Rijsdijk, F., Saudino, K. J, Asherson, P., & Kuntsi, J. Behavior genetics, 38(3):266–76, May, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex Despite the high heritability of children's activity level, which forms part of the core symptom domain of hyperactivity-impulsivity within attention deficit hyperactivity disorder (ADHD), there has only been a limited success with identifying candidate genes involved in its etiology. This may reflect a lack of understanding about the different measures used to define activity level across studies. We aimed to study the genetic and environmental etiology across three measures of activity level: parent and teacher ratings of hyperactivity-impulsivity and actigraph measurements, within a population-based sample of 463 7-9 year old twin pairs. We further examined ways in which the three measures could be combined for future molecular studies. Phenotypic correlations across measures were modest, but a common underlying phenotypic factor was highly heritable (92%); as was a simple aggregation of all three measurements (77%). This suggests that distilling what is common to all three measures may be a good method for generating a quantitative trait suitable for molecular studies of activity level in children. The high heritabilities found are encouraging in this respect.
@article{wood_high_2008,
title = {High heritability for a composite index of children's activity level measures.},
volume = {38},
issn = {0001-8244},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2493057&tool=pmcentrez&rendertype=abstract},
doi = {10.1007/s10519-008-9196-1},
abstract = {Despite the high heritability of children's activity level, which forms part of the core symptom domain of hyperactivity-impulsivity within attention deficit hyperactivity disorder (ADHD), there has only been a limited success with identifying candidate genes involved in its etiology. This may reflect a lack of understanding about the different measures used to define activity level across studies. We aimed to study the genetic and environmental etiology across three measures of activity level: parent and teacher ratings of hyperactivity-impulsivity and actigraph measurements, within a population-based sample of 463 7-9 year old twin pairs. We further examined ways in which the three measures could be combined for future molecular studies. Phenotypic correlations across measures were modest, but a common underlying phenotypic factor was highly heritable (92\%); as was a simple aggregation of all three measurements (77\%). This suggests that distilling what is common to all three measures may be a good method for generating a quantitative trait suitable for molecular studies of activity level in children. The high heritabilities found are encouraging in this respect.},
number = {3},
urldate = {2015-05-12},
journal = {Behavior genetics},
author = {Wood, Alexis C and Rijsdijk, Frühling and Saudino, Kimberly J and Asherson, Philip and Kuntsi, Jonna},
month = may,
year = {2008},
pmid = {18297388},
keywords = {Attention Deficit and Disruptive Behavior Disorder, Child, Family Health, Female, Genetic Predisposition to Disease, Humans, Impulsive Behavior, Impulsive Behavior: genetics, Male, Models, Genetic, Models, Statistical, Motor Activity, Multivariate Analysis, Parents, Phenotype},
pages = {266--76},
}Stability and kinetics of G-quadruplex structures. Lane, A. N, Chaires, J B., Gray, R. D, & Trent, J. O Nucleic acids research, 36(17):5482–515, October, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.
@article{Lane2008,
title = {Stability and kinetics of {G}-quadruplex structures.},
volume = {36},
issn = {1362-4962},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2553573&tool=pmcentrez&rendertype=abstract},
doi = {10.1093/nar/gkn517},
abstract = {In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.},
number = {17},
journal = {Nucleic acids research},
author = {Lane, Andrew N and Chaires, J Brad and Gray, Robert D and Trent, John O},
month = oct,
year = {2008},
pmid = {18718931},
keywords = {\#nosource, G-Quadruplexes, Ions, Ions: chemistry, Kinetics, Models, Molecular, Solvents, Solvents: chemistry, Thermodynamics},
pages = {5482--515},
}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},
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last_modified = {2015-01-15T02:26:53.000Z},
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citation_key = {Morris2008a},
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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}
}Elastic wave propagation in a microstructured acoustic fiber. Nikitov, S. a, Popov, R. S, Lisenkov, I. V, & Kim, C. K. IEEE transactions on ultrasonics, ferroelectrics, and frequency control, 55(8):1831–9, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex Elastic wave propagation along the structure of hollow cylinders in a linear isotropic medium is investigated. The multipole method for modeling elastic waves propagation in such structures is formulated and implemented. Using the multipole method, dispersion dependencies of the structures (microstructured fibers) containing 3, 6, and 7 hollow cylinders are calculated. Comparison with wave dispersion properties along one cylinder is made. Also, an approximate physical model based on an equivalent coaxial waveguide and multipole method is proposed. Exploiting this model, wave dispersion of the wave propagating along a structure with 18 hollow cylinders is calculated. Validation of the model is also proposed.
@article{nikitov_elastic_2008,
title = {Elastic wave propagation in a microstructured acoustic fiber.},
volume = {55},
issn = {1525-8955},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18986925},
doi = {10.1109/TUFFC.2008.866},
abstract = {Elastic wave propagation along the structure of hollow cylinders in a linear isotropic medium is investigated. The multipole method for modeling elastic waves propagation in such structures is formulated and implemented. Using the multipole method, dispersion dependencies of the structures (microstructured fibers) containing 3, 6, and 7 hollow cylinders are calculated. Comparison with wave dispersion properties along one cylinder is made. Also, an approximate physical model based on an equivalent coaxial waveguide and multipole method is proposed. Exploiting this model, wave dispersion of the wave propagating along a structure with 18 hollow cylinders is calculated. Validation of the model is also proposed.},
number = {8},
journal = {IEEE transactions on ultrasonics, ferroelectrics, and frequency control},
author = {Nikitov, Sergey a and Popov, Roman S and Lisenkov, Ivan V and Kim, Chul Koo},
year = {2008},
pmid = {18986925},
keywords = {Acoustics, Acoustics: instrumentation, Computer Simulation, Equipment Design, Equipment Failure Analysis, Manufactured Materials, Models, Theoretical, Scattering, Radiation},
pages = {1831--9},
}Bis(BF2)-2,2'-bidipyrrins (BisBODIPYs): highly fluorescent BODIPY dimers with large stokes shifts. Bröring, M., Krüger, R., Link, S., Kleeberg, C., Köhler, S., Xie, X., Ventura, B., & Flamigni, L. Chemistry (Weinheim an der Bergstrasse, Germany), 14(10):2976–83, January, 2008.
Paper doi abstract bibtex
Paper doi abstract bibtex Four new dimeric bis(BF(2))-2,2'-bidipyrrins (bisBODIPYs), and their corresponding BODIPY monomers, have been prepared and studied with respect to their structural and photophysical properties. The solid-state molecular structure of the dimers and the relative orientation of the subunits have been revealed by an X-ray diffraction study, which showed that the molecules contain two directly linked BODIPY chromophores in a conformationally fixed, almost orthogonal arrangement. Two of the fluorine atoms are in close contact with each other and the (19)F NMR spectra show a characteristic through-space coupling in solution. The new chromophores all exhibit a clear exciton splitting in the absorption spectra with maxima at about 490 and 560 nm, and are highly luminescent with an intense emission band at around 640 nm. The Stokes shift, which is the difference between the maximum of the lowest-energy absorption band and the maximum of the emission band, has a typical value of 5 to 15 nm for simple BODIPYs, whereas this value increases to 80 nm or more for the dimers, along with a slight decrease in fluorescence quantum yields and lifetimes. These properties indicate potential uses of these new fluorophoric materials as functional dyes in biomedical and materials applications and also in model compounds for BODIPY aggregates.
@article{broring_bisbf2-22-bidipyrrins_2008,
title = {Bis({BF2})-2,2'-bidipyrrins ({BisBODIPYs}): highly fluorescent {BODIPY} dimers with large stokes shifts.},
volume = {14},
issn = {0947-6539},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18306269},
doi = {10.1002/chem.200701912},
abstract = {Four new dimeric bis(BF(2))-2,2'-bidipyrrins (bisBODIPYs), and their corresponding BODIPY monomers, have been prepared and studied with respect to their structural and photophysical properties. The solid-state molecular structure of the dimers and the relative orientation of the subunits have been revealed by an X-ray diffraction study, which showed that the molecules contain two directly linked BODIPY chromophores in a conformationally fixed, almost orthogonal arrangement. Two of the fluorine atoms are in close contact with each other and the (19)F NMR spectra show a characteristic through-space coupling in solution. The new chromophores all exhibit a clear exciton splitting in the absorption spectra with maxima at about 490 and 560 nm, and are highly luminescent with an intense emission band at around 640 nm. The Stokes shift, which is the difference between the maximum of the lowest-energy absorption band and the maximum of the emission band, has a typical value of 5 to 15 nm for simple BODIPYs, whereas this value increases to 80 nm or more for the dimers, along with a slight decrease in fluorescence quantum yields and lifetimes. These properties indicate potential uses of these new fluorophoric materials as functional dyes in biomedical and materials applications and also in model compounds for BODIPY aggregates.},
number = {10},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
author = {Bröring, Martin and Krüger, Robin and Link, Stephan and Kleeberg, Christian and Köhler, Silke and Xie, Xiulian and Ventura, Barbara and Flamigni, Lucia},
month = jan,
year = {2008},
pmid = {18306269},
keywords = {\#nosource, Boron Compounds, Boron Compounds: chemical synthesis, Boron Compounds: chemistry, Crystallography, Dimerization, Fluorescence, Fluorescent Dyes, Fluorescent Dyes: chemical synthesis, Fluorescent Dyes: chemistry, Magnetic Resonance Spectroscopy, Magnetic Resonance Spectroscopy: methods, Magnetic Resonance Spectroscopy: standards, Models, Molecular, Molecular Structure, Pyrroles, Pyrroles: chemical synthesis, Pyrroles: chemistry, Reference Standards, Stereoisomerism, X-Ray},
pages = {2976--83},
}2007 (5)
Intraguild predation promotes complex alternative states along a productivity gradient. Takimoto, G., Miki, T., & Kagami, M. Theoretical population biology, 72(2):264–273, September, 2007. Place: United States Publisher: Academic Press
Paper abstract bibtex
Paper abstract bibtex Intraguild predation is the simplest, ubiquitous form of trophic omnivory, known to greatly influence the structure and functioning of natural and managed food webs. Although alternative states are fundamental to intraguild predation dynamics, only necessary conditions for alternative states have been previously reported. Using simple models, we found complex but systematic patterns in which different alternative states occur along a productivity gradient, and clarified the sufficient conditions to separate these patterns. We found that two quantities known to control the necessary conditions also determine the sufficient conditions: (1) relative energy transfer efficiency through alternative trophic pathways to an intraguild predator, and (2) relative resource exploitation ability between intraguild prey and predator. These governing quantities suggest how body size and stoichiometric relations between intraguild prey and predators can influence the possibility of alternative states. Our results indicate that food webs involving intraguild predation have a high potential of complex alternative states, and their management can be highly precarious.
@article{takimoto_intraguild_2007,
title = {Intraguild predation promotes complex alternative states along a productivity gradient.},
volume = {72},
issn = {0040-5809},
url = {http://search.ebscohost.com/login.aspx?direct=true&db=cmedm&AN=17573086&site=ehost-live},
abstract = {Intraguild predation is the simplest, ubiquitous form of trophic omnivory, known to greatly influence the structure and functioning of natural and managed food webs. Although alternative states are fundamental to intraguild predation dynamics, only necessary conditions for alternative states have been previously reported. Using simple models, we found complex but systematic patterns in which different alternative states occur along a productivity gradient, and clarified the sufficient conditions to separate these patterns. We found that two quantities known to control the necessary conditions also determine the sufficient conditions: (1) relative energy transfer efficiency through alternative trophic pathways to an intraguild predator, and (2) relative resource exploitation ability between intraguild prey and predator. These governing quantities suggest how body size and stoichiometric relations between intraguild prey and predators can influence the possibility of alternative states. Our results indicate that food webs involving intraguild predation have a high potential of complex alternative states, and their management can be highly precarious.},
number = {2},
journal = {Theoretical population biology},
author = {Takimoto, Gaku and Miki, Takeshi and Kagami, Maiko},
month = sep,
year = {2007},
note = {Place: United States
Publisher: Academic Press},
keywords = {Animals, Body Size, Ecosystem*, Food Chain*, Models, Statistical, Predatory Behavior*},
pages = {264--273},
}Weight estimation in resuscitation: is the current formula still valid?. Luscombe, M. & Owens, B. Archives of Disease in Childhood, 92(5):412–415, May, 2007.
Paper doi abstract bibtex
Paper doi abstract bibtex OBJECTIVES: To gather data on the ages and weights of paediatric patients between 1 and 10 years of age, and to compare these data with the current weight estimation formula weight(kg) = 2(age+4). If a significant difference was found, the data would be used to derive a more accurate formula. DESIGN: Retrospective study using data collected from paediatric attendances at an emergency department (ED). SETTING: A large ED in a major UK city, treating both children and adults. Patients: 17 244 children aged 1-10 years, attending the ED between June and December 2005. MAIN OUTCOME MEASURES: Weight difference between the measured weight and the expected weight, the latter given by weight = 2(age+4). RESULTS: The weights of seriously ill children were recorded in only 41.5% of cases, necessitating a weight estimate in the remainder. The formula weight = 2(age+4) underestimated children's weights by a mean of 18.8% (95% confidence interval (95% CI) 18.42% to 19.18%). Using linear regression and analysis of each individual age group, ten new formulas were tested. Of these formulas, weight(kg) = 3(age)+7 proved the most accurate with a mean underestimate of just 2.48% (95% CI 2.17% to 2.79%). CONCLUSIONS: Weight estimation remains of paramount importance in paediatric resuscitation. This study shows that the current estimation formula provides a significant underestimate of children's weights. When used to calculate drug and fluid dosages, this may lead to the under-resuscitation of a critically ill child. The formula weight(kg) = 3(age)+7 provided a safe and more accurate estimate of the weight of today's child.
@article{luscombe_weight_2007,
title = {Weight estimation in resuscitation: is the current formula still valid?},
volume = {92},
issn = {1468-2044},
shorttitle = {Weight estimation in resuscitation},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17213259},
doi = {10.1136/adc.2006.107284},
abstract = {OBJECTIVES: To gather data on the ages and weights of paediatric patients between 1 and 10 years of age, and to compare these data with the current weight estimation formula weight(kg) = 2(age+4). If a significant difference was found, the data would be used to derive a more accurate formula. DESIGN: Retrospective study using data collected from paediatric attendances at an emergency department (ED). SETTING: A large ED in a major UK city, treating both children and adults. Patients: 17 244 children aged 1-10 years, attending the ED between June and December 2005. MAIN OUTCOME MEASURES: Weight difference between the measured weight and the expected weight, the latter given by weight = 2(age+4). RESULTS: The weights of seriously ill children were recorded in only 41.5\% of cases, necessitating a weight estimate in the remainder. The formula weight = 2(age+4) underestimated children's weights by a mean of 18.8\% (95\% confidence interval (95\% CI) 18.42\% to 19.18\%). Using linear regression and analysis of each individual age group, ten new formulas were tested. Of these formulas, weight(kg) = 3(age)+7 proved the most accurate with a mean underestimate of just 2.48\% (95\% CI 2.17\% to 2.79\%). CONCLUSIONS: Weight estimation remains of paramount importance in paediatric resuscitation. This study shows that the current estimation formula provides a significant underestimate of children's weights. When used to calculate drug and fluid dosages, this may lead to the under-resuscitation of a critically ill child. The formula weight(kg) = 3(age)+7 provided a safe and more accurate estimate of the weight of today's child.},
number = {5},
urldate = {2010-03-18},
journal = {Archives of Disease in Childhood},
author = {Luscombe, Mark and Owens, Ben},
month = may,
year = {2007},
pmid = {17213259},
keywords = {Aging, Anthropometry, Body Weight, Child, Child, Preschool, Emergency Service, Hospital, Female, Humans, Infant, Male, Models, Biological, Reference Values, Resuscitation},
pages = {412--415},
}Looking for answers: eye movements in non-visual cognitive tasks. Ehrlichman, H., Micic, D., Sousa, A., & Zhu, J. Brain Cogn, 64(1):7–20, 2007.
Paper doi abstract bibtex
Paper doi abstract bibtex It is not known why people move their eyes when engaged in non-visual cognition. The current study tested the hypothesis that differences in saccadic eye movement rate (EMR) during non-visual cognitive tasks reflect different requirements for searching long-term memory. Participants performed non-visual tasks requiring relatively low or high long-term memory retrieval while eye movements were recorded. In three experiments, EMR was substantially lower for low-retrieval than for high-retrieval tasks, including in an eyes closed condition in Experiment 3. Neither visual imagery nor between-task difficulty was related to EMR, although there was some evidence for a minor effect of within-task difficulty. Comparison of task-related EMRs to EMR during a no-task waiting period suggests that eye movements may be suppressed or activated depending on task requirements. We discuss a number of possible interpretations of saccadic eye movements during non-visual cognition and propose an evolutionary model that links these eye movements to memory search through an elaboration of circuitry involved in visual perception.
@article{ehrlichman_looking_2007,
title = {Looking for answers: eye movements in non-visual cognitive tasks},
volume = {64},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17113204},
doi = {10/b852jr},
abstract = {It is not known why people move their eyes when engaged in non-visual cognition. The current study tested the hypothesis that differences in saccadic eye movement rate (EMR) during non-visual cognitive tasks reflect different requirements for searching long-term memory. Participants performed non-visual tasks requiring relatively low or high long-term memory retrieval while eye movements were recorded. In three experiments, EMR was substantially lower for low-retrieval than for high-retrieval tasks, including in an eyes closed condition in Experiment 3. Neither visual imagery nor between-task difficulty was related to EMR, although there was some evidence for a minor effect of within-task difficulty. Comparison of task-related EMRs to EMR during a no-task waiting period suggests that eye movements may be suppressed or activated depending on task requirements. We discuss a number of possible interpretations of saccadic eye movements during non-visual cognition and propose an evolutionary model that links these eye movements to memory search through an elaboration of circuitry involved in visual perception.},
number = {1},
journal = {Brain Cogn},
author = {Ehrlichman, H. and Micic, D. and Sousa, A. and Zhu, J.},
year = {2007},
keywords = {\#nosource, *Memory, *Saccades, Analysis of Variance, Auditory Perception, Female, Humans, Imagery (Psychotherapy), Male, Mental Recall, Models, Neurological, Reaction Time, Visual Pathways/physiology},
pages = {7--20},
}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}
}OligoCalc: an online oligonucleotide properties calculator. Kibbe, W. a Nucleic acids research, 35(Web Server issue):W43–6, July, 2007.
Paper doi abstract bibtex
Paper doi abstract bibtex We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar 'calculator' look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900,000 accesses of OligoCalc from nearly 200,000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.northwestern.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.
@article{Kibbe2007,
title = {{OligoCalc}: an online oligonucleotide properties calculator.},
volume = {35},
issn = {1362-4962},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933198&tool=pmcentrez&rendertype=abstract},
doi = {10.1093/nar/gkm234},
abstract = {We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar 'calculator' look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900,000 accesses of OligoCalc from nearly 200,000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.northwestern.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.},
number = {Web Server issue},
journal = {Nucleic acids research},
author = {Kibbe, Warren a},
month = jul,
year = {2007},
pmid = {17452344},
keywords = {\#nosource, Algorithms, Animals, Base Composition, Chemical, Computational Biology, Computational Biology: methods, DNA, DNA: chemistry, Humans, Internet, Models, Oligonucleotides, Oligonucleotides: chemistry, Oligonucleotides: genetics, RNA, RNA: chemistry, Software, Temperature, User-Computer Interface},
pages = {W43--6},
}2006 (5)
Synthesis of distamycin A polyamides targeting G-quadruplex DNA. Moore, M. J B, Cuenca, F., Searcey, M., & Neidle, S. Organic & biomolecular chemistry, 4(18):3479–88, October, 2006.
Paper doi abstract bibtex
Paper doi abstract bibtex A number of amide-linked oligopyrroles based on distamycin molecules have been synthesized by solid-state methods, and their interactions with a human intramolecular G-quadruplex have been measured by a melting procedure. Several of these molecules show an enhanced ratio of quadruplex vs. duplex DNA binding compared to distamycin itself, including one with a 2,5-disubstituted pyrrole group. Quadruplex affinity increases with the number of pyrrole groups, and it is suggested that this is consistent with a mixed groove/G-quartet stacking binding mode.
@article{Moore2006,
title = {Synthesis of distamycin {A} polyamides targeting {G}-quadruplex {DNA}.},
volume = {4},
issn = {1477-0520},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17036143},
doi = {10.1039/b607707b},
abstract = {A number of amide-linked oligopyrroles based on distamycin molecules have been synthesized by solid-state methods, and their interactions with a human intramolecular G-quadruplex have been measured by a melting procedure. Several of these molecules show an enhanced ratio of quadruplex vs. duplex DNA binding compared to distamycin itself, including one with a 2,5-disubstituted pyrrole group. Quadruplex affinity increases with the number of pyrrole groups, and it is suggested that this is consistent with a mixed groove/G-quartet stacking binding mode.},
number = {18},
journal = {Organic \& biomolecular chemistry},
author = {Moore, Michael J B and Cuenca, Francisco and Searcey, Mark and Neidle, Stephen},
month = oct,
year = {2006},
pmid = {17036143},
keywords = {\#nosource, DNA, DNA: chemistry, Dimerization, Distamycins, Distamycins: chemical synthesis, Distamycins: chemistry, Fluorescence Resonance Energy Transfer, G-Quadruplexes, Humans, Models, Molecular, Nylons, Nylons: chemical synthesis, Nylons: chemistry, Thermodynamics},
pages = {3479--88},
}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}
}Neural correlations, population coding and computation. Averbeck, B. B, Latham, P. E, & Pouget, A. Nature reviews. Neuroscience, 7(5):358–66, May, 2006.
Paper doi abstract bibtex
Paper doi abstract bibtex How the brain encodes information in population activity, and how it combines and manipulates that activity as it carries out computations, are questions that lie at the heart of systems neuroscience. During the past decade, with the advent of multi-electrode recording and improved theoretical models, these questions have begun to yield answers. However, a complete understanding of neuronal variability, and, in particular, how it affects population codes, is missing. This is because variability in the brain is typically correlated, and although the exact effects of these correlations are not known, it is known that they can be large. Here, we review studies that address the interaction between neuronal noise and population codes, and discuss their implications for population coding in general.
@article{Averbeck2006,
title = {Neural correlations, population coding and computation.},
volume = {7},
issn = {1471-003X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16760916},
doi = {10.1038/nrn1888},
abstract = {How the brain encodes information in population activity, and how it combines and manipulates that activity as it carries out computations, are questions that lie at the heart of systems neuroscience. During the past decade, with the advent of multi-electrode recording and improved theoretical models, these questions have begun to yield answers. However, a complete understanding of neuronal variability, and, in particular, how it affects population codes, is missing. This is because variability in the brain is typically correlated, and although the exact effects of these correlations are not known, it is known that they can be large. Here, we review studies that address the interaction between neuronal noise and population codes, and discuss their implications for population coding in general.},
number = {5},
urldate = {2013-08-10},
journal = {Nature reviews. Neuroscience},
author = {Averbeck, Bruno B and Latham, Peter E and Pouget, Alexandre},
month = may,
year = {2006},
pmid = {16760916},
keywords = {\#nosource, Action Potentials, Action Potentials: physiology, Animals, Brain, Brain: physiology, Humans, Models, Neurological, Nerve Net, Nerve Net: physiology, Neural Networks (Computer), Neurons, Neurons: classification, Neurons: physiology},
pages = {358--66},
}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}
}Optimal representation of sensory information by neural populations. Jazayeri, M. & Movshon, J. A. Nat Neurosci, 9(5):690-6, 2006.
doi abstract bibtex
doi abstract bibtex
Sensory information is encoded by populations of neurons. The responses of individual neurons are inherently noisy, so the brain must interpret this information as reliably as possible. In most situations, the optimal strategy for decoding the population signal is to compute the likelihoods of the stimuli that are consistent with an observed neural response. But it has not been clear how the brain can directly compute likelihoods. Here we present a simple and biologically plausible model that can realize the likelihood function by computing a weighted sum of sensory neuron responses. The model provides the basis for an optimal decoding of sensory information. It explains a variety of psychophysical observations on detection, discrimination and identification, and it also directly predicts the relative contributions that different sensory neurons make to perceptual judgments.
@Article{Jazayeri2006,
author = {Mehrdad Jazayeri and J. Anthony Movshon},
journal = {Nat Neurosci},
title = {Optimal representation of sensory information by neural populations.},
year = {2006},
number = {5},
pages = {690-6},
volume = {9},
abstract = {Sensory information is encoded by populations of neurons. The responses
of individual neurons are inherently noisy, so the brain must interpret
this information as reliably as possible. In most situations, the
optimal strategy for decoding the population signal is to compute
the likelihoods of the stimuli that are consistent with an observed
neural response. But it has not been clear how the brain can directly
compute likelihoods. Here we present a simple and biologically plausible
model that can realize the likelihood function by computing a weighted
sum of sensory neuron responses. The model provides the basis for
an optimal decoding of sensory information. It explains a variety
of psychophysical observations on detection, discrimination and identification,
and it also directly predicts the relative contributions that different
sensory neurons make to perceptual judgments.},
doi = {10.1038/nn1691},
keywords = {Afferent, Animals, Automatic Data Processing, Brain, Discrimination (Psychology), Humans, Likelihood Functions, Models, Nerve Net, Neurological, Neurons, Stochastic Processes, Visual Fields, Visual Perception, 16617339},
}2005 (5)
Computational analysis in vitro: dynamics and plasticity of a neuro-robotic system. Karniel, A., Kositsky, M., Fleming, K. M, Chiappalone, M., Sanguineti, V., Alford, S. T, & Mussa-Ivaldi, F. a J. Neural Eng., 2(3):S250–65, September, 2005.
Paper doi abstract bibtex
Paper doi abstract bibtex When the brain interacts with the environment it constantly adapts by representing the environment in a form that is called an internal model. The neurobiological basis for internal models is provided by the connectivity and the dynamical properties of neurons. Thus, the interactions between neural tissues and external devices provide a fundamental means for investigating the connectivity and dynamical properties of neural populations. We developed this idea, suggested in the 1980s by Valentino Braitenberg, for investigating and representing the dynamical behavior of neuronal populations in the brainstem of the lamprey. The brainstem was maintained in vitro and connected in a closed loop with two types of artificial device: (a) a simulated dynamical system and (b) a small mobile robot. In both cases, the device was controlled by recorded extracellular signals and its output was translated into electrical stimuli delivered to the neural system. The goal of the first study was to estimate the dynamical dimension of neural preparation in a single-input/single-output configuration. The dynamical dimension is the number of state variables that together with the applied input determine the output of a system. The results indicate that while this neural system has significant dynamical properties, its effective complexity, as established by the dynamical dimension, is rather moderate. In the second study, we considered a more specific situation, in which the same portion of the nervous system controls a robotic device in a two-input/two-output configuration. We fitted the input-output data from the neuro-robotic preparation to neural network models having different internal dynamics and we observed the generalization error of each model. Consistent with the first study, this second experiment showed that a simple recurrent dynamical model was able to capture the behavior of the hybrid system. This experimental and computational framework provides the means for investigating neural plasticity and internal representations in the context of brain-machine interfaces.
@article{Karniel2005,
title = {Computational analysis in vitro: dynamics and plasticity of a neuro-robotic system.},
volume = {2},
issn = {1741-2560},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135888},
doi = {10.1088/1741-2560/2/3/S08},
abstract = {When the brain interacts with the environment it constantly adapts by representing the environment in a form that is called an internal model. The neurobiological basis for internal models is provided by the connectivity and the dynamical properties of neurons. Thus, the interactions between neural tissues and external devices provide a fundamental means for investigating the connectivity and dynamical properties of neural populations. We developed this idea, suggested in the 1980s by Valentino Braitenberg, for investigating and representing the dynamical behavior of neuronal populations in the brainstem of the lamprey. The brainstem was maintained in vitro and connected in a closed loop with two types of artificial device: (a) a simulated dynamical system and (b) a small mobile robot. In both cases, the device was controlled by recorded extracellular signals and its output was translated into electrical stimuli delivered to the neural system. The goal of the first study was to estimate the dynamical dimension of neural preparation in a single-input/single-output configuration. The dynamical dimension is the number of state variables that together with the applied input determine the output of a system. The results indicate that while this neural system has significant dynamical properties, its effective complexity, as established by the dynamical dimension, is rather moderate. In the second study, we considered a more specific situation, in which the same portion of the nervous system controls a robotic device in a two-input/two-output configuration. We fitted the input-output data from the neuro-robotic preparation to neural network models having different internal dynamics and we observed the generalization error of each model. Consistent with the first study, this second experiment showed that a simple recurrent dynamical model was able to capture the behavior of the hybrid system. This experimental and computational framework provides the means for investigating neural plasticity and internal representations in the context of brain-machine interfaces.},
number = {3},
urldate = {2012-07-20},
journal = {J. Neural Eng.},
author = {Karniel, Amir and Kositsky, Michael and Fleming, Karen M and Chiappalone, Michela and Sanguineti, Vittorio and Alford, Simon T and Mussa-Ivaldi, Ferdinando a},
month = sep,
year = {2005},
pmid = {16135888},
keywords = {Animals, Brain, Brain: physiology, Cybernetics, Cybernetics: methods, Humans, Lampreys, Man-Machine Systems, Models, Nerve Net, Nerve Net: physiology, Neurological, Neuronal Plasticity, Neuronal Plasticity: physiology, Robotics, Robotics: methods, User-Computer Interface},
pages = {S250--65},
}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}
}Modelling and prediction in a complex world. Batty, M. & Torrens, P. M. Futures, 37(7):745–766, September, 2005.
Paper doi abstract bibtex
Paper doi abstract bibtex A complex system is an entity, coherent in some recognisable way but whose elements, interactions, and dynamics generate structures and admit surprise and novelty that cannot be defined a priori. Complex systems are more than the sum of their parts, and a consequence of this is that any model of their structure is necessarily incomplete and partial. Models thus represent simplifications in which salient parts and processes are simulated, and given this definition, many models will exist of any particular system. In this chapter, we explore the impact of this complexity on validating models of such systems. We begin with definitions and then identify key issues as being concerned with the characterisation of system equilibrium, system environment, and the way systems and their elements extend and scale. As our perspective on these issues changes, then so do our models with implications for their testing and validation. We argue that changes in the meaning of validity, posed by the use to which such models are to be put, are central to this debate, drawing these ideas together as conclusions about the limits posed to prediction in complex systems.
@article{batty_modelling_2005,
title = {Modelling and prediction in a complex world},
volume = {37},
issn = {0016-3287},
url = {http://www.sciencedirect.com/science/article/pii/S0016328704001788},
doi = {10.1016/j.futures.2004.11.003},
abstract = {A complex system is an entity, coherent in some recognisable way but whose elements, interactions, and dynamics generate structures and admit surprise and novelty that cannot be defined a priori. Complex systems are more than the sum of their parts, and a consequence of this is that any model of their structure is necessarily incomplete and partial. Models thus represent simplifications in which salient parts and processes are simulated, and given this definition, many models will exist of any particular system. In this chapter, we explore the impact of this complexity on validating models of such systems. We begin with definitions and then identify key issues as being concerned with the characterisation of system equilibrium, system environment, and the way systems and their elements extend and scale. As our perspective on these issues changes, then so do our models with implications for their testing and validation. We argue that changes in the meaning of validity, posed by the use to which such models are to be put, are central to this debate, drawing these ideas together as conclusions about the limits posed to prediction in complex systems.},
number = {7},
urldate = {2014-02-12},
journal = {Futures},
author = {Batty, Michael and Torrens, Paul M.},
month = sep,
year = {2005},
keywords = {collapse, models},
pages = {745--766},
file = {Batty and Torrens - 2005 - Modelling and prediction in a complex world.pdf:C\:\\Users\\rsrs\\Documents\\Zotero Database\\storage\\UB4NNSSJ\\Batty and Torrens - 2005 - Modelling and prediction in a complex world.pdf:application/pdf}
}Emotion as a thermostat: representing emotion regulation using a damped oscillator model. Chow, S., Ram, N., Boker, S. M., Fujita, F., & Clore, G. Emotion (Washington, D.C.), 5:208–25, 2005.
Paper doi abstract bibtex
Paper doi abstract bibtex The authors present in this study a damped oscillator model that provides a direct mathematical basis for testing the notion of emotion as a self-regulatory thermostat. Parameters from this model reflect individual differences in emotional lability and the ability to regulate emotion. The authors discuss concepts such as intensity, rate of change, and acceleration in the context of emotion, and they illustrate the strengths of this approach in comparison with spectral analysis and growth curve models. The utility of this modeling approach is illustrated using daily emotion ratings from 179 college students over 52 consecutive days. Overall, the damped oscillator model provides a meaningful way of representing emotion regulation as a dynamic process and helps identify the dominant periodicities in individuals' emotions.
@article{chow_emotion_2005,
title = {Emotion as a thermostat: representing emotion regulation using a damped oscillator model},
volume = {5},
issn = {1528-3542},
shorttitle = {Emotion as a thermostat},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15982086},
doi = {2005-06671-008},
abstract = {The authors present in this study a damped oscillator model that provides a direct mathematical basis for testing the notion of emotion as a self-regulatory thermostat. Parameters from this model reflect individual differences in emotional lability and the ability to regulate emotion. The authors discuss concepts such as intensity, rate of change, and acceleration in the context of emotion, and they illustrate the strengths of this approach in comparison with spectral analysis and growth curve models. The utility of this modeling approach is illustrated using daily emotion ratings from 179 college students over 52 consecutive days. Overall, the damped oscillator model provides a meaningful way of representing emotion regulation as a dynamic process and helps identify the dominant periodicities in individuals' emotions.},
urldate = {2008-12-08},
journal = {Emotion (Washington, D.C.)},
author = {Chow, S.-M. and Ram, N. and Boker, S. M. and Fujita, F. and Clore, G.},
year = {2005},
keywords = {Adult, Emotions, Female, Homeostasis, Humans, Male, Models, Theoretical, Periodicity},
pages = {208--25}
}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},
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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}
}Animal behaviour: Coalition among male fiddler crabs. Backwell, P. R Y & Jennions, M. D Nature, 430(6998):417, 2004.
doi abstract bibtex
doi abstract bibtex
Until now, no compelling evidence has emerged from studies of animal territoriality to indicate that a resident will strategically help a neighbour to defend its territory against an intruder. We show here that territory-owning Australian fiddler crabs will judiciously assist other crabs in defending their neighbouring territories. This cooperation supports the prediction that it is sometimes less costly to assist a familiar neighbour than to renegotiate boundaries with a new, and possibly stronger, neighbour.
@Article{Backwell2004,
author = {Patricia R Y Backwell and Michael D Jennions},
journal = {Nature},
title = {Animal behaviour: {C}oalition among male fiddler crabs.},
year = {2004},
number = {6998},
pages = {417},
volume = {430},
abstract = {Until now, no compelling evidence has emerged from studies of animal
territoriality to indicate that a resident will strategically help
a neighbour to defend its territory against an intruder. We show
here that territory-owning Australian fiddler crabs will judiciously
assist other crabs in defending their neighbouring territories. This
cooperation supports the prediction that it is sometimes less costly
to assist a familiar neighbour than to renegotiate boundaries with
a new, and possibly stronger, neighbour.},
doi = {10.1038/430417a},
keywords = {Animals, Attention, Brain, Decision Making, Face, Female, Haplorhini, Housing, Humans, Magnetic Resonance Imaging, Male, Models, Neurological, Pattern Recognition, Visual, Photic Stimulation, Prefrontal Cortex, Research Support, Non-U.S. Gov't, U.S. Gov't, P.H.S., Visual Perception, Choice Behavior, Cognition, Dopamine, Learning, Schizophrenia, Substance-Related Disorders, Generalization (Psychology), Motor Skills, Non-P.H.S., Nerve Net, Neuronal Plasticity, Perception, Cerebral Cortex, Memory, Neurons, Sound Localization, Synapses, Synaptic Transmission, Neural Pathways, Non-, Acoustic Stimulation, Adult, Age of Onset, Aging, Blindness, Child, Preschool, Infant, Newborn, Pitch Perception, Analysis of Variance, Animal Welfare, Laboratory, Behavior, Animal, Hybridization, Genetic, Maze Learning, Mice, Inbred C57BL, Inbred DBA, Phenotype, Reproducibility of Results, Darkness, Deafness, Finches, Sleep, Sound, Sunlight, Time Factors, Vocalization, Energy Metabolism, Evolution, Fossils, History, Ancient, Hominidae, Biological, Physical Endurance, Running, Skeleton, Walking, Acoustics, Auditory Perception, Cues, Discrimination Learning, Pair Bond, Social Behavior, Songbirds, Adolescent, England, Habituation (Psychophysiology), Korea, Language, Semantics, Vocabulary, Action Potentials, Hippocampus, Pyramidal Cells, Rats, Rotation, Australia, Brachyura, Cooperative Behavior, Logistic Models, Territoriality, 15269757},
}Thiazole orange-peptide conjugates: sensitivity of DNA binding to chemical structure. Carreon, J. R, Mahon, K. P, & Kelley, S. O Organic letters, 6(4):517–9, March, 2004.
Paper doi abstract bibtex
Paper doi abstract bibtex [structure: see text] Derivatives of the highly fluorescent and DNA-binding dye thiazole orange (TO) are described that feature appended peptides. Functionalization of TO can be achieved at either of the endocyclic nitrogens, and the photophysical properties and DNA-binding modes are sensitive to the position of the tethered peptide. A series of TO-peptide conjugates are described, demonstrating the utility of a solid-phase synthesis approach to their preparation and illustrating how the photophysical and DNA-binding properties of the compounds are influenced by chemical structure.
@article{Carreon2004,
title = {Thiazole orange-peptide conjugates: sensitivity of {DNA} binding to chemical structure.},
volume = {6},
issn = {1523-7060},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14961612},
doi = {10.1021/ol0362818},
abstract = {[structure: see text] Derivatives of the highly fluorescent and DNA-binding dye thiazole orange (TO) are described that feature appended peptides. Functionalization of TO can be achieved at either of the endocyclic nitrogens, and the photophysical properties and DNA-binding modes are sensitive to the position of the tethered peptide. A series of TO-peptide conjugates are described, demonstrating the utility of a solid-phase synthesis approach to their preparation and illustrating how the photophysical and DNA-binding properties of the compounds are influenced by chemical structure.},
number = {4},
journal = {Organic letters},
author = {Carreon, Jay R and Mahon, Kerry P and Kelley, Shana O},
month = mar,
year = {2004},
pmid = {14961612},
keywords = {\#nosource, Amino Acid Sequence, Benzothiazoles, DNA, DNA: chemistry, Fluorescent Dyes, Fluorescent Dyes: chemistry, Models, Molecular, Molecular Structure, Peptides, Peptides: chemistry, Quinolines, Structure-Activity Relationship, Thiazoles, Thiazoles: chemistry},
pages = {517--9},
}2003 (3)
Activity-dependent presynaptic facilitation and hebbian LTP are both required and interact during classical conditioning in Aplysia. Antonov, I., Antonova, I., Kandel, E. R, & Hawkins, R. D Neuron, 37(1):135-47, 2003.
abstract bibtex
abstract bibtex
Using a simplified preparation of the Aplysia siphon-withdrawal reflex, we previously found that associative plasticity at synapses between sensory neurons and motor neurons contributes importantly to classical conditioning of the reflex. We have now tested the roles in that plasticity of two associative cellular mechanisms: activity-dependent enhancement of presynaptic facilitation and postsynaptically induced long-term potentiation. By perturbing molecular signaling pathways in individual neurons, we have provided the most direct evidence to date that each of these mechanisms contributes to behavioral learning. In addition, our results suggest that the two mechanisms are not independent but rather interact through retrograde signaling.
@Article{Antonov2003,
author = {Igor Antonov and Irina Antonova and Eric R Kandel and Robert D Hawkins},
journal = {Neuron},
title = {Activity-dependent presynaptic facilitation and hebbian {LTP} are both required and interact during classical conditioning in {A}plysia.},
year = {2003},
number = {1},
pages = {135-47},
volume = {37},
abstract = {Using a simplified preparation of the Aplysia siphon-withdrawal reflex,
we previously found that associative plasticity at synapses between
sensory neurons and motor neurons contributes importantly to classical
conditioning of the reflex. We have now tested the roles in that
plasticity of two associative cellular mechanisms: activity-dependent
enhancement of presynaptic facilitation and postsynaptically induced
long-term potentiation. By perturbing molecular signaling pathways
in individual neurons, we have provided the most direct evidence
to date that each of these mechanisms contributes to behavioral learning.
In addition, our results suggest that the two mechanisms are not
independent but rather interact through retrograde signaling.},
keywords = {Amygdala, Animals, Evaluation Studies, Hippocampus, Human, Learning, Long-Term Potentiation, Memory, Models, Neurological, Neural Pathways, Neuronal Plasticity, Support, Non-U.S. Gov't, Synapses, 2-Amino-5-phosphonovalerate, Electric Stimulation, Isomerism, Rats, Receptors, N-Methyl-D-Aspartate, Neurotransmitter, Valine, Visual Perception, Action Potentials, Calcium Signaling, Central Nervous System, Chelating Agents, Conditioning (Psychology), Cyclic AMP-Dependent Protein Kinases, Enzyme Inhibitors, Excitatory Amino Acid Antagonists, Motor Neurons, Neurons, Afferent, Reaction Time, Reflex, Signal Transduction, U.S. Gov't, P.H.S., Synaptic Transmission, 12526779},
}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},
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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}
}Neural model for physiological responses to frequency and amplitude transitions uncovers topographical order in the auditory cortex. Fishbach, A., Yeshurun, Y., & Nelken, I. J Neurophysiol, 90(6):3663-78, 2003.
doi abstract bibtex
doi abstract bibtex
We characterize primary auditory cortex (AI) units using a neural model for the detection of frequency and amplitude transitions. The model is a generalization of a model for the detection of amplitude transition. A set of neurons, tuned in the spectrotemporal domain, is created by means of neural delays and frequency filtering. The sensitivity of the model to frequency and amplitude transitions is achieved by applying a 2-dimensional rotatable receptive field to the set of spectrotemporally tuned neurons. We evaluated the model using data recorded in AI of anesthetized ferrets. We show that the model is able to fit the responses of AI units to variety of stimuli, including single tones, delayed 2-tone stimuli and various frequency-modulated tones, using only a small number of parameters. Furthermore, we show that the topographical order in maps of the model parameters is higher than in maps created from response indices extracted directly from the responses to any single stimulus. These results suggest a possible ordered organization of a simple rotatable spectrotemporal receptive field in the mammalian AI.
@Article{Fishbach2003,
author = {Alon Fishbach and Yehezkel Yeshurun and Israel Nelken},
journal = {J Neurophysiol},
title = {Neural model for physiological responses to frequency and amplitude transitions uncovers topographical order in the auditory cortex.},
year = {2003},
number = {6},
pages = {3663-78},
volume = {90},
abstract = {We characterize primary auditory cortex (AI) units using a neural
model for the detection of frequency and amplitude transitions. The
model is a generalization of a model for the detection of amplitude
transition. A set of neurons, tuned in the spectrotemporal domain,
is created by means of neural delays and frequency filtering. The
sensitivity of the model to frequency and amplitude transitions is
achieved by applying a 2-dimensional rotatable receptive field to
the set of spectrotemporally tuned neurons. We evaluated the model
using data recorded in AI of anesthetized ferrets. We show that the
model is able to fit the responses of AI units to variety of stimuli,
including single tones, delayed 2-tone stimuli and various frequency-modulated
tones, using only a small number of parameters. Furthermore, we show
that the topographical order in maps of the model parameters is higher
than in maps created from response indices extracted directly from
the responses to any single stimulus. These results suggest a possible
ordered organization of a simple rotatable spectrotemporal receptive
field in the mammalian AI.},
doi = {10.1152/jn.00654.2003},
keywords = {Acoustic Stimulation, Algorithms, Artificial Intelligence, Auditory Cortex, Brain Mapping, Cluster Analysis, Computer Simulation, Human, Loudness Perception, Models, Neurological, Neurons, Pitch Perception, Reproducibility of Results, Support, U.S. Gov, ', t, Non-P.H.S., 14665682},
}2002 (6)
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}
}Selective targeting of zebrafish olfactory receptor neurons by the endogenous OMP promoter. Celik, A., Fuss, S. H, & Korsching, S I The European journal of neuroscience, 15(5):798–806, March, 2002.
Paper abstract bibtex
Paper abstract bibtex The olfactory nervous system of fish, in particular zebrafish, has become a valid model for that of higher vertebrates. However, no genetic markers for olfactory specific cell types, e.g. the olfactory receptor neurons, have been established in this species. Olfactory marker protein (OMP) is a reliable marker for olfactory receptor neurons in several other vertebrates. We have cloned zOMP, the zebrafish homologue of olfactory marker protein. During development, zOMP is expressed exclusively in the olfactory placode, presumably in olfactory receptor neurons, as shown by in situ hybridization. In the adult nasal epithelium zOMP is found restricted to the sensory region. zOMP appears to be a single gene, without close family members. The 5'-flanking region lacks most of the expected regulatory sequence motifs, both general and cell type-specific ones. Nevertheless, it drives reporter gene expression strongly and specifically in olfactory receptor neurons during the whole developmental period examined. Thus the zOMP promoter constitutes a powerful tool which should be useful to selectively introduce a wide variety of genetic modifications into olfactory receptor neurons.
@article{Celik2002,
title = {Selective targeting of zebrafish olfactory receptor neurons by the endogenous {OMP} promoter.},
volume = {15},
issn = {0953-816X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11906521},
abstract = {The olfactory nervous system of fish, in particular zebrafish, has become a valid model for that of higher vertebrates. However, no genetic markers for olfactory specific cell types, e.g. the olfactory receptor neurons, have been established in this species. Olfactory marker protein (OMP) is a reliable marker for olfactory receptor neurons in several other vertebrates. We have cloned zOMP, the zebrafish homologue of olfactory marker protein. During development, zOMP is expressed exclusively in the olfactory placode, presumably in olfactory receptor neurons, as shown by in situ hybridization. In the adult nasal epithelium zOMP is found restricted to the sensory region. zOMP appears to be a single gene, without close family members. The 5'-flanking region lacks most of the expected regulatory sequence motifs, both general and cell type-specific ones. Nevertheless, it drives reporter gene expression strongly and specifically in olfactory receptor neurons during the whole developmental period examined. Thus the zOMP promoter constitutes a powerful tool which should be useful to selectively introduce a wide variety of genetic modifications into olfactory receptor neurons.},
number = {5},
urldate = {2015-12-09},
journal = {The European journal of neuroscience},
author = {Celik, Arzu and Fuss, Stefan H and Korsching, S I},
month = mar,
year = {2002},
pmid = {11906521},
keywords = {\#nosource, Animals, Bacterial Proteins, Bacterial Proteins: diagnostic use, Bacterial Proteins: genetics, Cell Differentiation, Cell Differentiation: genetics, Cell Division, Cell Division: physiology, Cloning, Molecular, DNA, Complementary, DNA, Complementary: genetics, DNA, Complementary: isolation \& purification, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Gene Expression Regulation, Developmental: genetic, Gene Targeting, Gene Targeting: methods, Genetic Vectors, Genetic Vectors: genetics, Larva, Luminescent Proteins, Luminescent Proteins: diagnostic use, Luminescent Proteins: genetics, Models, Biological, Molecular Sequence Data, Nerve Tissue Proteins, Nerve Tissue Proteins: genetics, Nerve Tissue Proteins: metabolism, Olfactory Marker Protein, Olfactory Receptor Neurons, Olfactory Receptor Neurons: embryology, Olfactory Receptor Neurons: growth \& development, Olfactory Receptor Neurons: metabolism, Phylogeny, Promoter Regions, Genetic, Promoter Regions, Genetic: genetics, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Stem Cells, Stem Cells: cytology, Stem Cells: metabolism, Transgenes, Transgenes: genetics, Zebrafish, Zebrafish Proteins, Zebrafish: embryology, Zebrafish: growth \& development, Zebrafish: metabolism, olfaction, zebrafish},
pages = {798--806},
}Variance components models for gene-environment interaction in twin analysis. Purcell, S. Twin research : the official journal of the International Society for Twin Studies, 5(6):554–71, December, 2002.
Paper doi abstract bibtex
Paper doi abstract bibtex Gene-environment interaction is likely to be a common and important source of variation for complex behavioral traits. Often conceptualized as the genetic control of sensitivity to the environment, it can be incorporated in variance components twin analyses by partitioning genetic effects into a mean part, which is independent of the environment, and a part that is a linear function of the environment. The model allows for one or more environmental moderator variables (that possibly interact with each other) that may i). be continuous or binary ii). differ between twins within a pair iii). interact with residual environmental as well as genetic effects iv) have nonlinear moderating properties v). show scalar (different magnitudes) or qualitative (different genes) interactions vi). be correlated with genetic effects acting upon the trait, to allow for a test of gene-environment interaction in the presence of gene-environment correlation. Aspects and applications of a class of models are explored by simulation, in the context of both individual differences twin analysis and, in a companion paper (Purcell & Sham, 2002) sibpair quantitative trait locus linkage analysis. As well as elucidating environmental pathways, consideration of gene-environment interaction in quantitative and molecular studies will potentially direct and enhance gene-mapping efforts.
@article{purcell_variance_2002,
title = {Variance components models for gene-environment interaction in twin analysis.},
volume = {5},
issn = {1369-0523},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12573187},
doi = {10.1375/136905202762342026},
abstract = {Gene-environment interaction is likely to be a common and important source of variation for complex behavioral traits. Often conceptualized as the genetic control of sensitivity to the environment, it can be incorporated in variance components twin analyses by partitioning genetic effects into a mean part, which is independent of the environment, and a part that is a linear function of the environment. The model allows for one or more environmental moderator variables (that possibly interact with each other) that may i). be continuous or binary ii). differ between twins within a pair iii). interact with residual environmental as well as genetic effects iv) have nonlinear moderating properties v). show scalar (different magnitudes) or qualitative (different genes) interactions vi). be correlated with genetic effects acting upon the trait, to allow for a test of gene-environment interaction in the presence of gene-environment correlation. Aspects and applications of a class of models are explored by simulation, in the context of both individual differences twin analysis and, in a companion paper (Purcell \& Sham, 2002) sibpair quantitative trait locus linkage analysis. As well as elucidating environmental pathways, consideration of gene-environment interaction in quantitative and molecular studies will potentially direct and enhance gene-mapping efforts.},
number = {6},
urldate = {2015-05-16},
journal = {Twin research : the official journal of the International Society for Twin Studies},
author = {Purcell, Shaun},
month = dec,
year = {2002},
pmid = {12573187},
keywords = {Computer Simulation, Environment, Genetics, Behavioral, Humans, Models, Genetic, Twins, Twins: genetics},
pages = {554--71},
}Model for a robust neural integrator. Koulakov, A. a, Raghavachari, S., Kepecs, A., & Lisman, J. E Nature neuroscience, 5(8):775–82, August, 2002.
Paper doi abstract bibtex
Paper doi abstract bibtex Integrator circuits in the brain show persistent firing that reflects the sum of previous excitatory and inhibitory inputs from external sources. Integrator circuits have been implicated in parametric working memory, decision making and motor control. Previous work has shown that stable integrator function can be achieved by an excitatory recurrent neural circuit, provided synaptic strengths are tuned with extreme precision (better than 1% accuracy). Here we show that integrator circuits can function without fine tuning if the neuronal units have bistable properties. Two specific mechanisms of bistability are analyzed, one based on local recurrent excitation, and the other on the voltage-dependence of the NMDA (N-methyl-D-aspartate) channel. Neither circuit requires fine tuning to perform robust integration, and the latter actually exploits the variability of neuronal conductances.
@article{Koulakov2002,
title = {Model for a robust neural integrator.},
volume = {5},
issn = {1097-6256},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12134153},
doi = {10.1038/nn893},
abstract = {Integrator circuits in the brain show persistent firing that reflects the sum of previous excitatory and inhibitory inputs from external sources. Integrator circuits have been implicated in parametric working memory, decision making and motor control. Previous work has shown that stable integrator function can be achieved by an excitatory recurrent neural circuit, provided synaptic strengths are tuned with extreme precision (better than 1\% accuracy). Here we show that integrator circuits can function without fine tuning if the neuronal units have bistable properties. Two specific mechanisms of bistability are analyzed, one based on local recurrent excitation, and the other on the voltage-dependence of the NMDA (N-methyl-D-aspartate) channel. Neither circuit requires fine tuning to perform robust integration, and the latter actually exploits the variability of neuronal conductances.},
number = {8},
urldate = {2013-08-16},
journal = {Nature neuroscience},
author = {Koulakov, Alexei a and Raghavachari, Sridhar and Kepecs, Adam and Lisman, John E},
month = aug,
year = {2002},
pmid = {12134153},
keywords = {\#nosource, Computer Simulation, Models, Neurological, Neural Networks (Computer), Neurons, Neurons: physiology, Receptors, N-Methyl-D-Aspartate, Receptors, N-Methyl-D-Aspartate: physiology, Reproducibility of Results},
pages = {775--82},
}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}
}Fundamentals of experimental design for cDNA microarrays. Churchill, G. A Nature genetics, 32 Suppl:490–5, December, 2002.
Paper doi bibtex
Paper doi bibtex 2001 (1)
Activation of the auditory pre-attentive change detection system by tone repetitions with fast stimulation rate. Wolff, C & Schröger, E Brain Res Cogn Brain Res, 10(3):323-7, 2001.
abstract bibtex
abstract bibtex
The human automatic pre-attentive change detection system indexed by the mismatch negativity (MMN) component of the auditory event-related brain potential is known to be highly adaptive. The present study showed that even infrequent repetitions of tones can elicit MMN, independently of attention, when tones of varying frequency are rapidly presented in an isochronous rhythm. This demonstrates that frequency variation can be extracted as an invariant feature of the acoustic environment revealing the capacity for adaptation of the auditory pre-attentive change detection system. It is argued that this capacity is related to the temporal-window of integration.
@Article{Wolff2001,
author = {C Wolff and E Schr\"oger},
journal = {Brain Res Cogn Brain Res},
title = {Activation of the auditory pre-attentive change detection system by tone repetitions with fast stimulation rate.},
year = {2001},
number = {3},
pages = {323-7},
volume = {10},
abstract = {The human automatic pre-attentive change detection system indexed
by the mismatch negativity (MMN) component of the auditory event-related
brain potential is known to be highly adaptive. The present study
showed that even infrequent repetitions of tones can elicit MMN,
independently of attention, when tones of varying frequency are rapidly
presented in an isochronous rhythm. This demonstrates that frequency
variation can be extracted as an invariant feature of the acoustic
environment revealing the capacity for adaptation of the auditory
pre-attentive change detection system. It is argued that this capacity
is related to the temporal-window of integration.},
keywords = {Computing Methodologies, Human, Language, Learning, Mental Processes, Models, Theoretical, Stochastic Processes, Support, U.S. Gov't, Non-P.H.S., Cognition, Linguistics, Neural Networks (Computer), Practice (Psychology), Non-U.S. Gov't, Memory, Psychological, Task Performance and Analysis, Time Factors, Visual Perception, Adult, Attention, Discrimination Learning, Female, Male, Short-Term, Mental Recall, Orientation, Pattern Recognition, Visual, Perceptual Masking, Reading, Concept Formation, Form Perception, Animals, Corpus Striatum, Shrews, P.H.S., Visual Cortex, Visual Pathways, Acoustic Stimulation, Auditory Cortex, Auditory Perception, Cochlea, Ear, Gerbillinae, Glycine, Hearing, Neurons, Space Perception, Strychnine, Adolescent, Decision Making, Reaction Time, Astrocytoma, Brain Mapping, Brain Neoplasms, Cerebral Cortex, Electric Stimulation, Electrophysiology, Epilepsy, Temporal Lobe, Evoked Potentials, Frontal Lobe, Noise, Parietal Lobe, Scalp, Child, Language Development, Psycholinguistics, Brain, Perception, Speech, Vocalization, Animal, Discrimination (Psychology), Hippocampus, Rats, Calcium, Chelating Agents, Excitatory Postsynaptic Potentials, Glutamic Acid, Guanosine Diphosphate, In Vitro, Neuronal Plasticity, Pyramidal Cells, Receptors, AMPA, Metabotropic Glutamate, N-Methyl-D-Aspartate, Somatosensory Cortex, Synapses, Synaptic Transmission, Thionucleotides, Action Potentials, Calcium Channels, L-Type, Electric Conductivity, Entorhinal Cortex, Neurological, Long-Evans, Infant, Mathematics, Statistics, Probability Learning, Problem Solving, Psychophysics, Association Learning, Child Psychology, Habituation (Psychophysiology), Probability Theory, Analysis of Variance, Semantics, Symbolism, Behavior, Eye Movements, Macaca mulatta, Prefrontal Cortex, Cats, Dogs, Haplorhini, Photic Stimulation, Electroencephalography, Nervous System Physiology, Darkness, Grasshoppers, Light, Membrane Potentials, Neural Inhibition, Afferent, Picrotoxin, Vision, Deoxyglucose, Injections, Microspheres, Neural Pathways, Rhodamines, Choice Behavior, Speech Perception, Verbal Learning, Dominance, Cerebral, Fixation, Ocular, Language Tests, Random Allocation, Comparative Study, Saguinus, Sound Spectrography, Species Specificity, Audiometry, Auditory Threshold, Calibration, Data Interpretation, Statistical, Anesthesia, General, Electrodes, Implanted, Pitch Perception, Sound Localization, Paired-Associate Learning, Serial Learning, Auditory, Age Factors, Motion Perception, Brain Injuries, Computer Simulation, Blindness, Psychomotor Performance, Color Perception, Signal Detection (Psychology), Judgment, ROC Curve, Regression Analysis, Music, Probability, Arm, Cerebrovascular Disorders, Hemiplegia, Movement, Muscle, Skeletal, Myoclonus, Robotics, Magnetoencephalography, Phonetics, Software, Speech Production Measurement, Epilepsies, Partial, Laterality, Stereotaxic Techniques, Germany, Speech Acoustics, Verbal Behavior, Child Development, Instinct, Brain Stem, Coma, Diagnosis, Differential, Hearing Disorders, Hearing Loss, Central, Neuroma, Acoustic, Dendrites, Down-Regulation, Patch-Clamp Techniques, Wistar, Up-Regulation, Aged, Aphasia, Middle Aged, Cones (Retina), Primates, Retina, Retinal Ganglion Cells, Tympanic Membrane, Cell Communication, Extremities, Biological, Motor Activity, Rana catesbeiana, Spinal Cord, Central Nervous System, Motion, Motor Cortex, Intelligence, Macaca fascicularis, Adoption, Critical Period (Psychology), France, Korea, Magnetic Resonance Imaging, Multilingualism, Auditory Pathways, Cochlear Nerve, Loudness Perception, Neural Conduction, Sensory Thresholds, Sound, Language Disorders, Preschool, Generalization (Psychology), Vocabulary, Biophysics, Nerve Net, Potassium Channels, Sodium Channels, Cues, Differential Threshold, Arousal, Newborn, Sucking Behavior, Ferrets, Microelectrodes, Gestalt Theory, Mathematical Computing, Perceptual Closure, Vestibulocochlear Nerve, Brain Damage, Chronic, Regional Blood Flow, Thinking, Tomography, Emission-Computed, Case-Control Studies, Multivariate Analysis, Artificial Intelligence, Depth Perception, Broca, Encephalitis, Herpes Simplex, Infarction, Middle Cerebral Artery, X-Ray Computed, 11167055},
}2000 (4)
Learning of action through adaptive combination of motor primitives. Thoroughman, K. & Shadmehr, R Nature, 407(6805):742-7, 2000.
doi abstract bibtex
doi abstract bibtex
Understanding how the brain constructs movements remains a fundamental challenge in neuroscience. The brain may control complex movements through flexible combination of motor primitives, where each primitive is an element of computation in the sensorimotor map that transforms desired limb trajectories into motor commands. Theoretical studies have shown that a system's ability to learn action depends on the shape of its primitives. Using a time-series analysis of error patterns, here we show that humans learn the dynamics of reaching movements through a flexible combination of primitives that have gaussian-like tuning functions encoding hand velocity. The wide tuning of the inferred primitives predicts limitations on the brain's ability to represent viscous dynamics. We find close agreement between the predicted limitations and the subjects' adaptation to new force fields. The mathematical properties of the derived primitives resemble the tuning curves of Purkinje cells in the cerebellum. The activity of these cells may encode primitives that underlie the learning of dynamics.
@Article{Thoroughman2000,
author = {KA Thoroughman and R Shadmehr},
journal = {Nature},
title = {Learning of action through adaptive combination of motor primitives.},
year = {2000},
number = {6805},
pages = {742-7},
volume = {407},
abstract = {Understanding how the brain constructs movements remains a fundamental
challenge in neuroscience. The brain may control complex movements
through flexible combination of motor primitives, where each primitive
is an element of computation in the sensorimotor map that transforms
desired limb trajectories into motor commands. Theoretical studies
have shown that a system's ability to learn action depends on the
shape of its primitives. Using a time-series analysis of error patterns,
here we show that humans learn the dynamics of reaching movements
through a flexible combination of primitives that have gaussian-like
tuning functions encoding hand velocity. The wide tuning of the inferred
primitives predicts limitations on the brain's ability to represent
viscous dynamics. We find close agreement between the predicted limitations
and the subjects' adaptation to new force fields. The mathematical
properties of the derived primitives resemble the tuning curves of
Purkinje cells in the cerebellum. The activity of these cells may
encode primitives that underlie the learning of dynamics.},
doi = {10.1038/35037588},
keywords = {Computing Methodologies, Human, Language, Learning, Mental Processes, Models, Theoretical, Stochastic Processes, Support, U.S. Gov't, Non-P.H.S., Cognition, Linguistics, Neural Networks (Computer), Practice (Psychology), Non-U.S. Gov't, Memory, Psychological, Task Performance and Analysis, Time Factors, Visual Perception, Adult, Attention, Discrimination Learning, Female, Male, Short-Term, Mental Recall, Orientation, Pattern Recognition, Visual, Perceptual Masking, Reading, Concept Formation, Form Perception, Animals, Corpus Striatum, Shrews, P.H.S., Visual Cortex, Visual Pathways, Acoustic Stimulation, Auditory Cortex, Auditory Perception, Cochlea, Ear, Gerbillinae, Glycine, Hearing, Neurons, Space Perception, Strychnine, Adolescent, Decision Making, Reaction Time, Astrocytoma, Brain Mapping, Brain Neoplasms, Cerebral Cortex, Electric Stimulation, Electrophysiology, Epilepsy, Temporal Lobe, Evoked Potentials, Frontal Lobe, Noise, Parietal Lobe, Scalp, Child, Language Development, Psycholinguistics, Brain, Perception, Speech, Vocalization, Animal, Discrimination (Psychology), Hippocampus, Rats, Calcium, Chelating Agents, Excitatory Postsynaptic Potentials, Glutamic Acid, Guanosine Diphosphate, In Vitro, Neuronal Plasticity, Pyramidal Cells, Receptors, AMPA, Metabotropic Glutamate, N-Methyl-D-Aspartate, Somatosensory Cortex, Synapses, Synaptic Transmission, Thionucleotides, Action Potentials, Calcium Channels, L-Type, Electric Conductivity, Entorhinal Cortex, Neurological, Long-Evans, Infant, Mathematics, Statistics, Probability Learning, Problem Solving, Psychophysics, Association Learning, Child Psychology, Habituation (Psychophysiology), Probability Theory, Analysis of Variance, Semantics, Symbolism, Behavior, Eye Movements, Macaca mulatta, Prefrontal Cortex, Cats, Dogs, Haplorhini, Photic Stimulation, Electroencephalography, Nervous System Physiology, Darkness, Grasshoppers, Light, Membrane Potentials, Neural Inhibition, Afferent, Picrotoxin, Vision, Deoxyglucose, Injections, Microspheres, Neural Pathways, Rhodamines, Choice Behavior, Speech Perception, Verbal Learning, Dominance, Cerebral, Fixation, Ocular, Language Tests, Random Allocation, Comparative Study, Saguinus, Sound Spectrography, Species Specificity, Audiometry, Auditory Threshold, Calibration, Data Interpretation, Statistical, Anesthesia, General, Electrodes, Implanted, Pitch Perception, Sound Localization, Paired-Associate Learning, Serial Learning, Auditory, Age Factors, Motion Perception, Brain Injuries, Computer Simulation, Blindness, Psychomotor Performance, Color Perception, Signal Detection (Psychology), Judgment, ROC Curve, Regression Analysis, Music, Probability, Arm, Cerebrovascular Disorders, Hemiplegia, Movement, Muscle, Skeletal, Myoclonus, Robotics, Magnetoencephalography, Phonetics, Software, Speech Production Measurement, Epilepsies, Partial, Laterality, Stereotaxic Techniques, Germany, Speech Acoustics, Verbal Behavior, Child Development, Instinct, Brain Stem, Coma, Diagnosis, Differential, Hearing Disorders, Hearing Loss, Central, Neuroma, Acoustic, Dendrites, Down-Regulation, Patch-Clamp Techniques, Wistar, Up-Regulation, Aged, Aphasia, Middle Aged, Cones (Retina), Primates, Retina, Retinal Ganglion Cells, Tympanic Membrane, Cell Communication, Extremities, Biological, Motor Activity, Rana catesbeiana, Spinal Cord, Central Nervous System, Motion, Motor Cortex, Intelligence, Macaca fascicularis, Adoption, Critical Period (Psychology), France, Korea, Magnetic Resonance Imaging, Multilingualism, Auditory Pathways, Cochlear Nerve, Loudness Perception, Neural Conduction, Sensory Thresholds, Sound, Language Disorders, Preschool, Generalization (Psychology), Vocabulary, Biophysics, Nerve Net, Potassium Channels, Sodium Channels, Cues, Differential Threshold, Arousal, Newborn, Sucking Behavior, Ferrets, Microelectrodes, Gestalt Theory, Mathematical Computing, Perceptual Closure, Vestibulocochlear Nerve, Brain Damage, Chronic, Regional Blood Flow, Thinking, Tomography, Emission-Computed, Case-Control Studies, Multivariate Analysis, Artificial Intelligence, Depth Perception, 11048700},
}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}
}The radiosensitizing agent 7-hydroxystaurosporine (UCN-01) inhibits the DNA damage checkpoint kinase hChk1. Busby, E. C., Leistritz, D. F., Abraham, R. T., Karnitz, L. M., & Sarkaria, J. N. Cancer Research, 60(8):2108–2112, April, 2000.
abstract bibtex
abstract bibtex
The investigational anticancer agent 7-hydroxystaurosporine (UCN-01) abrogates the G2 checkpoint in tumor cells and sensitizes them to the lethal effects of genotoxic anticancer agents. On the basis of the role of the Cdc25C phosphatase in maintenance of this damage-inducible checkpoint, we hypothesized that UCN-01 inhibits a component of the signal transduction pathway that modulates Cdc25C phosphorylation. Of the three kinases known to phosphorylate Cdc25C on Ser216, both checkpoint kinase 1 (hChk1) and Cdc25C-associated protein kinase 1 (cTAK1) were potently inhibited by UCN-01 with IC50s of 11 and 27 nM, respectively. Treatment of K562 erythroblastoid leukemia cells with similar drug concentrations resulted in decreased levels of Ser216 phosphorylation of Cdc25C and complete disruption of the y-radiation-induced G2 checkpoint. In contrast to hChk1, the hChk2 kinase was 100-fold more resistant to inhibition by UCN-01 (IC50, 1040 nM). These results suggest that disruption of the DNA damage-induced G2 checkpoint by UCN-01 is mediated through the inhibition of the Cdc25C kinases, hChk1 and cTAK1, and that hChk2 activity is not sufficient to enforce the G2 checkpoint in cells treated with a pharmacological inhibitor of hChk1.
@article{busby_radiosensitizing_2000,
title = {The radiosensitizing agent 7-hydroxystaurosporine ({UCN}-01) inhibits the {DNA} damage checkpoint kinase {hChk1}},
volume = {60},
issn = {0008-5472},
abstract = {The investigational anticancer agent 7-hydroxystaurosporine (UCN-01) abrogates the G2 checkpoint in tumor cells and sensitizes them to the lethal effects of genotoxic anticancer agents. On the basis of the role of the Cdc25C phosphatase in maintenance of this damage-inducible checkpoint, we hypothesized that UCN-01 inhibits a component of the signal transduction pathway that modulates Cdc25C phosphorylation. Of the three kinases known to phosphorylate Cdc25C on Ser216, both checkpoint kinase 1 (hChk1) and Cdc25C-associated protein kinase 1 (cTAK1) were potently inhibited by UCN-01 with IC50s of 11 and 27 nM, respectively. Treatment of K562 erythroblastoid leukemia cells with similar drug concentrations resulted in decreased levels of Ser216 phosphorylation of Cdc25C and complete disruption of the y-radiation-induced G2 checkpoint. In contrast to hChk1, the hChk2 kinase was 100-fold more resistant to inhibition by UCN-01 (IC50, 1040 nM). These results suggest that disruption of the DNA damage-induced G2 checkpoint by UCN-01 is mediated through the inhibition of the Cdc25C kinases, hChk1 and cTAK1, and that hChk2 activity is not sufficient to enforce the G2 checkpoint in cells treated with a pharmacological inhibitor of hChk1.},
language = {eng},
number = {8},
journal = {Cancer Research},
author = {Busby, E. C. and Leistritz, D. F. and Abraham, R. T. and Karnitz, L. M. and Sarkaria, J. N.},
month = apr,
year = {2000},
keywords = {Alkaloids, Antineoplastic Agents, Cell Cycle Proteins, Checkpoint Kinase 1, Checkpoint Kinase 2, DNA Damage, G2 Phase, Humans, Inhibitory Concentration 50, K562 Cells, Models, Biological, Phosphorylation, Phosphoserine, Protein Kinase Inhibitors, Protein Kinases, Protein-Serine-Threonine Kinases, Radiation-Sensitizing Agents, Signal Transduction, Staurosporine, cdc25 Phosphatases},
pages = {2108--2112},
}Genetic and environmental influences on behavioral disinhibition. Young, S E, Stallings, M C, Corley, R P, Krauter, K S, & Hewitt, J K American journal of medical genetics, 96(5):684–95, October, 2000.
Paper abstract bibtex
Paper abstract bibtex Comorbidity among childhood disruptive behavioral disorders is commonly reported in both epidemiologic and clinical studies. These problems are also associated with early substance use and other markers of behavioral disinhibition. Previous twin research has suggested that much of the covariation between antisocial behavior and alcohol dependence is due to common genetic influences. Similar results have been reported for conduct problems and hyperactivity. For the present study, an adolescent sample consisting of 172 MZ and 162 DZ twin pairs, recruited through the Colorado Twin Registry and the Colorado Longitudinal Twin Study were assessed using standardized psychiatric interviews and personality assessments. DSM-IV symptom counts for conduct disorder and attention deficit hyperactivity disorder, along with a measure of substance experimentation and novelty seeking, were used as indices of a latent behavioral disinhibition trait. A confirmatory factor model fit to individual-level data showed a strong common factor accounting for 16-42% of the observed variance in each measure. A common pathway model evaluating the genetic and environmental architecture of the latent phenotype suggested that behavioral disinhibition is highly heritable (a(2) = 0.84), and is not influenced significantly by shared environmental factors. A residual correlation between conduct disorder and substance experimentation was explained by shared environmental effects, and a residual correlation between attention deficit hyperactivity disorder and novelty seeking was accounted for by genetic dominance. These results suggest that a variety of adolescent problem behaviors may share a common underlying genetic risk.
@article{young_genetic_2000,
title = {Genetic and environmental influences on behavioral disinhibition.},
volume = {96},
issn = {0148-7299},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11054778},
abstract = {Comorbidity among childhood disruptive behavioral disorders is commonly reported in both epidemiologic and clinical studies. These problems are also associated with early substance use and other markers of behavioral disinhibition. Previous twin research has suggested that much of the covariation between antisocial behavior and alcohol dependence is due to common genetic influences. Similar results have been reported for conduct problems and hyperactivity. For the present study, an adolescent sample consisting of 172 MZ and 162 DZ twin pairs, recruited through the Colorado Twin Registry and the Colorado Longitudinal Twin Study were assessed using standardized psychiatric interviews and personality assessments. DSM-IV symptom counts for conduct disorder and attention deficit hyperactivity disorder, along with a measure of substance experimentation and novelty seeking, were used as indices of a latent behavioral disinhibition trait. A confirmatory factor model fit to individual-level data showed a strong common factor accounting for 16-42\% of the observed variance in each measure. A common pathway model evaluating the genetic and environmental architecture of the latent phenotype suggested that behavioral disinhibition is highly heritable (a(2) = 0.84), and is not influenced significantly by shared environmental factors. A residual correlation between conduct disorder and substance experimentation was explained by shared environmental effects, and a residual correlation between attention deficit hyperactivity disorder and novelty seeking was accounted for by genetic dominance. These results suggest that a variety of adolescent problem behaviors may share a common underlying genetic risk.},
number = {5},
urldate = {2015-04-13},
journal = {American journal of medical genetics},
author = {Young, S E and Stallings, M C and Corley, R P and Krauter, K S and Hewitt, J K},
month = oct,
year = {2000},
pmid = {11054778},
keywords = {Adolescent, Adolescent Behavior, Adolescent Behavior: psychology, Attention Deficit Disorder with Hyperactivity, Attention Deficit Disorder with Hyperactivity: gen, Comorbidity, Conduct Disorder, Conduct Disorder: genetics, Data Interpretation, Statistical, Environment, Humans, Inhibition (Psychology), Models, Genetic, Personality Disorders, Personality Disorders: genetics, Phenotype, Psychiatric Status Rating Scales, Psychology, Adolescent, Substance-Related Disorders, Substance-Related Disorders: genetics, Twins, Dizygotic, Twins, Dizygotic: genetics, Twins, Dizygotic: psychology, Twins, Monozygotic, Twins, Monozygotic: genetics, Twins, Monozygotic: psychology},
pages = {684--95},
}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}
}Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model. Williams, D J & Hall, K B Biophysical journal, 76(6):3192–205, June, 1999.
Paper doi abstract bibtex
Paper doi abstract bibtex Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.
@article{Williams1999,
title = {Unrestrained stochastic dynamics simulations of the {UUCG} tetraloop using an implicit solvation model.},
volume = {76},
issn = {0006-3495},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300288&tool=pmcentrez&rendertype=abstract},
doi = {10.1016/s0006-3495(99)77471-0},
abstract = {Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.},
number = {6},
journal = {Biophysical journal},
author = {Williams, D J and Hall, K B},
month = jun,
year = {1999},
pmid = {10354444},
keywords = {\#nosource, Base Sequence, Biophysical Phenomena, Biophysics, Computer Simulation, Models, Molecular, Nucleic Acid Conformation, RNA, RNA: chemistry, Solvents, Stochastic Processes, Thermodynamics},
pages = {3192--205},
}The conceptual structure of research utilization. Estabrooks, C., A. 1999.
bibtex
bibtex
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title = {The conceptual structure of research utilization},
type = {article},
year = {1999},
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author = {Estabrooks, C A}
}Do infants learn grammar with algebra or statistics?. Eimas, P. Science, 284(5413):435-6; author reply 436-7, 1999.
bibtex
bibtex
@Article{Eimas1999,
author = {PD Eimas},
journal = {Science},
title = {Do infants learn grammar with algebra or statistics?},
year = {1999},
number = {5413},
pages = {435-6; author reply 436-7},
volume = {284},
keywords = {Computing Methodologies, Human, Language, Learning, Mental Processes, Models, Theoretical, Stochastic Processes, Support, U.S. Gov't, Non-P.H.S., Cognition, Linguistics, Neural Networks (Computer), Practice (Psychology), Non-U.S. Gov't, Memory, Psychological, Task Performance and Analysis, Time Factors, Visual Perception, Adult, Attention, Discrimination Learning, Female, Male, Short-Term, Mental Recall, Orientation, Pattern Recognition, Visual, Perceptual Masking, Reading, Concept Formation, Form Perception, Animals, Corpus Striatum, Shrews, P.H.S., Visual Cortex, Visual Pathways, Acoustic Stimulation, Auditory Cortex, Auditory Perception, Cochlea, Ear, Gerbillinae, Glycine, Hearing, Neurons, Space Perception, Strychnine, Adolescent, Decision Making, Reaction Time, Astrocytoma, Brain Mapping, Brain Neoplasms, Cerebral Cortex, Electric Stimulation, Electrophysiology, Epilepsy, Temporal Lobe, Evoked Potentials, Frontal Lobe, Noise, Parietal Lobe, Scalp, Child, Language Development, Psycholinguistics, Brain, Perception, Speech, Vocalization, Animal, Discrimination (Psychology), Hippocampus, Rats, Calcium, Chelating Agents, Excitatory Postsynaptic Potentials, Glutamic Acid, Guanosine Diphosphate, In Vitro, Neuronal Plasticity, Pyramidal Cells, Receptors, AMPA, Metabotropic Glutamate, N-Methyl-D-Aspartate, Somatosensory Cortex, Synapses, Synaptic Transmission, Thionucleotides, Action Potentials, Calcium Channels, L-Type, Electric Conductivity, Entorhinal Cortex, Neurological, Long-Evans, Infant, Mathematics, Statistics, 9872745},
}1998 (1)
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},
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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}
}1997 (1)
Flow and Creativity. Csikszentmihalyi, M. NAMTA Journal, 22(2):60–97, 1997.
Paper abstract bibtex
Paper abstract bibtex Describes phases of the creative process, and historical and contemporary views of creativity, then presents a systems model of "Creativity," distinguished from the everyday creativity displayed by many people. Describes backgrounds and traits of "Creative" people, and concludes with comments on flow experience and "Creativity," asserting that understanding the principles of "Creativity" can help transform everyone's daily routine. (EV)
@article{csikszentmihalyi_flow_1997,
title = {Flow and {Creativity}},
volume = {22},
url = {https://eric.ed.gov/?id=EJ547968},
abstract = {Describes phases of the creative process, and historical and contemporary views of creativity, then presents a systems model of "Creativity," distinguished from the everyday creativity displayed by many people. Describes backgrounds and traits of "Creative" people, and concludes with comments on flow experience and "Creativity," asserting that understanding the principles of "Creativity" can help transform everyone's daily routine. (EV)},
language = {eng},
number = {2},
journal = {NAMTA Journal},
author = {Csikszentmihalyi, Mihaly},
year = {1997},
keywords = {Creativity, Models, Creative Thinking, Creative Development, Self Motivation, Personality Traits, Change Agents},
pages = {60--97}
}1996 (4)
Response properties of units in the posterior auditory field deprived of input from the ipsilateral primary auditory cortex. Kitzes, L. & Hollrigel, G. Hear Res, 100(1-2):120-30, 1996. as cited in i̧teNPHeil1998
abstract bibtex
abstract bibtex
The influence of the ipsilateral primary auditory field (AI) on the response properties of neurons in the posterior auditory field (Field P) was examined in three cats anesthetized with sodium pentobarbital. Rate/level functions were obtained, by extracellular recording, from single units in Field P before (n = 38) and after (n = 50) subpial aspiration of AI. The ablations were primarily confined to the medial ectosylvian gyrus, although in one case extended into the high-frequency portion of the anterior auditory field. Comparisons between the behavior of units isolated before and after AI ablation failed to demonstrate any changes in the response properties of neurons in Field P attributable to the ablation. Nonmonotonic response profiles, first spike latency, variability in latency, threshold and maximal discharge rates of the units to acoustic stimuli were not significantly altered by the AI ablation. These results indicate that the basic response properties of neurons in Field P do not depend on input from the ipsilateral AI. This suggests that these properties are most likely determined by thalamic input or by circuitry within Field P.
@Article{Kitzes1996,
author = {LM Kitzes and GS Hollrigel},
journal = {Hear Res},
title = {Response properties of units in the posterior auditory field deprived of input from the ipsilateral primary auditory cortex.},
year = {1996},
note = {as cited in \citeNP{Heil1998}},
number = {1-2},
pages = {120-30},
volume = {100},
abstract = {The influence of the ipsilateral primary auditory field (AI) on the
response properties of neurons in the posterior auditory field (Field
P) was examined in three cats anesthetized with sodium pentobarbital.
Rate/level functions were obtained, by extracellular recording, from
single units in Field P before (n = 38) and after (n = 50) subpial
aspiration of AI. The ablations were primarily confined to the medial
ectosylvian gyrus, although in one case extended into the high-frequency
portion of the anterior auditory field. Comparisons between the behavior
of units isolated before and after AI ablation failed to demonstrate
any changes in the response properties of neurons in Field P attributable
to the ablation. Nonmonotonic response profiles, first spike latency,
variability in latency, threshold and maximal discharge rates of
the units to acoustic stimuli were not significantly altered by the
AI ablation. These results indicate that the basic response properties
of neurons in Field P do not depend on input from the ipsilateral
AI. This suggests that these properties are most likely determined
by thalamic input or by circuitry within Field P.},
keywords = {Computing Methodologies, Human, Language, Learning, Mental Processes, Models, Theoretical, Stochastic Processes, Support, U.S. Gov't, Non-P.H.S., Cognition, Linguistics, Neural Networks (Computer), Practice (Psychology), Non-U.S. Gov't, Memory, Psychological, Task Performance and Analysis, Time Factors, Visual Perception, Adult, Attention, Discrimination Learning, Female, Male, Short-Term, Mental Recall, Orientation, Pattern Recognition, Visual, Perceptual Masking, Reading, Concept Formation, Form Perception, Animals, Corpus Striatum, Shrews, P.H.S., Visual Cortex, Visual Pathways, Acoustic Stimulation, Auditory Cortex, Auditory Perception, Cochlea, Ear, Gerbillinae, Glycine, Hearing, Neurons, Space Perception, Strychnine, Adolescent, Decision Making, Reaction Time, Astrocytoma, Brain Mapping, Brain Neoplasms, Cerebral Cortex, Electric Stimulation, Electrophysiology, Epilepsy, Temporal Lobe, Evoked Potentials, Frontal Lobe, Noise, Parietal Lobe, Scalp, Child, Language Development, Psycholinguistics, Brain, Perception, Speech, Vocalization, Animal, Discrimination (Psychology), Hippocampus, Rats, Calcium, Chelating Agents, Excitatory Postsynaptic Potentials, Glutamic Acid, Guanosine Diphosphate, In Vitro, Neuronal Plasticity, Pyramidal Cells, Receptors, AMPA, Metabotropic Glutamate, N-Methyl-D-Aspartate, Somatosensory Cortex, Synapses, Synaptic Transmission, Thionucleotides, Action Potentials, Calcium Channels, L-Type, Electric Conductivity, Entorhinal Cortex, Neurological, Long-Evans, Infant, Mathematics, Statistics, Probability Learning, Problem Solving, Psychophysics, Association Learning, Child Psychology, Habituation (Psychophysiology), Probability Theory, Analysis of Variance, Semantics, Symbolism, Behavior, Eye Movements, Macaca mulatta, Prefrontal Cortex, Cats, Dogs, Haplorhini, Photic Stimulation, Electroencephalography, Nervous System Physiology, Darkness, Grasshoppers, Light, Membrane Potentials, Neural Inhibition, Afferent, Picrotoxin, Vision, Deoxyglucose, Injections, Microspheres, Neural Pathways, Rhodamines, Choice Behavior, Speech Perception, Verbal Learning, Dominance, Cerebral, Fixation, Ocular, Language Tests, Random Allocation, Comparative Study, Saguinus, Sound Spectrography, Species Specificity, Audiometry, Auditory Threshold, Calibration, Data Interpretation, Statistical, Anesthesia, General, Electrodes, Implanted, Pitch Perception, Sound Localization, Paired-Associate Learning, Serial Learning, Auditory, Age Factors, Motion Perception, Brain Injuries, Computer Simulation, Blindness, Psychomotor Performance, Color Perception, Signal Detection (Psychology), Judgment, ROC Curve, Regression Analysis, 8922986},
}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},
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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}
}Isolation, characterization and electron microscopy analysis of a hemidiscoidal phycobilisome type from the cyanobacterium Anabaena sp PCC 7120. Ducret, A, Sidler, W, Wehrli, E, Frank, G, & Zuber, H European Journal of Biochemistry, 236(3):1010–1024, 1996.
Paper doi abstract bibtex
Paper doi abstract bibtex In this work we present the characterization of a hemidiscoidal phycobilisome type of the heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. The phycobilisome of this organism contains allophycocyanin, phycocyanin and phycoerythrocyanin, similar to the closely related thermophilic cyanobacterium Mastigocladus laminosus. Intact phycobilisomes exhibit an absorption maximum at 619 nm and two fluorescence maxima at 664 nm and 680 nm, corroborating the presence of a complete energy pathway along the antenna. Upon dissociation, the phycobiliproteins were released from the phycobilisome. One phycoerythrocyanin, one phycocyanin and three allophycocyanin complexes were isolated by ion-exchange chromatography and characterized by absorption and fluorescence spectroscopy and by SDS/PAGE. The polypeptides contained in the phycobilisome of Anabaena sp. PCC 7120 were subjected to SDS/PAGE, blotted onto poly(vinylidendifluoride) membranes and identified by amino-terminal sequence analysis. The amino-terminal sequences of the polypeptides belonging to the phycoerythrocyanin and phycocyanin families were identical with the derived sequences of their corresponding genes. Partial amino-terminal sequences of the polypeptides belonging to the allophycocyanin family are presented here. Our results show that the phycobiliproteins and linker polypeptides from Anabaena sp. PCC 7120 are similar to the phycobilisome components characterized in other cyanobacteria. The phycobilisome of Anabaena sp. PCC 7120 was extensively analyzed by electron microscopy. It differs from the common hemidiscoidal tricylindrical, six-rod phycobilisome type by a core domain consisting of five core cylinders surrounded by up to eight rods radiating in a hemidiscoidal manner. One rod is Linked to each basal core cylinder, whereas the remaining core cylinders bind two rods each, On the basis of the data presented in this work, a revised model for the hemidiscoidal pentacylindrical phycobilisome of Anabaena sp. PCC 7120, M. laminosus and Anabaena variabilis is proposed. This model accounts more accurately for the 'grape' pattern typically exhibited by these phycobilisomes in electron micrographs.
@article{ducret_isolation_1996,
title = {Isolation, characterization and electron microscopy analysis of a hemidiscoidal phycobilisome type from the cyanobacterium {Anabaena} sp {PCC} 7120},
volume = {236},
issn = {0014-2956},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8665889},
doi = {10.1111/j.1432-1033.1996.01010.x},
abstract = {In this work we present the characterization of a hemidiscoidal phycobilisome type of the heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. The phycobilisome of this organism contains allophycocyanin, phycocyanin and phycoerythrocyanin, similar to the closely related thermophilic cyanobacterium Mastigocladus laminosus. Intact phycobilisomes exhibit an absorption maximum at 619 nm and two fluorescence maxima at 664 nm and 680 nm, corroborating the presence of a complete energy pathway along the antenna. Upon dissociation, the phycobiliproteins were released from the phycobilisome. One phycoerythrocyanin, one phycocyanin and three allophycocyanin complexes were isolated by ion-exchange chromatography and characterized by absorption and fluorescence spectroscopy and by SDS/PAGE. The polypeptides contained in the phycobilisome of Anabaena sp. PCC 7120 were subjected to SDS/PAGE, blotted onto poly(vinylidendifluoride) membranes and identified by amino-terminal sequence analysis. The amino-terminal sequences of the polypeptides belonging to the phycoerythrocyanin and phycocyanin families were identical with the derived sequences of their corresponding genes. Partial amino-terminal sequences of the polypeptides belonging to the allophycocyanin family are presented here. Our results show that the phycobiliproteins and linker polypeptides from Anabaena sp. PCC 7120 are similar to the phycobilisome components characterized in other cyanobacteria. The phycobilisome of Anabaena sp. PCC 7120 was extensively analyzed by electron microscopy. It differs from the common hemidiscoidal tricylindrical, six-rod phycobilisome type by a core domain consisting of five core cylinders surrounded by up to eight rods radiating in a hemidiscoidal manner. One rod is Linked to each basal core cylinder, whereas the remaining core cylinders bind two rods each, On the basis of the data presented in this work, a revised model for the hemidiscoidal pentacylindrical phycobilisome of Anabaena sp. PCC 7120, M. laminosus and Anabaena variabilis is proposed. This model accounts more accurately for the 'grape' pattern typically exhibited by these phycobilisomes in electron micrographs.},
language = {English},
number = {3},
journal = {European Journal of Biochemistry},
author = {Ducret, A and Sidler, W and Wehrli, E and Frank, G and Zuber, H},
year = {1996},
keywords = {Amino Acid, Amino Acid Sequence, Anabaena, Bacterial Proteins, Cyanobacteria, Electrophoresis, Fluorescence, Light-Harvesting Protein Complexes, Models, Molecular Sequence Data, Molecular Weight, Peptide Fragments, Phycobilins, Phycobilisomes, Phycocyanin, Plant Proteins, Polyacrylamide Gel, Sequence Homology, Spectrometry, Spectrophotometry, Structural, Ultrafiltration, allophycocyanin-b, amino-acid-sequence, c-phycocyanin, core substructure, crystal-structure analysis, cyanobacterium, electron microscopy, light-harvesting antenna, linker-polypeptide complexes, mastigocladus-laminosus phycobilisomes, molecular characterization, photosynthesis, phycobiliprotein, phycobilisome, terminal energy acceptor},
pages = {1010--1024},
}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},
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citation_key = {Nelson1996},
folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
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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}
}1994 (3)
Repetition blindness between visually different items: The case of pictures and words. Bavelier, D Cognition, 51(3):199-236, 1994.
abstract bibtex
abstract bibtex
Repetition blindness (RB) is the failure to see or recall the second of two visually similar or identical items in rapid serial visual presentation. It was initially demonstrated by Kanwisher (1987), who proposed that a second token of a given word or object type cannot be established when the two items occur close in time. Bavelier and Potter (1992) showed that RB also occurs between visually different items that are phonologically similar. They proposed that RB may occur not only when the targets are physically similar, but also when they have to be registered or encoded in short-term memory (STM) along dimensions on which they are similar. This hypothesis predicts that RB between visually different items should not be restricted to words, but should occur with any stimuli, as long as the task requires these stimuli to be encoded along dimensions on which they are similar. Moreover, it also implies that a task that changes the preferred code of targets will affect the size of RB. The first prediction was confirmed by establishing RB between phonologically similar pictures and words, whether semantically related (the picture of a cat and the word "cat") or not (the picture of a sun and the word "son"), when using a task that requires phonological encoding (Experiments 1 and 2). The second prediction was also supported: the magnitude of RB depended on whether the task required similar or different codes for pictures and words (Experiments 3 and 4). These experiments confirm that RB between visually different items is due to the similarity of the codes initially used in STM. The results suggest that RB can occur at any step during the instantiation of a token, arising not only from a failure to create a new token, but also from a failure to stabilize an opened token. In this view, tokens are to be seen as dynamical entities, built over time as a function of type activation and task requirements, and varying in stability as a function of the information that is entered into them.
@Article{Bavelier1994,
author = {D Bavelier},
journal = {Cognition},
title = {Repetition blindness between visually different items: {T}he case of pictures and words.},
year = {1994},
number = {3},
pages = {199-236},
volume = {51},
abstract = {Repetition blindness (RB) is the failure to see or recall the second
of two visually similar or identical items in rapid serial visual
presentation. It was initially demonstrated by Kanwisher (1987),
who proposed that a second token of a given word or object type cannot
be established when the two items occur close in time. Bavelier and
Potter (1992) showed that RB also occurs between visually different
items that are phonologically similar. They proposed that RB may
occur not only when the targets are physically similar, but also
when they have to be registered or encoded in short-term memory (STM)
along dimensions on which they are similar. This hypothesis predicts
that RB between visually different items should not be restricted
to words, but should occur with any stimuli, as long as the task
requires these stimuli to be encoded along dimensions on which they
are similar. Moreover, it also implies that a task that changes the
preferred code of targets will affect the size of RB. The first prediction
was confirmed by establishing RB between phonologically similar pictures
and words, whether semantically related (the picture of a cat and
the word "cat") or not (the picture of a sun and the word "son"),
when using a task that requires phonological encoding (Experiments
1 and 2). The second prediction was also supported: the magnitude
of RB depended on whether the task required similar or different
codes for pictures and words (Experiments 3 and 4). These experiments
confirm that RB between visually different items is due to the similarity
of the codes initially used in STM. The results suggest that RB can
occur at any step during the instantiation of a token, arising not
only from a failure to create a new token, but also from a failure
to stabilize an opened token. In this view, tokens are to be seen
as dynamical entities, built over time as a function of type activation
and task requirements, and varying in stability as a function of
the information that is entered into them.},
keywords = {Computing Methodologies, Human, Language, Learning, Mental Processes, Models, Theoretical, Stochastic Processes, Support, U.S. Gov't, Non-P.H.S., Cognition, Linguistics, Neural Networks (Computer), Practice (Psychology), Non-U.S. Gov't, Memory, Psychological, Task Performance and Analysis, Time Factors, Visual Perception, Adult, Attention, Discrimination Learning, Female, Male, Short-Term, Mental Recall, Orientation, Pattern Recognition, Visual, Perceptual Masking, Reading, 8194301},
}Structure and stability of human telomeric sequence. Balagurumoorthy, P & Brahmachari, S K The Journal of biological chemistry, 269(34):21858–69, August, 1994.
Paper abstract bibtex
Paper abstract bibtex Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)n. We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T2AG3)4, d(G3T2A)3G3, and d(G3T2AG3) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G3T2A)3G3 and d(T2AG3)4 assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G3T2AG3) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide d(G3T2AG3) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T2AG3)4 suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.
@article{Balagurumoorthy1994,
title = {Structure and stability of human telomeric sequence.},
volume = {269},
issn = {0021-9258},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8063830},
abstract = {Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)n. We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T2AG3)4, d(G3T2A)3G3, and d(G3T2AG3) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G3T2A)3G3 and d(T2AG3)4 assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G3T2AG3) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide d(G3T2AG3) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T2AG3)4 suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.},
number = {34},
journal = {The Journal of biological chemistry},
author = {Balagurumoorthy, P and Brahmachari, S K},
month = aug,
year = {1994},
pmid = {8063830},
keywords = {\#nosource, Circular Dichroism, Diethyl Pyrocarbonate, Diethyl Pyrocarbonate: pharmacology, Humans, Hydrogen Bonding, Models, Molecular, Nucleic Acid, Nucleic Acid Conformation, Nucleic Acid Conformation: drug effects, Nucleic Acid Denaturation, Oligonucleotides, Oligonucleotides: chemistry, Potassium, Potassium Permanganate, Potassium Permanganate: pharmacology, Potassium: pharmacology, Repetitive Sequences, Sodium, Sodium: pharmacology, Sulfuric Acid Esters, Sulfuric Acid Esters: pharmacology, Telomere, Telomere: chemistry, Thermodynamics},
pages = {21858--69},
}Variability and stability in cognitive abilities are largely genetic later in life. Plomin, R, Pedersen, N L, Lichtenstein, P, & McClearn, G E Behavior genetics, 24(3):207–15, May, 1994.
Paper abstract bibtex
Paper abstract bibtex The powerful quantitative genetic design of identical and fraternal twins reared apart (112 pairs) and matched twins reared together (111 pairs) was employed to assess the extent of genetic influence on individual differences in cognitive abilities during the last half of the life span. General cognitive ability yielded a heritability estimate of about .80 in two assessments 3 years apart as part of the Swedish Adoption/Twin Study of Aging. This is one of the highest heritabilities reported for a behavioral trait. Across the two ages, average heritabilities are about .60 for verbal tests, .50 for spatial and speed-of-processing tests, and .40 for memory tests. For general cognitive ability, the phenotypic stability across the 3 years is .92 and stable genetic factors account for nearly 90% this stability. These findings suggest that general cognitive ability is a reasonable target for research that aims to identify specific genes for complex traits.
@article{plomin_variability_1994,
title = {Variability and stability in cognitive abilities are largely genetic later in life.},
volume = {24},
issn = {0001-8244},
url = {http://www.ncbi.nlm.nih.gov/pubmed/7945151},
abstract = {The powerful quantitative genetic design of identical and fraternal twins reared apart (112 pairs) and matched twins reared together (111 pairs) was employed to assess the extent of genetic influence on individual differences in cognitive abilities during the last half of the life span. General cognitive ability yielded a heritability estimate of about .80 in two assessments 3 years apart as part of the Swedish Adoption/Twin Study of Aging. This is one of the highest heritabilities reported for a behavioral trait. Across the two ages, average heritabilities are about .60 for verbal tests, .50 for spatial and speed-of-processing tests, and .40 for memory tests. For general cognitive ability, the phenotypic stability across the 3 years is .92 and stable genetic factors account for nearly 90\% this stability. These findings suggest that general cognitive ability is a reasonable target for research that aims to identify specific genes for complex traits.},
number = {3},
urldate = {2013-09-30},
journal = {Behavior genetics},
author = {Plomin, R and Pedersen, N L and Lichtenstein, P and McClearn, G E},
month = may,
year = {1994},
pmid = {7945151},
keywords = {Aging, Aging: psychology, Aptitude, Female, Humans, Intelligence, Intelligence: genetics, Male, Middle Aged, Models, Genetic, Social Environment, Twins, Twins, Dizygotic, Twins, Dizygotic: genetics, Twins, Dizygotic: psychology, Twins, Monozygotic, Twins, Monozygotic: genetics, Twins, Monozygotic: psychology, Twins: genetics, Twins: psychology},
pages = {207--15},
}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}
}1985 (1)
Responses of single neurones in cat auditory cortex to time-varying stimuli: Frequency-modulated tones of narrow excursion. Phillips, D., Mendelson, J., Cynader, M., & Douglas, R. Exp Brain Res, 58(3):443-54, 1985.
abstract bibtex
abstract bibtex
In the primary auditory cortex of cats anaesthetized with nitrous oxide, single neurones were examined with respect to their responses to tone bursts and linear modulations of the frequency of an on-going continuous tone. Using FM ramps of 2.0 kHz excursion and varying centre frequency, each of 39 neurones was examined for its preference for the direction of frequency change of a ramp whose centre frequency was varied in and around the neurone's response area. Direction preference was strictly associated with the slopes of the cell's spike count-versus-frequency function over the frequency range covered by the ramp. Preferences for upward- and downward-directed ramps were associated with the low- and high-frequency slopes of the spike count function, respectively. The strength of the cell's direction preference was associated with the relative steepness of the spike count function over the frequency range covered by the ramp. The timing of discharges elicited by the frequency modulations was found to be the sum of the cell's latent period for tone bursts plus the time after ramp onset that the stimulus frequency fell within the neurone's response area. The implications of these data for the processing of narrow and broad frequency-modulated ramps are discussed.
@Article{Phillips1985,
author = {DP Phillips and JR Mendelson and MS Cynader and RM Douglas},
journal = {Exp Brain Res},
title = {Responses of single neurones in cat auditory cortex to time-varying stimuli: {F}requency-modulated tones of narrow excursion.},
year = {1985},
number = {3},
pages = {443-54},
volume = {58},
abstract = {In the primary auditory cortex of cats anaesthetized with nitrous
oxide, single neurones were examined with respect to their responses
to tone bursts and linear modulations of the frequency of an on-going
continuous tone. Using FM ramps of 2.0 kHz excursion and varying
centre frequency, each of 39 neurones was examined for its preference
for the direction of frequency change of a ramp whose centre frequency
was varied in and around the neurone's response area. Direction preference
was strictly associated with the slopes of the cell's spike count-versus-frequency
function over the frequency range covered by the ramp. Preferences
for upward- and downward-directed ramps were associated with the
low- and high-frequency slopes of the spike count function, respectively.
The strength of the cell's direction preference was associated with
the relative steepness of the spike count function over the frequency
range covered by the ramp. The timing of discharges elicited by the
frequency modulations was found to be the sum of the cell's latent
period for tone bursts plus the time after ramp onset that the stimulus
frequency fell within the neurone's response area. The implications
of these data for the processing of narrow and broad frequency-modulated
ramps are discussed.},
keywords = {Computing Methodologies, Human, Language, Learning, Mental Processes, Models, Theoretical, Stochastic Processes, Support, U.S. Gov't, Non-P.H.S., Cognition, Linguistics, Neural Networks (Computer), Practice (Psychology), Non-U.S. Gov't, Memory, Psychological, Task Performance and Analysis, Time Factors, Visual Perception, Adult, Attention, Discrimination Learning, Female, Male, Short-Term, Mental Recall, Orientation, Pattern Recognition, Visual, Perceptual Masking, Reading, Concept Formation, Form Perception, Animals, Corpus Striatum, Shrews, P.H.S., Visual Cortex, Visual Pathways, Acoustic Stimulation, Auditory Cortex, Auditory Perception, Cochlea, Ear, Gerbillinae, Glycine, Hearing, Neurons, Space Perception, Strychnine, Adolescent, Decision Making, Reaction Time, Astrocytoma, Brain Mapping, Brain Neoplasms, Cerebral Cortex, Electric Stimulation, Electrophysiology, Epilepsy, Temporal Lobe, Evoked Potentials, Frontal Lobe, Noise, Parietal Lobe, Scalp, Child, Language Development, Psycholinguistics, Brain, Perception, Speech, Vocalization, Animal, Discrimination (Psychology), Hippocampus, Rats, Calcium, Chelating Agents, Excitatory Postsynaptic Potentials, Glutamic Acid, Guanosine Diphosphate, In Vitro, Neuronal Plasticity, Pyramidal Cells, Receptors, AMPA, Metabotropic Glutamate, N-Methyl-D-Aspartate, Somatosensory Cortex, Synapses, Synaptic Transmission, Thionucleotides, Action Potentials, Calcium Channels, L-Type, Electric Conductivity, Entorhinal Cortex, Neurological, Long-Evans, Infant, Mathematics, Statistics, Probability Learning, Problem Solving, Psychophysics, Association Learning, Child Psychology, Habituation (Psychophysiology), Probability Theory, Analysis of Variance, Semantics, Symbolism, Behavior, Eye Movements, Macaca mulatta, Prefrontal Cortex, Cats, Dogs, Haplorhini, Photic Stimulation, Electroencephalography, Nervous System Physiology, Darkness, Grasshoppers, Light, Membrane Potentials, Neural Inhibition, Afferent, Picrotoxin, Vision, Deoxyglucose, Injections, Microspheres, Neural Pathways, Rhodamines, Choice Behavior, Speech Perception, Verbal Learning, Dominance, Cerebral, Fixation, Ocular, Language Tests, Random Allocation, Comparative Study, Saguinus, Sound Spectrography, Species Specificity, Audiometry, Auditory Threshold, Calibration, Data Interpretation, Statistical, Anesthesia, General, Electrodes, Implanted, Pitch Perception, Sound Localization, Paired-Associate Learning, Serial Learning, Auditory, Age Factors, Motion Perception, Brain Injuries, Computer Simulation, Blindness, Psychomotor Performance, Color Perception, Signal Detection (Psychology), Judgment, ROC Curve, Regression Analysis, Music, Probability, Arm, Cerebrovascular Disorders, Hemiplegia, Movement, Muscle, Skeletal, Myoclonus, Robotics, Magnetoencephalography, Phonetics, Software, Speech Production Measurement, Epilepsies, Partial, Laterality, Stereotaxic Techniques, Germany, Speech Acoustics, Verbal Behavior, Child Development, Instinct, Brain Stem, Coma, Diagnosis, Differential, Hearing Disorders, Hearing Loss, Central, Neuroma, Acoustic, Dendrites, Down-Regulation, Patch-Clamp Techniques, Wistar, Up-Regulation, Aged, Aphasia, Middle Aged, Cones (Retina), Primates, Retina, Retinal Ganglion Cells, Tympanic Membrane, Cell Communication, Extremities, Biological, Motor Activity, Rana catesbeiana, Spinal Cord, Central Nervous System, Motion, Motor Cortex, Intelligence, Macaca fascicularis, Adoption, Critical Period (Psychology), France, Korea, Magnetic Resonance Imaging, Multilingualism, Auditory Pathways, Cochlear Nerve, Loudness Perception, Neural Conduction, 4007088},
}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}
}