Keyword: research support
2014 (1)
Performance-optimized hierarchical models predict neural responses in higher visual cortex. Yamins, D. L K, Hong, H., Cadieu, C. F, Solomon, E. A, Seibert, D., & DiCarlo, J. J Proc Natl Acad Sci U S A, 111(23):8619–8624, 2014. Place: United States ISBN: 1091-6490
doi abstract bibtex
doi abstract bibtex
The ventral visual stream underlies key human visual object recognition abilities. However, neural encoding in the higher areas of the ventral stream remains poorly understood. Here, we describe a modeling approach that yields a quantitatively accurate model of inferior temporal (IT) cortex, the highest ventral cortical area. Using high-throughput computational techniques, we discovered that, within a class of biologically plausible hierarchical neural network models, there is a strong correlation between a model's categorization performance and its ability to predict individual IT neural unit response data. To pursue this idea, we then identified a high-performing neural network that matches human performance on a range of recognition tasks. Critically, even though we did not constrain this model to match neural data, its top output layer turns out to be highly predictive of IT spiking responses to complex naturalistic images at both the single site and population levels. Moreover, the model's intermediate layers are highly predictive of neural responses in the V4 cortex, a midlevel visual area that provides the dominant cortical input to IT. These results show that performance optimization–applied in a biologically appropriate model class–can be used to build quantitative predictive models of neural processing
@article{Yamins2014,
title = {Performance-optimized hierarchical models predict neural responses in higher visual cortex.},
volume = {111},
doi = {10.1073/pnas.1403112111},
abstract = {The ventral visual stream underlies key human visual object recognition abilities. However, neural encoding in the higher areas of the ventral stream remains poorly understood. Here, we describe a modeling approach that yields a quantitatively accurate model of inferior temporal (IT) cortex, the highest ventral cortical area. Using high-throughput computational techniques, we discovered that, within a class of biologically plausible hierarchical neural network models, there is a strong correlation between a model's categorization performance and its ability to predict individual IT neural unit response data. To pursue this idea, we then identified a high-performing neural network that matches human performance on a range of recognition tasks. Critically, even though we did not constrain this model to match neural data, its top output layer turns out to be highly predictive of IT spiking responses to complex naturalistic images at both the single site and population levels. Moreover, the model's intermediate layers are highly predictive of neural responses in the V4 cortex, a midlevel visual area that provides the dominant cortical input to IT. These results show that performance optimization--applied in a biologically appropriate model class--can be used to build quantitative predictive models of neural processing},
language = {eng},
number = {23},
journal = {Proc Natl Acad Sci U S A},
author = {Yamins, Daniel L K and Hong, Ha and Cadieu, Charles F and Solomon, Ethan A and Seibert, Darren and DiCarlo, James J},
year = {2014},
pmid = {24812127},
note = {Place: United States
ISBN: 1091-6490},
keywords = {Algorithms, Animals, Deep, Humans, Macaca mulatta, Models, Neurological, Nerve Net, Neural Networks (Computer), Photic Stimulation, Psychomotor Performance, Recognition (Psychology), Visual Cortex, Visual Pathways, Visual Perception, research support, n.i.h., extramural, research support, u.s. gov't, non-p.h.s.},
pages = {8619--8624},
}2012 (1)
Preferential encoding of visual categories in parietal cortex compared with prefrontal cortex. Swaminathan, S. K & Freedman, D. J Nat Neurosci, 15(2):315–320, 2012. Place: United States ISBN: 1546-1726
doi abstract bibtex
doi abstract bibtex
The ability to recognize the behavioral relevance, or category membership, of sensory stimuli is critical for interpreting the meaning of events in our environment. Neurophysiological studies of visual categorization have found categorical representations of stimuli in prefrontal cortex (PFC), an area that is closely associated with cognitive and executive functions. Recent studies have also identified neuronal category signals in parietal areas that are typically associated with visual-spatial processing. It has been proposed that category-related signals in parietal cortex and other visual areas may result from 'top-down' feedback from PFC. We directly compared neuronal activity in the lateral intraparietal (LIP) area and PFC in monkeys performing a visual motion categorization task. We found that LIP showed stronger, more reliable and shorter latency category signals than PFC. These findings suggest that LIP is strongly involved in visual categorization and argue against the idea that parietal category signals arise as a result of feedback from PFC during this task
@article{swaminathan_preferential_2012,
title = {Preferential encoding of visual categories in parietal cortex compared with prefrontal cortex.},
volume = {15},
doi = {10.1038/nn.3016},
abstract = {The ability to recognize the behavioral relevance, or category membership, of sensory stimuli is critical for interpreting the meaning of events in our environment. Neurophysiological studies of visual categorization have found categorical representations of stimuli in prefrontal cortex (PFC), an area that is closely associated with cognitive and executive functions. Recent studies have also identified neuronal category signals in parietal areas that are typically associated with visual-spatial processing. It has been proposed that category-related signals in parietal cortex and other visual areas may result from 'top-down' feedback from PFC. We directly compared neuronal activity in the lateral intraparietal (LIP) area and PFC in monkeys performing a visual motion categorization task. We found that LIP showed stronger, more reliable and shorter latency category signals than PFC. These findings suggest that LIP is strongly involved in visual categorization and argue against the idea that parietal category signals arise as a result of feedback from PFC during this task},
language = {eng},
number = {2},
journal = {Nat Neurosci},
author = {Swaminathan, Sruthi K and Freedman, David J},
year = {2012},
pmid = {22246435},
note = {Place: United States
ISBN: 1546-1726},
keywords = {Action Potentials, Analysis of Variance, Animals, Brain Mapping, Macaca mulatta, Male, Parietal Lobe, Photic Stimulation, Prefrontal Cortex, ROC Curve, Sensory Receptor Cells, Visual Fields, Visual Pathways, research support, n.i.h., extramural, research support, non-u.s. gov't, research support, u.s. gov't, non-p.h.s.},
pages = {315--320},
}2011 (1)
Unraveling the distributed neural code of facial identity through spatiotemporal pattern analysis. Nestor, A., Plaut, D. C, & Behrmann, M. Proc Natl Acad Sci U S A, 108(24):9998–10003, 2011. Place: United States ISBN: 1091-6490
doi abstract bibtex
doi abstract bibtex
Face individuation is one of the most impressive achievements of our visual system, and yet uncovering the neural mechanisms subserving this feat appears to elude traditional approaches to functional brain data analysis. The present study investigates the neural code of facial identity perception with the aim of ascertaining its distributed nature and informational basis. To this end, we use a sequence of multivariate pattern analyses applied to functional magnetic resonance imaging (fMRI) data. First, we combine information-based brain mapping and dynamic discrimination analysis to locate spatiotemporal patterns that support face classification at the individual level. This analysis reveals a network of fusiform and anterior temporal areas that carry information about facial identity and provides evidence that the fusiform face area responds with distinct patterns of activation to different face identities. Second, we assess the information structure of the network using recursive feature elimination. We find that diagnostic information is distributed evenly among anterior regions of the mapped network and that a right anterior region of the fusiform gyrus plays a central role within the information network mediating face individuation. These findings serve to map out and characterize a cortical system responsible for individuation. More generally, in the context of functionally defined networks, they provide an account of distributed processing grounded in information-based architectures
@article{nestor_unraveling_2011,
title = {Unraveling the distributed neural code of facial identity through spatiotemporal pattern analysis.},
volume = {108},
doi = {10.1073/pnas.1102433108},
abstract = {Face individuation is one of the most impressive achievements of our visual system, and yet uncovering the neural mechanisms subserving this feat appears to elude traditional approaches to functional brain data analysis. The present study investigates the neural code of facial identity perception with the aim of ascertaining its distributed nature and informational basis. To this end, we use a sequence of multivariate pattern analyses applied to functional magnetic resonance imaging (fMRI) data. First, we combine information-based brain mapping and dynamic discrimination analysis to locate spatiotemporal patterns that support face classification at the individual level. This analysis reveals a network of fusiform and anterior temporal areas that carry information about facial identity and provides evidence that the fusiform face area responds with distinct patterns of activation to different face identities. Second, we assess the information structure of the network using recursive feature elimination. We find that diagnostic information is distributed evenly among anterior regions of the mapped network and that a right anterior region of the fusiform gyrus plays a central role within the information network mediating face individuation. These findings serve to map out and characterize a cortical system responsible for individuation. More generally, in the context of functionally defined networks, they provide an account of distributed processing grounded in information-based architectures},
language = {eng},
number = {24},
journal = {Proc Natl Acad Sci U S A},
author = {Nestor, Adrian and Plaut, David C and Behrmann, Marlene},
year = {2011},
pmid = {21628569},
note = {Place: United States
ISBN: 1091-6490},
keywords = {Adult, Brain Mapping, European Continental Ancestry Group, Face, Humans, Magnetic Resonance Imaging, Male, Pattern Recognition, Visual, Task Performance and Analysis, Temporal Lobe, Visual Perception, Young Adult, clinical trial, research support, non-u.s. gov't, research support, u.s. gov't, non-p.h.s.},
pages = {9998--10003},
}2010 (1)
The Basics of Scientific Writing in APA Style. Marek, P. Technical Report American Psychological Association, Washington DC, 2010.
bibtex
bibtex
@techreport{marek_basics_2010,
address = {Washington DC},
title = {The {Basics} of {Scientific} {Writing} in {APA} {Style}},
institution = {American Psychological Association},
author = {Marek, Pam},
year = {2010},
keywords = {APA, Adult, Age Factors, Aging, Economics, Employment, Female, Humans, Male, Middle Aged, Personnel Selection, PhD, Stereotyping, básicos tesis, escribir, non-u.s. gov't, publicar, research, research support, tesis}
}2009 (3)
A face feature space in the macaque temporal lobe. Freiwald, W. A, Tsao, D. Y, & Livingstone, M. S Nat Neurosci, 12(9):1187–1196, 2009. Place: United States ISBN: 1546-1726
doi abstract bibtex
doi abstract bibtex
The ability of primates to effortlessly recognize faces has been attributed to the existence of specialized face areas. One such area, the macaque middle face patch, consists almost entirely of cells that are selective for faces, but the principles by which these cells analyze faces are unknown. We found that middle face patch neurons detect and differentiate faces using a strategy that is both part based and holistic. Cells detected distinct constellations of face parts. Furthermore, cells were tuned to the geometry of facial features. Tuning was most often ramp-shaped, with a one-to-one mapping of feature magnitude to firing rate. Tuning amplitude depended on the presence of a whole, upright face and features were interpreted according to their position in a whole, upright face. Thus, cells in the middle face patch encode axes of a face space specialized for whole, upright faces
@article{freiwald_face_2009,
title = {A face feature space in the macaque temporal lobe.},
volume = {12},
doi = {10.1038/nn.2363},
abstract = {The ability of primates to effortlessly recognize faces has been attributed to the existence of specialized face areas. One such area, the macaque middle face patch, consists almost entirely of cells that are selective for faces, but the principles by which these cells analyze faces are unknown. We found that middle face patch neurons detect and differentiate faces using a strategy that is both part based and holistic. Cells detected distinct constellations of face parts. Furthermore, cells were tuned to the geometry of facial features. Tuning was most often ramp-shaped, with a one-to-one mapping of feature magnitude to firing rate. Tuning amplitude depended on the presence of a whole, upright face and features were interpreted according to their position in a whole, upright face. Thus, cells in the middle face patch encode axes of a face space specialized for whole, upright faces},
language = {eng},
number = {9},
journal = {Nat Neurosci},
author = {Freiwald, Winrich A and Tsao, Doris Y and Livingstone, Margaret S},
year = {2009},
pmid = {19668199},
note = {Place: United States
ISBN: 1546-1726},
keywords = {Action Potentials, Analysis of Variance, Animals, Face, Macaca mulatta, Magnetic Resonance Imaging, Male, Microelectrodes, Neurons, Photic Stimulation, Temporal Lobe, Time Factors, Visual Perception, research support, n.i.h., extramural, research support, non-u.s. gov't},
pages = {1187--1196},
}A high-throughput screening approach to discovering good forms of biologically inspired visual representation. Pinto, N., Doukhan, D., DiCarlo, J. J, & Cox, D. D PLoS Comput Biol, 5(11):e1000579, 2009. Place: United States ISBN: 1553-7358
doi abstract bibtex
doi abstract bibtex
While many models of biological object recognition share a common set of "broad-stroke" properties, the performance of any one model depends strongly on the choice of parameters in a particular instantiation of that model–e.g., the number of units per layer, the size of pooling kernels, exponents in normalization operations, etc. Since the number of such parameters (explicit or implicit) is typically large and the computational cost of evaluating one particular parameter set is high, the space of possible model instantiations goes largely unexplored. Thus, when a model fails to approach the abilities of biological visual systems, we are left uncertain whether this failure is because we are missing a fundamental idea or because the correct "parts" have not been tuned correctly, assembled at sufficient scale, or provided with enough training. Here, we present a high-throughput approach to the exploration of such parameter sets, leveraging recent advances in stream processing hardware (high-end NVIDIA graphic cards and the PlayStation 3's IBM Cell Processor). In analogy to high-throughput screening approaches in molecular biology and genetics, we explored thousands of potential network architectures and parameter instantiations, screening those that show promising object recognition performance for further analysis. We show that this approach can yield significant, reproducible gains in performance across an array of basic object recognition tasks, consistently outperforming a variety of state-of-the-art purpose-built vision systems from the literature. As the scale of available computational power continues to expand, we argue that this approach has the potential to greatly accelerate progress in both artificial vision and our understanding of the computational underpinning of biological vision.
@article{pinto_high-throughput_2009,
title = {A high-throughput screening approach to discovering good forms of biologically inspired visual representation.},
volume = {5},
doi = {10.1371/journal.pcbi.1000579},
abstract = {While many models of biological object recognition share a common set of "broad-stroke" properties, the performance of any one model depends strongly on the choice of parameters in a particular instantiation of that model--e.g., the number of units per layer, the size of pooling kernels, exponents in normalization operations, etc. Since the number of such parameters (explicit or implicit) is typically large and the computational cost of evaluating one particular parameter set is high, the space of possible model instantiations goes largely unexplored. Thus, when a model fails to approach the abilities of biological visual systems, we are left uncertain whether this failure is because we are missing a fundamental idea or because the correct "parts" have not been tuned correctly, assembled at sufficient scale, or provided with enough training. Here, we present a high-throughput approach to the exploration of such parameter sets, leveraging recent advances in stream processing hardware (high-end NVIDIA graphic cards and the PlayStation 3's IBM Cell Processor). In analogy to high-throughput screening approaches in molecular biology and genetics, we explored thousands of potential network architectures and parameter instantiations, screening those that show promising object recognition performance for further analysis. We show that this approach can yield significant, reproducible gains in performance across an array of basic object recognition tasks, consistently outperforming a variety of state-of-the-art purpose-built vision systems from the literature. As the scale of available computational power continues to expand, we argue that this approach has the potential to greatly accelerate progress in both artificial vision and our understanding of the computational underpinning of biological vision.},
language = {eng},
number = {11},
journal = {PLoS Comput Biol},
author = {Pinto, Nicolas and Doukhan, David and DiCarlo, James J and Cox, David D},
year = {2009},
pmid = {19956750},
note = {Place: United States
ISBN: 1553-7358},
keywords = {Algorithms, Animals, Artificial Intelligence, Biomimetics, Computer Simulation, EUREKA, Humans, MR Methods, Models, Neurological, Pattern Recognition, Automated, Pattern Recognition, Visual, To Read, Visual Cortex, research support, n.i.h., extramural, research support, non-u.s. gov't},
pages = {e1000579},
}Circular analysis in systems neuroscience: the dangers of double dipping. Kriegeskorte, N., Simmons, W K., Bellgowan, P. S F, & Baker, C. I Nat Neurosci, 12(5):535–540, 2009. Place: United States ISBN: 1546-1726
doi abstract bibtex
doi abstract bibtex
A neuroscientific experiment typically generates a large amount of data, of which only a small fraction is analyzed in detail and presented in a publication. However, selection among noisy measurements can render circular an otherwise appropriate analysis and invalidate results. Here we argue that systems neuroscience needs to adjust some widespread practices to avoid the circularity that can arise from selection. In particular, 'double dipping', the use of the same dataset for selection and selective analysis, will give distorted descriptive statistics and invalid statistical inference whenever the results statistics are not inherently independent of the selection criteria under the null hypothesis. To demonstrate the problem, we apply widely used analyses to noise data known to not contain the experimental effects in question. Spurious effects can appear in the context of both univariate activation analysis and multivariate pattern-information analysis. We suggest a policy for avoiding circularity.
@article{kriegeskorte_circular_2009,
title = {Circular analysis in systems neuroscience: the dangers of double dipping.},
volume = {12},
doi = {10.1038/nn.2303},
abstract = {A neuroscientific experiment typically generates a large amount of data, of which only a small fraction is analyzed in detail and presented in a publication. However, selection among noisy measurements can render circular an otherwise appropriate analysis and invalidate results. Here we argue that systems neuroscience needs to adjust some widespread practices to avoid the circularity that can arise from selection. In particular, 'double dipping', the use of the same dataset for selection and selective analysis, will give distorted descriptive statistics and invalid statistical inference whenever the results statistics are not inherently independent of the selection criteria under the null hypothesis. To demonstrate the problem, we apply widely used analyses to noise data known to not contain the experimental effects in question. Spurious effects can appear in the context of both univariate activation analysis and multivariate pattern-information analysis. We suggest a policy for avoiding circularity.},
language = {eng},
number = {5},
journal = {Nat Neurosci},
author = {Kriegeskorte, Nikolaus and Simmons, W Kyle and Bellgowan, Patrick S F and Baker, Chris I},
year = {2009},
pmid = {19396166},
note = {Place: United States
ISBN: 1546-1726},
keywords = {Animals, Artifacts, Data Collection, Data Interpretation, Statistical, Humans, Image Processing, Computer-Assisted, MR Methods, Magnetic Resonance Imaging, Neurosciences, Reproducibility of Results, Selection Bias, Systems Biology, research support, n.i.h., intramural, review},
pages = {535--540},
}2008 (3)
Effects of familiarity on neural activity in monkey inferior temporal lobe. Anderson, B., Mruczek, R. E B, Kawasaki, K., & Sheinberg, D. Cereb Cortex, 18(11):2540–2552, 2008. Place: United States ISBN: 1460-2199
doi abstract bibtex
doi abstract bibtex
Long-term familiarity facilitates recognition of visual stimuli. To better understand the neural basis for this effect, we measured the local field potential (LFP) and multiunit spiking activity (MUA) from the inferior temporal (IT) lobe of behaving monkeys in response to novel and familiar images. In general, familiar images evoked larger amplitude LFPs whereas MUA responses were greater for novel images. Familiarity effects were attenuated by image rotations in the picture plane of 45 degrees. Decreasing image contrast led to more pronounced decreases in LFP response magnitude for novel, compared with familiar images, and resulted in more selective MUA response profiles for familiar images. The shape of individual LFP traces could be used for stimulus classification, and classification performance was better for the familiar image category. Recording the visual and auditory evoked LFP at multiple depths showed significant alterations in LFP morphology with distance changes of 2 mm. In summary, IT cortex shows local processing differences for familiar and novel images at a time scale and in a manner consistent with the observed behavioral advantage for classifying familiar images and rapidly detecting novel stimuli.
@article{anderson_effects_2008,
title = {Effects of familiarity on neural activity in monkey inferior temporal lobe.},
volume = {18},
doi = {10.1093/cercor/bhn015},
abstract = {Long-term familiarity facilitates recognition of visual stimuli. To better understand the neural basis for this effect, we measured the local field potential (LFP) and multiunit spiking activity (MUA) from the inferior temporal (IT) lobe of behaving monkeys in response to novel and familiar images. In general, familiar images evoked larger amplitude LFPs whereas MUA responses were greater for novel images. Familiarity effects were attenuated by image rotations in the picture plane of 45 degrees. Decreasing image contrast led to more pronounced decreases in LFP response magnitude for novel, compared with familiar images, and resulted in more selective MUA response profiles for familiar images. The shape of individual LFP traces could be used for stimulus classification, and classification performance was better for the familiar image category. Recording the visual and auditory evoked LFP at multiple depths showed significant alterations in LFP morphology with distance changes of 2 mm. In summary, IT cortex shows local processing differences for familiar and novel images at a time scale and in a manner consistent with the observed behavioral advantage for classifying familiar images and rapidly detecting novel stimuli.},
language = {eng},
number = {11},
journal = {Cereb Cortex},
author = {Anderson, Britt and Mruczek, Ryan E B and Kawasaki, Keisuke and Sheinberg, David},
year = {2008},
pmid = {18296433},
note = {Place: United States
ISBN: 1460-2199},
keywords = {Acoustic Stimulation, Animals, Evoked Potentials, Visual, Eye Movements, Macaca mulatta, Male, Photic Stimulation, Psychomotor Performance, Recognition (Psychology), Temporal Lobe, research support, n.i.h., extramural, research support, u.s. gov't, non-p.h.s.},
pages = {2540--2552},
}Perceptual grouping and inverse fMRI activity patterns in human visual cortex. Fang, F., Kersten, D., & Murray, S. O J Vis, 8(7):2.1–9, 2008. Place: United States ISBN: 1534-7362
doi abstract bibtex
doi abstract bibtex
We used functional magnetic resonance imaging (fMRI) to measure activity in human visual cortex, including a higher object processing area, the lateral occipital complex (LOC), and primary visual cortex (V1), in response to a perceptually bistable stimulus whose elements were perceived as either grouped into a shape or randomly arranged. We found activity increases in the LOC and simultaneous reductions of activity in V1 when the elements were perceived as a coherent shape. Consistent with a number of inferential models of visual processing, our results suggest that feedback from higher visual areas to lower visual areas serves to reduce activity during perceptual grouping. The implications of these findings with respect to these models are discussed.
@article{fang_perceptual_2008,
title = {Perceptual grouping and inverse {fMRI} activity patterns in human visual cortex.},
volume = {8},
doi = {10.1167/8.7.2},
abstract = {We used functional magnetic resonance imaging (fMRI) to measure activity in human visual cortex, including a higher object processing area, the lateral occipital complex (LOC), and primary visual cortex (V1), in response to a perceptually bistable stimulus whose elements were perceived as either grouped into a shape or randomly arranged. We found activity increases in the LOC and simultaneous reductions of activity in V1 when the elements were perceived as a coherent shape. Consistent with a number of inferential models of visual processing, our results suggest that feedback from higher visual areas to lower visual areas serves to reduce activity during perceptual grouping. The implications of these findings with respect to these models are discussed.},
language = {eng},
number = {7},
journal = {J Vis},
author = {Fang, Fang and Kersten, Daniel and Murray, Scott O},
year = {2008},
pmid = {19146235},
note = {Place: United States
ISBN: 1534-7362},
keywords = {Adult, Eye Movements, Female, Humans, Magnetic Resonance Imaging, Male, Photic Stimulation, Reference Values, Visual Cortex, Visual Perception, comparative study, research support, n.i.h., extramural, research support, non-u.s. gov't},
pages = {2.1--9},
}The effects of visual stimulation and selective visual attention on rhythmic neuronal synchronization in macaque area V4. Fries, P., Womelsdorf, T., Oostenveld, R., & Desimone, R. J Neurosci, 28(18):4823–4835, 2008. Place: United States ISBN: 1529-2401
doi abstract bibtex
doi abstract bibtex
Selective attention lends relevant sensory input priority access to higher-level brain areas and ultimately to behavior. Recent studies have suggested that those neurons in visual areas that are activated by an attended stimulus engage in enhanced gamma-band (30-70 Hz) synchronization compared with neurons activated by a distracter. Such precise synchronization could enhance the postsynaptic impact of cells carrying behaviorally relevant information. Previous studies have used the local field potential (LFP) power spectrum or spike-LFP coherence (SFC) to indirectly estimate spike synchronization. Here, we directly demonstrate zero-phase gamma-band coherence among spike trains of V4 neurons. This synchronization was particularly evident during visual stimulation and enhanced by selective attention, thus confirming the pattern inferred from LFP power and SFC. We therefore investigated the time course of LFP gamma-band power and found rapid dynamics consistent with interactions of top-down spatial and feature attention with bottom-up saliency. In addition to the modulation of synchronization during visual stimulation, selective attention significantly changed the prestimulus pattern of synchronization. Attention inside the receptive field of the recorded neuronal population enhanced gamma-band synchronization and strongly reduced alpha-band (9-11 Hz) synchronization in the prestimulus period. These results lend further support for a functional role of rhythmic neuronal synchronization in attentional stimulus selection.
@article{fries_effects_2008,
title = {The effects of visual stimulation and selective visual attention on rhythmic neuronal synchronization in macaque area {V4}.},
volume = {28},
doi = {10.1523/JNEUROSCI.4499-07.2008},
abstract = {Selective attention lends relevant sensory input priority access to higher-level brain areas and ultimately to behavior. Recent studies have suggested that those neurons in visual areas that are activated by an attended stimulus engage in enhanced gamma-band (30-70 Hz) synchronization compared with neurons activated by a distracter. Such precise synchronization could enhance the postsynaptic impact of cells carrying behaviorally relevant information. Previous studies have used the local field potential (LFP) power spectrum or spike-LFP coherence (SFC) to indirectly estimate spike synchronization. Here, we directly demonstrate zero-phase gamma-band coherence among spike trains of V4 neurons. This synchronization was particularly evident during visual stimulation and enhanced by selective attention, thus confirming the pattern inferred from LFP power and SFC. We therefore investigated the time course of LFP gamma-band power and found rapid dynamics consistent with interactions of top-down spatial and feature attention with bottom-up saliency. In addition to the modulation of synchronization during visual stimulation, selective attention significantly changed the prestimulus pattern of synchronization. Attention inside the receptive field of the recorded neuronal population enhanced gamma-band synchronization and strongly reduced alpha-band (9-11 Hz) synchronization in the prestimulus period. These results lend further support for a functional role of rhythmic neuronal synchronization in attentional stimulus selection.},
language = {eng},
number = {18},
journal = {J Neurosci},
author = {Fries, Pascal and Womelsdorf, Thilo and Oostenveld, Robert and Desimone, Robert},
year = {2008},
pmid = {18448659},
note = {Place: United States
ISBN: 1529-2401},
keywords = {Animals, Attention, Color Perception, Cortical Synchronization, Evoked Potentials, Visual, Fourier Analysis, Macaca mulatta, Male, Neurons, Photic Stimulation, Psychophysics, Time Factors, Visual Cortex, research support, n.i.h., extramural, research support, n.i.h., intramural, research support, non-u.s. gov't},
pages = {4823--4835},
}2007 (7)
Object category structure in response patterns of neuronal population in monkey inferior temporal cortex. Kiani, R., Esteky, H., Mirpour, K., & Tanaka, K. J Neurophysiol, 97(6):4296–4309, 2007. Place: United States ISBN: 0022-3077
doi abstract bibtex
doi abstract bibtex
Our mental representation of object categories is hierarchically organized, and our rapid and seemingly effortless categorization ability is crucial for our daily behavior. Here, we examine responses of a large number (\textgreater600) of neurons in monkey inferior temporal (IT) cortex with a large number (\textgreater1,000) of natural and artificial object images. During the recordings, the monkeys performed a passive fixation task. We found that the categorical structure of objects is represented by the pattern of activity distributed over the cell population. Animate and inanimate objects created distinguishable clusters in the population code. The global category of animate objects was divided into bodies, hands, and faces. Faces were divided into primate and nonprimate faces, and the primate-face group was divided into human and monkey faces. Bodies of human, birds, and four-limb animals clustered together, whereas lower animals such as fish, reptile, and insects made another cluster. Thus the cluster analysis showed that IT population responses reconstruct a large part of our intuitive category structure, including the global division into animate and inanimate objects, and further hierarchical subdivisions of animate objects. The representation of categories was distributed in several respects, e.g., the similarity of response patterns to stimuli within a category was maintained by both the cells that maximally responded to the category and the cells that responded weakly to the category. These results advance our understanding of the nature of the IT neural code, suggesting an inherently categorical representation that comprises a range of categories including the amply investigated face category.
@article{kiani_object_2007,
title = {Object category structure in response patterns of neuronal population in monkey inferior temporal cortex.},
volume = {97},
doi = {10.1152/jn.00024.2007},
abstract = {Our mental representation of object categories is hierarchically organized, and our rapid and seemingly effortless categorization ability is crucial for our daily behavior. Here, we examine responses of a large number ({\textgreater}600) of neurons in monkey inferior temporal (IT) cortex with a large number ({\textgreater}1,000) of natural and artificial object images. During the recordings, the monkeys performed a passive fixation task. We found that the categorical structure of objects is represented by the pattern of activity distributed over the cell population. Animate and inanimate objects created distinguishable clusters in the population code. The global category of animate objects was divided into bodies, hands, and faces. Faces were divided into primate and nonprimate faces, and the primate-face group was divided into human and monkey faces. Bodies of human, birds, and four-limb animals clustered together, whereas lower animals such as fish, reptile, and insects made another cluster. Thus the cluster analysis showed that IT population responses reconstruct a large part of our intuitive category structure, including the global division into animate and inanimate objects, and further hierarchical subdivisions of animate objects. The representation of categories was distributed in several respects, e.g., the similarity of response patterns to stimuli within a category was maintained by both the cells that maximally responded to the category and the cells that responded weakly to the category. These results advance our understanding of the nature of the IT neural code, suggesting an inherently categorical representation that comprises a range of categories including the amply investigated face category.},
language = {eng},
number = {6},
journal = {J Neurophysiol},
author = {Kiani, Roozbeh and Esteky, Hossein and Mirpour, Koorosh and Tanaka, Keiji},
year = {2007},
pmid = {17428910},
note = {Place: United States
ISBN: 0022-3077},
keywords = {Action Potentials, Animals, Behavior, Animal, Brain Mapping, Cluster Analysis, Humans, Macaca mulatta, Neurons, Pattern Recognition, Visual, Photic Stimulation, Probability, Reaction Time, Temporal Lobe, Visual Pathways, research support, non-u.s. gov't},
pages = {4296--4309},
}Invariant object recognition with trace learning and multiple stimuli present during training. Stringer, S M, Rolls, E T, & Tromans, J M Network, 18(2):161–187, 2007. Place: England ISBN: 0954-898X
doi abstract bibtex
doi abstract bibtex
Over successive stages, the ventral visual system develops neurons that respond with view, size and position invariance to objects including faces. A major challenge is to explain how invariant representations of individual objects could develop given visual input from environments containing multiple objects. Here we show that the neurons in a 1-layer competitive network learn to represent combinations of three objects simultaneously present during training if the number of objects in the training set is low (e.g. 4), to represent combinations of two objects as the number of objects is increased to for e.g. 10, and to represent individual objects as the number of objects in the training set is increased further to for e.g. 20. We next show that translation invariant representations can be formed even when multiple stimuli are always present during training, by including a temporal trace in the learning rule. Finally, we show that these concepts can be extended to a multi-layer hierarchical network model (VisNet) of the ventral visual system. This approach provides a way to understand how a visual system can, by self-organizing competitive learning, form separate invariant representations of each object even when each object is presented in a scene with multiple other objects present, as in natural visual scenes.
@article{stringer_invariant_2007,
title = {Invariant object recognition with trace learning and multiple stimuli present during training.},
volume = {18},
doi = {10.1080/09548980701556055},
abstract = {Over successive stages, the ventral visual system develops neurons that respond with view, size and position invariance to objects including faces. A major challenge is to explain how invariant representations of individual objects could develop given visual input from environments containing multiple objects. Here we show that the neurons in a 1-layer competitive network learn to represent combinations of three objects simultaneously present during training if the number of objects in the training set is low (e.g. 4), to represent combinations of two objects as the number of objects is increased to for e.g. 10, and to represent individual objects as the number of objects in the training set is increased further to for e.g. 20. We next show that translation invariant representations can be formed even when multiple stimuli are always present during training, by including a temporal trace in the learning rule. Finally, we show that these concepts can be extended to a multi-layer hierarchical network model (VisNet) of the ventral visual system. This approach provides a way to understand how a visual system can, by self-organizing competitive learning, form separate invariant representations of each object even when each object is presented in a scene with multiple other objects present, as in natural visual scenes.},
language = {eng},
number = {2},
journal = {Network},
author = {Stringer, S M and Rolls, E T and Tromans, J M},
year = {2007},
pmid = {17966074},
note = {Place: England
ISBN: 0954-898X},
keywords = {Animals, Computer Simulation, Generalization (Psychology), Humans, Learning, Models, Neurological, Neural Networks (Computer), Neurons, Pattern Recognition, Visual, Photic Stimulation, Visual Cortex, Visual Pathways, research support, non-u.s. gov't},
pages = {161--187},
}Unsupervised learning of visual features through spike timing dependent plasticity. Masquelier, T. & Thorpe, S. J PLoS Comput Biol, 3(2):e31, 2007. Place: United States ISBN: 1553-7358
doi abstract bibtex
doi abstract bibtex
Spike timing dependent plasticity (STDP) is a learning rule that modifies synaptic strength as a function of the relative timing of pre- and postsynaptic spikes. When a neuron is repeatedly presented with similar inputs, STDP is known to have the effect of concentrating high synaptic weights on afferents that systematically fire early, while postsynaptic spike latencies decrease. Here we use this learning rule in an asynchronous feedforward spiking neural network that mimics the ventral visual pathway and shows that when the network is presented with natural images, selectivity to intermediate-complexity visual features emerges. Those features, which correspond to prototypical patterns that are both salient and consistently present in the images, are highly informative and enable robust object recognition, as demonstrated on various classification tasks. Taken together, these results show that temporal codes may be a key to understanding the phenomenal processing speed achieved by the visual system and that STDP can lead to fast and selective responses.
@article{masquelier_unsupervised_2007,
title = {Unsupervised learning of visual features through spike timing dependent plasticity.},
volume = {3},
doi = {10.1371/journal.pcbi.0030031},
abstract = {Spike timing dependent plasticity (STDP) is a learning rule that modifies synaptic strength as a function of the relative timing of pre- and postsynaptic spikes. When a neuron is repeatedly presented with similar inputs, STDP is known to have the effect of concentrating high synaptic weights on afferents that systematically fire early, while postsynaptic spike latencies decrease. Here we use this learning rule in an asynchronous feedforward spiking neural network that mimics the ventral visual pathway and shows that when the network is presented with natural images, selectivity to intermediate-complexity visual features emerges. Those features, which correspond to prototypical patterns that are both salient and consistently present in the images, are highly informative and enable robust object recognition, as demonstrated on various classification tasks. Taken together, these results show that temporal codes may be a key to understanding the phenomenal processing speed achieved by the visual system and that STDP can lead to fast and selective responses.},
language = {eng},
number = {2},
journal = {PLoS Comput Biol},
author = {Masquelier, Timothée and Thorpe, Simon J},
year = {2007},
pmid = {17305422},
note = {Place: United States
ISBN: 1553-7358},
keywords = {Action Potentials, Artificial Intelligence, Computer Simulation, Feedback, Models, Neurological, Nerve Net, Neuronal Plasticity, Neurons, Afferent, Pattern Recognition, Visual, Synaptic Transmission, Visual Cortex, research support, non-u.s. gov't},
pages = {e31},
}Modulation of neuronal interactions through neuronal synchronization. Womelsdorf, T., Schoffelen, J., Oostenveld, R., Singer, W., Desimone, R., Engel, A. K, & Fries, P. Science, 316(5831):1609–1612, 2007. Place: United States ISBN: 1095-9203
doi abstract bibtex
doi abstract bibtex
Brain processing depends on the interactions between neuronal groups. Those interactions are governed by the pattern of anatomical connections and by yet unknown mechanisms that modulate the effective strength of a given connection. We found that the mutual influence among neuronal groups depends on the phase relation between rhythmic activities within the groups. Phase relations supporting interactions between the groups preceded those interactions by a few milliseconds, consistent with a mechanistic role. These effects were specific in time, frequency, and space, and we therefore propose that the pattern of synchronization flexibly determines the pattern of neuronal interactions.
@article{womelsdorf_modulation_2007,
title = {Modulation of neuronal interactions through neuronal synchronization.},
volume = {316},
doi = {10.1126/science.1139597},
abstract = {Brain processing depends on the interactions between neuronal groups. Those interactions are governed by the pattern of anatomical connections and by yet unknown mechanisms that modulate the effective strength of a given connection. We found that the mutual influence among neuronal groups depends on the phase relation between rhythmic activities within the groups. Phase relations supporting interactions between the groups preceded those interactions by a few milliseconds, consistent with a mechanistic role. These effects were specific in time, frequency, and space, and we therefore propose that the pattern of synchronization flexibly determines the pattern of neuronal interactions.},
language = {eng},
number = {5831},
journal = {Science},
author = {Womelsdorf, Thilo and Schoffelen, Jan-Mathijs and Oostenveld, Robert and Singer, Wolf and Desimone, Robert and Engel, Andreas K and Fries, Pascal},
year = {2007},
pmid = {17569862},
note = {Place: United States
ISBN: 1095-9203},
keywords = {Action Potentials, Animals, Cats, Electrodes, Implanted, Electrophysiology, Macaca nemestrina, Male, Nerve Net, Neurons, Parietal Lobe, Temporal Lobe, Visual Pathways, research support, n.i.h., extramural, research support, non-u.s. gov't},
pages = {1609--1612},
}A feedforward architecture accounts for rapid categorization. Serre, T., Oliva, A., & Poggio, T. Proc Natl Acad Sci U S A, 104(15):6424–6429, 2007. Place: United States ISBN: 0027-8424
doi abstract bibtex
doi abstract bibtex
Primates are remarkably good at recognizing objects. The level of performance of their visual system and its robustness to image degradations still surpasses the best computer vision systems despite decades of engineering effort. In particular, the high accuracy of primates in ultra rapid object categorization and rapid serial visual presentation tasks is remarkable. Given the number of processing stages involved and typical neural latencies, such rapid visual processing is likely to be mostly feedforward. Here we show that a specific implementation of a class of feedforward theories of object recognition (that extend the Hubel and Wiesel simple-to-complex cell hierarchy and account for many anatomical and physiological constraints) can predict the level and the pattern of performance achieved by humans on a rapid masked animal vs. non-animal categorization task.
@article{serre_feedforward_2007,
title = {A feedforward architecture accounts for rapid categorization.},
volume = {104},
doi = {10.1073/pnas.0700622104},
abstract = {Primates are remarkably good at recognizing objects. The level of performance of their visual system and its robustness to image degradations still surpasses the best computer vision systems despite decades of engineering effort. In particular, the high accuracy of primates in ultra rapid object categorization and rapid serial visual presentation tasks is remarkable. Given the number of processing stages involved and typical neural latencies, such rapid visual processing is likely to be mostly feedforward. Here we show that a specific implementation of a class of feedforward theories of object recognition (that extend the Hubel and Wiesel simple-to-complex cell hierarchy and account for many anatomical and physiological constraints) can predict the level and the pattern of performance achieved by humans on a rapid masked animal vs. non-animal categorization task.},
language = {eng},
number = {15},
journal = {Proc Natl Acad Sci U S A},
author = {Serre, Thomas and Oliva, Aude and Poggio, Tomaso},
year = {2007},
pmid = {17404214},
note = {Place: United States
ISBN: 0027-8424},
keywords = {Adult, Humans, Models, Neurological, OR Journal Club, Pattern Recognition, Visual, Photic Stimulation, Psychophysics, Recognition (Psychology), Visual Perception, comparative study, research support, n.i.h., extramural, research support, non-u.s. gov't, research support, u.s. gov't, non-p.h.s.},
pages = {6424--6429},
}A multichip neuromorphic system for spike-based visual information processing. Vogelstein, R J., Mallik, U., Culurciello, E., Cauwenberghs, G., & Etienne-Cummings, R. Neural Comput, 19(9):2281–2300, 2007. Place: United States ISBN: 0899-7667
doi abstract bibtex
doi abstract bibtex
We present a multichip, mixed-signal VLSI system for spike-based vision processing. The system consists of an 80 x 60 pixel neuromorphic retina and a 4800 neuron silicon cortex with 4,194,304 synapses. Its functionality is illustrated with experimental data on multiple components of an attention-based hierarchical model of cortical object recognition, including feature coding, salience detection, and foveation. This model exploits arbitrary and reconfigurable connectivity between cells in the multichip architecture, achieved by asynchronously routing neural spike events within and between chips according to a memory-based look-up table. Synaptic parameters, including conductance and reversal potential, are also stored in memory and are used to dynamically configure synapse circuits within the silicon neurons.
@article{vogelstein_multichip_2007,
title = {A multichip neuromorphic system for spike-based visual information processing.},
volume = {19},
doi = {10.1162/neco.2007.19.9.2281},
abstract = {We present a multichip, mixed-signal VLSI system for spike-based vision processing. The system consists of an 80 x 60 pixel neuromorphic retina and a 4800 neuron silicon cortex with 4,194,304 synapses. Its functionality is illustrated with experimental data on multiple components of an attention-based hierarchical model of cortical object recognition, including feature coding, salience detection, and foveation. This model exploits arbitrary and reconfigurable connectivity between cells in the multichip architecture, achieved by asynchronously routing neural spike events within and between chips according to a memory-based look-up table. Synaptic parameters, including conductance and reversal potential, are also stored in memory and are used to dynamically configure synapse circuits within the silicon neurons.},
language = {eng},
number = {9},
journal = {Neural Comput},
author = {Vogelstein, R Jacob and Mallik, Udayan and Culurciello, Eugenio and Cauwenberghs, Gert and Etienne-Cummings, Ralph},
year = {2007},
pmid = {17650061},
note = {Place: United States
ISBN: 0899-7667},
keywords = {Action Potentials, Attention, Humans, Micromanipulation, Models, Neurological, Neural Networks (Computer), Neurons, Visual Pathways, research support, n.i.h., extramural, research support, u.s. gov't, non-p.h.s.},
pages = {2281--2300},
}TMS evidence for the involvement of the right occipital face area in early face processing. Pitcher, D., Walsh, V., Yovel, G., & Duchaine, B. Curr Biol, 17(18):1568–1573, 2007. Place: England ISBN: 0960-9822
doi abstract bibtex
doi abstract bibtex
Extensive research has demonstrated that several specialized cortical regions respond preferentially to faces. One such region, located in the inferior occipital gyrus, has been dubbed the occipital face area (OFA). The OFA is the first stage in two influential face-processing models, both of which suggest that it constructs an initial representation of a face, but how and when it does so remains unclear. The present study revealed that repetitive transcranial magnetic stimulation (rTMS) targeted at the right OFA (rOFA) disrupted accurate discrimination of face parts but had no effect on the discrimination of spacing between these parts. rTMS to left OFA had no effect. A matched part and spacing discrimination task that used house stimuli showed no impairment. In a second experiment, rTMS to rOFA replicated the face-part impairment but did not produce the same effect in an adjacent area, the lateral occipital cortex. A third experiment delivered double pulses of TMS separated by 40 ms at six periods after stimulus presentation during face-part discrimination. Accuracy dropped when pulses were delivered at 60 and 100 ms only. These findings indicate that the rOFA processes face-part information at an early stage in the face-processing stream.
@article{pitcher_tms_2007,
title = {{TMS} evidence for the involvement of the right occipital face area in early face processing.},
volume = {17},
doi = {10.1016/j.cub.2007.07.063},
abstract = {Extensive research has demonstrated that several specialized cortical regions respond preferentially to faces. One such region, located in the inferior occipital gyrus, has been dubbed the occipital face area (OFA). The OFA is the first stage in two influential face-processing models, both of which suggest that it constructs an initial representation of a face, but how and when it does so remains unclear. The present study revealed that repetitive transcranial magnetic stimulation (rTMS) targeted at the right OFA (rOFA) disrupted accurate discrimination of face parts but had no effect on the discrimination of spacing between these parts. rTMS to left OFA had no effect. A matched part and spacing discrimination task that used house stimuli showed no impairment. In a second experiment, rTMS to rOFA replicated the face-part impairment but did not produce the same effect in an adjacent area, the lateral occipital cortex. A third experiment delivered double pulses of TMS separated by 40 ms at six periods after stimulus presentation during face-part discrimination. Accuracy dropped when pulses were delivered at 60 and 100 ms only. These findings indicate that the rOFA processes face-part information at an early stage in the face-processing stream.},
language = {eng},
number = {18},
journal = {Curr Biol},
author = {Pitcher, David and Walsh, Vincent and Yovel, Galit and Duchaine, Bradley},
year = {2007},
pmid = {17764942},
note = {Place: England
ISBN: 0960-9822},
keywords = {Adult, Face, Female, Humans, Male, Occipital Lobe, Photic Stimulation, Transcranial Magnetic Stimulation, Visual Perception, research support, non-u.s. gov't},
pages = {1568--1573},
}2006 (4)
Characterization of canine superficial tumors using gray-scale B mode, color flow mapping, and spectral doppler ultrasonography--a multivariate study. Nyman, H., T., Kristensen, A., T., Lee, M., H., Martinussen, T., & McEvoy, F., J. Veterinary radiology & ultrasound : the official journal of the American College of Veterinary Radiology and the International Veterinary Radiology Association, 47(2):192-198, 2006.
abstract bibtex
abstract bibtex
Superficial tumors are not routinely evaluated by two- or three-dimensional diagnostic imaging methods as part of the staging of canine cancer patients, although superficial tumors are readily imaged by ultrasound. The objectives of this study were to characterize the ultrasonographic patterns of superficial tumors and to evaluate whether ultrasound can help discriminate between benign and malignant tumors in dogs. Superficial tumors (n=132) in 86 dogs were evaluated by B mode, color flow mapping, and spectral Doppler ultrasonography. Size, echogenicity, tumor border definition, invasiveness, acoustic transmission, presence and distribution of vascular flow to and within the tumor, as well as perfusion indices were measured. The tumors were classified as lipomas, benign tumors, atypical mammary tumors, and malignant tumors. Multivariate statistics using discriminant analysis was used to determine which parameters may be used to predict the status of the tumor. Tumor echogenicity, border shape, acoustic shadowing, total number of vessels to the tumor and the total flow amount are the parameters that in combination resulted in the lowest classification error (24%), meaning that on average three out of four tumors were correctly classified using these parameters. All the lipomas and atypical mammary tumors were classified correctly by ultrasonography. The results of this study show that ultrasonography has an important role in the evaluation of canine superficial tumors, particularly in the evaluation of tissue homogeneity and tumor vascularity.
@article{
title = {Characterization of canine superficial tumors using gray-scale B mode, color flow mapping, and spectral doppler ultrasonography--a multivariate study},
type = {article},
year = {2006},
identifiers = {[object Object]},
keywords = {Animals,Dog Diseases/pathology/physiopathology/ultrasonogr,Dogs,Female,Lipoma/blood supply/ultrasonography/veterinary,Male,Multivariate Analysis,Neoplasm Metastasis,Predictive Value of Tests,Pulsatile Flow,Regional Blood Flow,Research Support, Non-U.S. Gov't,Soft Tissue Neoplasms/blood supply/ultrasonography,Ultrasonography, Doppler, Color/veterinary},
pages = {192-198},
volume = {47},
city = {Department of Small Animal Clinical Sciences, The Royal Veterinary and Agricultural University Copenhagen, Dyrlaegevej 16, 1870 Frederiksberg C, Denmark. helena@dsr.kvl.dv},
id = {bf3d3202-f876-3f19-b88c-c47b56be7064},
created = {2016-09-06T13:34:42.000Z},
file_attached = {false},
profile_id = {cacab941-be62-3845-982b-a7700857a11d},
last_modified = {2016-09-07T14:54:39.000Z},
read = {false},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
source_type = {JOUR},
notes = {LR: 20061107; PUBM: Print; JID: 9209635; ppublish},
abstract = {Superficial tumors are not routinely evaluated by two- or three-dimensional diagnostic imaging methods as part of the staging of canine cancer patients, although superficial tumors are readily imaged by ultrasound. The objectives of this study were to characterize the ultrasonographic patterns of superficial tumors and to evaluate whether ultrasound can help discriminate between benign and malignant tumors in dogs. Superficial tumors (n=132) in 86 dogs were evaluated by B mode, color flow mapping, and spectral Doppler ultrasonography. Size, echogenicity, tumor border definition, invasiveness, acoustic transmission, presence and distribution of vascular flow to and within the tumor, as well as perfusion indices were measured. The tumors were classified as lipomas, benign tumors, atypical mammary tumors, and malignant tumors. Multivariate statistics using discriminant analysis was used to determine which parameters may be used to predict the status of the tumor. Tumor echogenicity, border shape, acoustic shadowing, total number of vessels to the tumor and the total flow amount are the parameters that in combination resulted in the lowest classification error (24%), meaning that on average three out of four tumors were correctly classified using these parameters. All the lipomas and atypical mammary tumors were classified correctly by ultrasonography. The results of this study show that ultrasonography has an important role in the evaluation of canine superficial tumors, particularly in the evaluation of tissue homogeneity and tumor vascularity.},
bibtype = {article},
author = {Nyman, H T and Kristensen, A T and Lee, M H and Martinussen, T and McEvoy, F J},
journal = {Veterinary radiology & ultrasound : the official journal of the American College of Veterinary Radiology and the International Veterinary Radiology Association},
number = {2}
}The fate of mutations surfing on the wave of a range expansion. Klopfstein, S., Currat, M., & Excoffier, L. Mol Biol Evol, 23(3):482-490, 2006.
![The fate of mutations surfing on the wave of a range expansion [pdf]](https://bibbase.org/img/filetypes/pdf.svg "pdf")
Paper ![The fate of mutations surfing on the wave of a range expansion [link]](https://bibbase.org/img/filetypes/link.svg "link")
Website abstract bibtex
Paper Website abstract bibtex Many species, including humans, have dramatically expanded their range in the past, and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance and thus reach a larger spatial distribution and a much higher frequency than would be expected in stationary populations. We study here this surfing phenomenon in more detail, by performing extensive computer simulations under a two-dimensional stepping-stone model. We find that the probability of survival of a new mutation depends to a large degree on its proximity to the edge of the wave. Demographic factors such as deme size, migration rate, and local growth rate also influence the fate of these new mutations. We also find that the final spatial and frequency distributions depend on the local deme size of a subdivided population. This latter result is discussed in the light of human expansions in Europe as it should allow one to distinguish between mutations having spread with Paleolithic or Neolithic expansions. By favoring the spread of new mutations, a consequence of the surfing phenomenon is to increase the rate of evolution of spatially expanding populations.
@article{
title = {The fate of mutations surfing on the wave of a range expansion},
type = {article},
year = {2006},
identifiers = {[object Object]},
keywords = {*Genetics, Population,*Geography,*Models, Genetic,*Mutation,Animals,Computer Simulation,Demography,Europe,Humans,Population Density,Research Support, Non-U.S. Gov't,Software},
pages = {482-490},
volume = {23},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16280540},
id = {e8b34b18-45f3-3c34-9619-fa45f993815d},
created = {2017-06-19T13:43:37.402Z},
file_attached = {true},
profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:43:37.526Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0737-4038 (Print)<m:linebreak/>Journal Article</m:note>},
abstract = {Many species, including humans, have dramatically expanded their range in the past, and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance and thus reach a larger spatial distribution and a much higher frequency than would be expected in stationary populations. We study here this surfing phenomenon in more detail, by performing extensive computer simulations under a two-dimensional stepping-stone model. We find that the probability of survival of a new mutation depends to a large degree on its proximity to the edge of the wave. Demographic factors such as deme size, migration rate, and local growth rate also influence the fate of these new mutations. We also find that the final spatial and frequency distributions depend on the local deme size of a subdivided population. This latter result is discussed in the light of human expansions in Europe as it should allow one to distinguish between mutations having spread with Paleolithic or Neolithic expansions. By favoring the spread of new mutations, a consequence of the surfing phenomenon is to increase the rate of evolution of spatially expanding populations.},
bibtype = {article},
author = {Klopfstein, S and Currat, M and Excoffier, L},
journal = {Mol Biol Evol},
number = {3}
}Two retinotopic visual areas in human lateral occipital cortex. Larsson, J. & Heeger, D. J J Neurosci, 26(51):13128–13142, 2006. Place: United States ISBN: 1529-2401
doi abstract bibtex
doi abstract bibtex
We describe two visual field maps, lateral occipital areas 1 (LO1) and 2 (LO2), in the human lateral occipital cortex between the dorsal part of visual area V3 and visual area V5/MT+. Each map contained a topographic representation of the contralateral visual hemifield. The eccentricity representations were shared with V1/V2/V3. The polar angle representation in LO1 extended from the lower vertical meridian (at the boundary with dorsal V3) through the horizontal to the upper vertical meridian (at the boundary with LO2). The polar angle representation in LO2 was the mirror-reversal of that in LO1. LO1 and LO2 overlapped with the posterior part of the object-selective lateral occipital complex and the kinetic occipital region (KO). The retinotopy and functional properties of LO1 and LO2 suggest that they correspond to two new human visual areas, which lack exact homologues in macaque visual cortex. The topography, stimulus selectivity, and anatomical location of LO1 and LO2 indicate that they integrate shape information from multiple visual submodalities in retinotopic coordinates.
@article{larsson_two_2006,
title = {Two retinotopic visual areas in human lateral occipital cortex.},
volume = {26},
doi = {10.1523/JNEUROSCI.1657-06.2006},
abstract = {We describe two visual field maps, lateral occipital areas 1 (LO1) and 2 (LO2), in the human lateral occipital cortex between the dorsal part of visual area V3 and visual area V5/MT+. Each map contained a topographic representation of the contralateral visual hemifield. The eccentricity representations were shared with V1/V2/V3. The polar angle representation in LO1 extended from the lower vertical meridian (at the boundary with dorsal V3) through the horizontal to the upper vertical meridian (at the boundary with LO2). The polar angle representation in LO2 was the mirror-reversal of that in LO1. LO1 and LO2 overlapped with the posterior part of the object-selective lateral occipital complex and the kinetic occipital region (KO). The retinotopy and functional properties of LO1 and LO2 suggest that they correspond to two new human visual areas, which lack exact homologues in macaque visual cortex. The topography, stimulus selectivity, and anatomical location of LO1 and LO2 indicate that they integrate shape information from multiple visual submodalities in retinotopic coordinates.},
language = {eng},
number = {51},
journal = {J Neurosci},
author = {Larsson, Jonas and Heeger, David J},
year = {2006},
pmid = {17182764},
note = {Place: United States
ISBN: 1529-2401},
keywords = {Brain Mapping, Humans, Motion Perception, Occipital Lobe, Photic Stimulation, Retina, Visual Cortex, Visual Fields, Visual Pathways, research support, n.i.h., extramural, research support, non-u.s. gov't},
pages = {13128--13142},
}A cortical region consisting entirely of face-selective cells. Tsao, D. Y, Freiwald, W. A, Tootell, R. B H, & Livingstone, M. S Science, 311(5761):670–674, 2006. Place: United States ISBN: 1095-9203
doi abstract bibtex
doi abstract bibtex
Face perception is a skill crucial to primates. In both humans and macaque monkeys, functional magnetic resonance imaging (fMRI) reveals a system of cortical regions that show increased blood flow when the subject views images of faces, compared with images of objects. However, the stimulus selectivity of single neurons within these fMRI-identified regions has not been studied. We used fMRI to identify and target the largest face-selective region in two macaques for single-unit recording. Almost all (97%) of the visually responsive neurons in this region were strongly face selective, indicating that a dedicated cortical area exists to support face processing in the macaque.
@article{tsao_cortical_2006,
title = {A cortical region consisting entirely of face-selective cells.},
volume = {311},
doi = {10.1126/science.1119983},
abstract = {Face perception is a skill crucial to primates. In both humans and macaque monkeys, functional magnetic resonance imaging (fMRI) reveals a system of cortical regions that show increased blood flow when the subject views images of faces, compared with images of objects. However, the stimulus selectivity of single neurons within these fMRI-identified regions has not been studied. We used fMRI to identify and target the largest face-selective region in two macaques for single-unit recording. Almost all (97\%) of the visually responsive neurons in this region were strongly face selective, indicating that a dedicated cortical area exists to support face processing in the macaque.},
language = {eng},
number = {5761},
journal = {Science},
author = {Tsao, Doris Y and Freiwald, Winrich A and Tootell, Roger B H and Livingstone, Margaret S},
year = {2006},
pmid = {16456083},
note = {Place: United States
ISBN: 1095-9203},
keywords = {Animals, Brain Mapping, Electrophysiology, Face, Form Perception, Humans, Macaca mulatta, Magnetic Resonance Imaging, Male, Neurons, Photic Stimulation, Synaptic Transmission, Temporal Lobe, research support, n.i.h., extramural, research support, non-u.s. gov't},
pages = {670--674},
}2005 (10)
Mapping genes of complex psychiatric diseases in Daghestan genetic isolates. Bulayeva, K., B., Leal, S., M., Pavlova, T., A., Kurbanov, R., M., Glatt, S., J., Bulayev, O., A., & Tsuang, M., T. Am J Med Genet B Neuropsychiatr Genet, 132(1):76-84, 2005.
Paper Website abstract bibtex
Paper Website abstract bibtex Genetic isolates, which provide outstanding opportunities for identification of susceptibility genes for complex diseases, can be classified as primary (having an ancient demographic history in a stable environment) or secondary (having a younger demographic history) Neel [1992: Minority populations: Genetics, demography, and health, pp. 1-13]. Daghestan contains 26 out of 50 indigenous Caucasus ethnicities that have been in existence for hundreds of generations in the same highland region. The ethnic groups are subdivided into numerous primary isolates. The founder effect and gene drift in these primary isolates may have caused aggregation of specific haplotypes with limited numbers of pathogenic alleles and loci in some isolates relative to others. These are expressed as inter-population differences in lifetime prevalence and features of certain complex clinical phenotypes and in patterns of genetic linkage and linkage disequilibrium (LD). Stable highland and ethnic-cultural environments have led to increased penetrance and a reduced number of phenocopies, which typically hamper the identification of any susceptibility genes for complex diseases. Owing to these characteristics of the primary isolates, a comparative linkage study in the primary isolates allows us to define the number of susceptibility genes for any complex disease and to identify the source of variability and non-replication of linkage analysis results. As part of an ongoing study, seven extended schizophrenia and one nonspecific mental retardation kindreds have been ascertained from Daghestan isolates. Lifetime morbid risk for schizophrenia in the isolates varied from 0 to 5%. A genome scan with markers spaced 10 cM apart was carried out on these pedigrees and linkage analysis was performed using descent graph methods, as implemented in Simwalk2. To identify regions containing susceptibility genes within these kindreds, we followed up those regions with non-parametric and parametric linkage analyses, with the choice of genetic model guided by the results obtained in the NPL. While the analyses are ongoing, the most positive findings were made in different isolated pedigrees on chromosomes 17p11, 3q24, and 22q for schizophrenia and on chromosome 12q for nonspecific mental retardation.
@article{
title = {Mapping genes of complex psychiatric diseases in Daghestan genetic isolates},
type = {article},
year = {2005},
identifiers = {[object Object]},
keywords = {Chromosome Mapping,Chromosomes, Human, Pair 12/genetics,Chromosomes, Human, Pair 17/genetics,Chromosomes, Human, Pair 22/genetics,Chromosomes, Human, Pair 3/genetics,Female,Founder Effect,Genetic Predisposition to Disease/*genetics,Humans,Linkage Disequilibrium,Male,Mental Disorders/ethnology/*genetics,Microsatellite Repeats,Multivariate Analysis,Pedigree,Phenotype,Research Support, Non-U.S. Gov't,Russia,Schizophrenia/ethnology/genetics},
pages = {76-84},
volume = {132},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15389762},
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abstract = {Genetic isolates, which provide outstanding opportunities for identification of susceptibility genes for complex diseases, can be classified as primary (having an ancient demographic history in a stable environment) or secondary (having a younger demographic history) Neel [1992: Minority populations: Genetics, demography, and health, pp. 1-13]. Daghestan contains 26 out of 50 indigenous Caucasus ethnicities that have been in existence for hundreds of generations in the same highland region. The ethnic groups are subdivided into numerous primary isolates. The founder effect and gene drift in these primary isolates may have caused aggregation of specific haplotypes with limited numbers of pathogenic alleles and loci in some isolates relative to others. These are expressed as inter-population differences in lifetime prevalence and features of certain complex clinical phenotypes and in patterns of genetic linkage and linkage disequilibrium (LD). Stable highland and ethnic-cultural environments have led to increased penetrance and a reduced number of phenocopies, which typically hamper the identification of any susceptibility genes for complex diseases. Owing to these characteristics of the primary isolates, a comparative linkage study in the primary isolates allows us to define the number of susceptibility genes for any complex disease and to identify the source of variability and non-replication of linkage analysis results. As part of an ongoing study, seven extended schizophrenia and one nonspecific mental retardation kindreds have been ascertained from Daghestan isolates. Lifetime morbid risk for schizophrenia in the isolates varied from 0 to 5%. A genome scan with markers spaced 10 cM apart was carried out on these pedigrees and linkage analysis was performed using descent graph methods, as implemented in Simwalk2. To identify regions containing susceptibility genes within these kindreds, we followed up those regions with non-parametric and parametric linkage analyses, with the choice of genetic model guided by the results obtained in the NPL. While the analyses are ongoing, the most positive findings were made in different isolated pedigrees on chromosomes 17p11, 3q24, and 22q for schizophrenia and on chromosome 12q for nonspecific mental retardation.},
bibtype = {article},
author = {Bulayeva, K B and Leal, S M and Pavlova, T A and Kurbanov, R M and Glatt, S J and Bulayev, O A and Tsuang, M T},
journal = {Am J Med Genet B Neuropsychiatr Genet},
number = {1}
}A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations. Evans, D., M. & Cardon, L., R. Am J Hum Genet, 76(4):681-687, 2005.
Paper Website abstract bibtex
Paper Website abstract bibtex Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D' and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates ( rho ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D' within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of rho correlate well across populations, but there is still evidence of population-specific spikes and troughs in rho values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping.
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title = {A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations},
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year = {2005},
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pages = {681-687},
volume = {76},
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abstract = {Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D' and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates ( rho ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D' within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of rho correlate well across populations, but there is still evidence of population-specific spikes and troughs in rho values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping.},
bibtype = {article},
author = {Evans, D M and Cardon, L R},
journal = {Am J Hum Genet},
number = {4}
}A video database of moving faces and people. O'Toole, A. J, Harms, J., Snow, S. L, Hurst, D. R, Pappas, M. R, Ayyad, J. H, & Abdi, H. IEEE Trans Pattern Anal Mach Intell, 27(5):812–816, 2005. Place: United States ISBN: 0162-8828
doi abstract bibtex
doi abstract bibtex
We describe a database of static images and video clips of human faces and people that is useful for testing algorithms for face and person recognition, head/eye tracking, and computer graphics modeling of natural human motions. For each person there are nine static "facial mug shots" and a series of video streams. The videos include a "moving facial mug shot," a facial speech clip, one or more dynamic facial expression clips, two gait videos, and a conversation video taken at a moderate distance from the camera. Complete data sets are available for 284 subjects and duplicate data sets, taken subsequent to the original set, are available for 229 subjects.
@article{otoole_video_2005,
title = {A video database of moving faces and people.},
volume = {27},
doi = {10.1109/TPAMI.2005.90},
abstract = {We describe a database of static images and video clips of human faces and people that is useful for testing algorithms for face and person recognition, head/eye tracking, and computer graphics modeling of natural human motions. For each person there are nine static "facial mug shots" and a series of video streams. The videos include a "moving facial mug shot," a facial speech clip, one or more dynamic facial expression clips, two gait videos, and a conversation video taken at a moderate distance from the camera. Complete data sets are available for 284 subjects and duplicate data sets, taken subsequent to the original set, are available for 229 subjects.},
language = {eng},
number = {5},
journal = {IEEE Trans Pattern Anal Mach Intell},
author = {O'Toole, Alice J and Harms, Joshua and Snow, Sarah L and Hurst, Dawn R and Pappas, Matthew R and Ayyad, Janet H and Abdi, Hervé},
year = {2005},
pmid = {15875802},
note = {Place: United States
ISBN: 0162-8828},
keywords = {Adult, Cluster Analysis, Database Management Systems, Databases, Factual, Face, Female, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Male, Models, Biological, Movement, Pattern Recognition, Automated, Photography, Reproducibility of Results, Sensitivity and Specificity, Video Recording, clinical trial, research support, u.s. gov't, non-p.h.s.},
pages = {812--816},
}Decoding the visual and subjective contents of the human brain. Kamitani, Y. & Tong, F. Nat Neurosci, 8(5):679–685, 2005. Place: United States ISBN: 1097-6256
doi abstract bibtex
doi abstract bibtex
The potential for human neuroimaging to read out the detailed contents of a person's mental state has yet to be fully explored. We investigated whether the perception of edge orientation, a fundamental visual feature, can be decoded from human brain activity measured with functional magnetic resonance imaging (fMRI). Using statistical algorithms to classify brain states, we found that ensemble fMRI signals in early visual areas could reliably predict on individual trials which of eight stimulus orientations the subject was seeing. Moreover, when subjects had to attend to one of two overlapping orthogonal gratings, feature-based attention strongly biased ensemble activity toward the attended orientation. These results demonstrate that fMRI activity patterns in early visual areas, including primary visual cortex (V1), contain detailed orientation information that can reliably predict subjective perception. Our approach provides a framework for the readout of fine-tuned representations in the human brain and their subjective contents.
@article{kamitani_decoding_2005,
title = {Decoding the visual and subjective contents of the human brain.},
volume = {8},
doi = {10.1038/nn1444},
abstract = {The potential for human neuroimaging to read out the detailed contents of a person's mental state has yet to be fully explored. We investigated whether the perception of edge orientation, a fundamental visual feature, can be decoded from human brain activity measured with functional magnetic resonance imaging (fMRI). Using statistical algorithms to classify brain states, we found that ensemble fMRI signals in early visual areas could reliably predict on individual trials which of eight stimulus orientations the subject was seeing. Moreover, when subjects had to attend to one of two overlapping orthogonal gratings, feature-based attention strongly biased ensemble activity toward the attended orientation. These results demonstrate that fMRI activity patterns in early visual areas, including primary visual cortex (V1), contain detailed orientation information that can reliably predict subjective perception. Our approach provides a framework for the readout of fine-tuned representations in the human brain and their subjective contents.},
language = {eng},
number = {5},
journal = {Nat Neurosci},
author = {Kamitani, Yukiyasu and Tong, Frank},
year = {2005},
pmid = {15852014},
note = {Place: United States
ISBN: 1097-6256},
keywords = {Adult, Algorithms, Attention, Brain Mapping, Cognition, Evoked Potentials, Visual, Humans, MR Methods, Magnetic Resonance Imaging, Models, Neurological, Orientation, Pattern Recognition, Visual, Photic Stimulation, Visual Cortex, Visual Pathways, Visual Perception, research support, n.i.h., extramural, research support, non-u.s. gov't, research support, u.s. gov't, p.h.s.},
pages = {679--685},
}How close are we to understanding v1?. Olshausen, B. A & Field, D. J Neural Comput, 17(8):1665–1699, 2005. Place: United States ISBN: 0899-7667
doi abstract bibtex
doi abstract bibtex
A wide variety of papers have reviewed what is known about the function of primary visual cortex. In this review, rather than stating what is known, we attempt to estimate how much is still unknown about V1 function. In particular, we identify five problems with the current view of V1 that stem largely from experimental and theoretical biases, in addition to the contributions of nonlinearities in the cortex that are not well understood. Our purpose is to open the door to new theories, a number of which we describe, along with some proposals for testing them.
@article{olshausen_how_2005,
title = {How close are we to understanding v1?},
volume = {17},
doi = {10.1162/0899766054026639},
abstract = {A wide variety of papers have reviewed what is known about the function of primary visual cortex. In this review, rather than stating what is known, we attempt to estimate how much is still unknown about V1 function. In particular, we identify five problems with the current view of V1 that stem largely from experimental and theoretical biases, in addition to the contributions of nonlinearities in the cortex that are not well understood. Our purpose is to open the door to new theories, a number of which we describe, along with some proposals for testing them.},
language = {eng},
number = {8},
journal = {Neural Comput},
author = {Olshausen, Bruno A and Field, David J},
year = {2005},
pmid = {15969914},
note = {Place: United States
ISBN: 0899-7667},
keywords = {Animals, Bias (Epidemiology), Humans, Models, Neurological, Neurons, Nonlinear Dynamics, Visual Cortex, Visual Pathways, comparative study, research support, non-u.s. gov't, review},
pages = {1665--1699},
}Promoting the implementation of practices that are supported by research: The national implementing evidence-based practice project. Torrey, W., C., Lynde, D., W., & Gorman, P. Child and adolescent psychiatric clinics of North America, 14(2):297-306, 2005.
Website abstract bibtex
Website abstract bibtex The National Implementing Evidence-Based Practice Project is an ongoing effort to promote the implementation of effective practices for adults who have severe mental illnesses. The project members designed and developed integrated packages of materials and services to help practice sites implement evidence-based practices and is field-testing the approach in eight states. These implementations are being evaluated carefully to learn how to make the technology transfer process more efficient in the future. This article describes the project and provides some early reflections on the implementation experience.
@article{
title = {Promoting the implementation of practices that are supported by research: The national implementing evidence-based practice project},
type = {article},
year = {2005},
identifiers = {[object Object]},
keywords = {Adolescent Health Services,Adolescent Psychiatry,Adult,Child Health Services,Evidence-Based Medicine,Humans,Mental Health Services,Pilot Projects,Program Development,Research Design,Research Support,United States,adolescent,authority,child,child psychiatry,consensus development,consultation,correlation analysis,experience,feasibility study,health care management,health care system,health program,health promotion,health service,human,medical literature,medical practice,medical research,mental disease,mental health,practice guideline,priority journal,quality of life,review,schizophrenia,social psychiatry},
pages = {297-306},
volume = {14},
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city = {Affiliation: West Central Behavioral Health, Dartmouth-Hitchcock, 2 Whipple Place, Lebanon, NH 03766, United States; Affiliation: W. Inst. New Hampshire-Dartmouth P., Dartmouth Medical School, 2 Whipple Place, Lebanon, NH 03766, United States; Corresponde},
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abstract = {The National Implementing Evidence-Based Practice Project is an ongoing effort to promote the implementation of effective practices for adults who have severe mental illnesses. The project members designed and developed integrated packages of materials and services to help practice sites implement evidence-based practices and is field-testing the approach in eight states. These implementations are being evaluated carefully to learn how to make the technology transfer process more efficient in the future. This article describes the project and provides some early reflections on the implementation experience.},
bibtype = {article},
author = {Torrey, W C and Lynde, D W and Gorman, P},
journal = {Child and adolescent psychiatric clinics of North America},
number = {2}
}Heritability and genetic constraints of life-history trait evolution in preindustrial humans. Pettay, J., E., Kruuk, L., E., B., Jokela, J., & Lummaa, V. Proc Natl Acad Sci U S A, 102(8):2838-2843, 2, 2005.
Paper Website abstract bibtex
Paper Website abstract bibtex An increasing number of studies have documented phenotypic selection on life-history traits in human populations, but less is known of the heritability and genetic constraints that mediate the response to selection on life-history traits in humans. We collected pedigree data for four generations of preindustrial (1745-1900) Finns who lived in premodern fertility and mortality conditions, and by using a restricted maximum-likelihood animal-model framework, we estimated the heritability of and genetic correlations between a suite of life-history traits and two alternative measures of fitness. First, we demonstrate high heritability of key life-history traits (fecundity, interbirth interval, age at last reproduction, and adult longevity) and measures of fitness (individual lambda and lifetime reproductive success) for females but not for males. This sex difference may have arisen because most of the measured traits are under physiological control of the female, such that a male's fitness in monogamous societies may depend mainly on the reproductive quality of his spouse. We found strong positive genetic correlations between female age at first reproduction and longevity, and between interbirth intervals and longevity, suggesting reduced life spans in females who either started to breed relatively early or who then bred frequently. Our results suggest that key female life-history traits in this premodern human population had high heritability and may have responded to natural selection. However genetic constraints between longevity and reproductive life-history traits may have constrained the evolution of life history and facilitated the maintenance of additive genetic variance in key life-history traits.
@article{
title = {Heritability and genetic constraints of life-history trait evolution in preindustrial humans},
type = {article},
year = {2005},
identifiers = {[object Object]},
keywords = {*Evolution,*Selection (Genetics),Animal,Animals,Biological Evolution,Female,Genetic,Genetic Variation,Humans,Likelihood Functions,Male,Models,Non-U.S. Gov't,Reproduction,Reproduction/*genetics,Reproduction: genetics,Research Support,Selection,Sex Characteristics,Variation (Genetics)},
pages = {2838-2843},
volume = {102},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15701704,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=549452&tool=pmcentrez&rendertype=abstract},
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notes = {<m:note> <m:bold>From Duplicate 1 ( </m:bold> <m:bold> </m:bold><m:bold><m:italic>Heritability and genetic constraints of life-history trait evolution in preindustrial humans</m:italic></m:bold><m:bold> </m:bold> <m:bold> - Pettay, J E; Kruuk, L E; Jokela, J; Lummaa, V )<m:linebreak/> </m:bold> <m:linebreak/>0027-8424<m:linebreak/>Journal Article<m:linebreak/> <m:linebreak/> </m:note>},
abstract = {An increasing number of studies have documented phenotypic selection on life-history traits in human populations, but less is known of the heritability and genetic constraints that mediate the response to selection on life-history traits in humans. We collected pedigree data for four generations of preindustrial (1745-1900) Finns who lived in premodern fertility and mortality conditions, and by using a restricted maximum-likelihood animal-model framework, we estimated the heritability of and genetic correlations between a suite of life-history traits and two alternative measures of fitness. First, we demonstrate high heritability of key life-history traits (fecundity, interbirth interval, age at last reproduction, and adult longevity) and measures of fitness (individual lambda and lifetime reproductive success) for females but not for males. This sex difference may have arisen because most of the measured traits are under physiological control of the female, such that a male's fitness in monogamous societies may depend mainly on the reproductive quality of his spouse. We found strong positive genetic correlations between female age at first reproduction and longevity, and between interbirth intervals and longevity, suggesting reduced life spans in females who either started to breed relatively early or who then bred frequently. Our results suggest that key female life-history traits in this premodern human population had high heritability and may have responded to natural selection. However genetic constraints between longevity and reproductive life-history traits may have constrained the evolution of life history and facilitated the maintenance of additive genetic variance in key life-history traits.},
bibtype = {article},
author = {Pettay, Jenni E and Kruuk, Loeske E B and Jokela, Jukka and Lummaa, Virpi},
journal = {Proc Natl Acad Sci U S A},
number = {8}
}The effect of the Neolithic expansion on European molecular diversity. Currat, M. & Excoffier, L. Proc Biol Sci, 272(1564):679-688, 2005.
abstract bibtex
abstract bibtex
We performed extensive and realistic simulations of the colonization process of Europe by Neolithic farmers, as well as their potential admixture and competition with local Palaeolithic hunter-gatherers. We find that minute amounts of gene flow between Palaeolithic and Neolithic populations should lead to a massive Palaeolithic contribution to the current gene pool of Europeans. This large Palaeolithic contribution is not expected under the demic diffusion (DD) model, which postulates that agriculture diffused over Europe by a massive migration of individuals from the Near East. However, genetic evidence in favour of this model mainly consisted in the observation of allele frequency clines over Europe, which are shown here to be equally probable under a pure DD or a pure acculturation model. The examination of the consequence of range expansions on single nucleotide polymorphism (SNP) diversity reveals that an ascertainment bias consisting of selecting SNPs with high frequencies will promote the observation of genetic clines (which are not expected for random SNPs) and will lead to multimodal mismatch distributions. We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations.
@article{
title = {The effect of the Neolithic expansion on European molecular diversity},
type = {article},
year = {2005},
identifiers = {[object Object]},
keywords = {*Demography,*Genetics, Population,*Models, Genetic,*Variation (Genetics),Chromosomes, Human, Y/*genetics,Comparative Study,Computer Simulation,DNA, Mitochondrial/genetics,Europe,European Continental Ancestry Group/*genetics,Gene Frequency,Humans,Polymorphism, Single Nucleotide/genetics,Research Support, U.S. Gov't, Non-P.H.S.},
pages = {679-688},
volume = {272},
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notes = {<m:note>Journal Article</m:note>},
abstract = {We performed extensive and realistic simulations of the colonization process of Europe by Neolithic farmers, as well as their potential admixture and competition with local Palaeolithic hunter-gatherers. We find that minute amounts of gene flow between Palaeolithic and Neolithic populations should lead to a massive Palaeolithic contribution to the current gene pool of Europeans. This large Palaeolithic contribution is not expected under the demic diffusion (DD) model, which postulates that agriculture diffused over Europe by a massive migration of individuals from the Near East. However, genetic evidence in favour of this model mainly consisted in the observation of allele frequency clines over Europe, which are shown here to be equally probable under a pure DD or a pure acculturation model. The examination of the consequence of range expansions on single nucleotide polymorphism (SNP) diversity reveals that an ascertainment bias consisting of selecting SNPs with high frequencies will promote the observation of genetic clines (which are not expected for random SNPs) and will lead to multimodal mismatch distributions. We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations.},
bibtype = {article},
author = {Currat, M and Excoffier, L},
journal = {Proc Biol Sci},
number = {1564}
}Morphing Marilyn into Maggie dissociates physical and identity face representations in the brain. Rotshtein, P., Henson, R. N A, Treves, A., Driver, J., & Dolan, R. J Nat Neurosci, 8(1):107–113, 2005. Place: United States ISBN: 1097-6256
doi abstract bibtex
doi abstract bibtex
How the brain represents different aspects of faces remains controversial. Here we presented subjects with stimuli drawn from morph continua between pairs of famous faces. In the paired presentations, a second face could be identical to the first, could share perceived identity but differ physically (30% along the morph continuum), or could differ physically by the same distance along the continuum (30%) but in the other direction. We show that, behaviorally, subjects are more likely to classify face pairs in the third paired presentation as different and that this effect is more pronounced for subjects who are more familiar with the faces. In functional magnetic resonance imaging (fMRI), inferior occipital gyrus (IOG) shows sensitivity to physical rather than to identity changes, whereas right fusiform gyrus (FFG) shows sensitivity to identity rather than to physical changes. Bilateral anterior temporal regions show sensitivity to identity change that varies with the subjects' pre-experimental familiarity with the faces. These findings provide neurobiological support for a hierarchical model of face perception.
@article{rotshtein_morphing_2005,
title = {Morphing {Marilyn} into {Maggie} dissociates physical and identity face representations in the brain.},
volume = {8},
doi = {10.1038/nn1370},
abstract = {How the brain represents different aspects of faces remains controversial. Here we presented subjects with stimuli drawn from morph continua between pairs of famous faces. In the paired presentations, a second face could be identical to the first, could share perceived identity but differ physically (30\% along the morph continuum), or could differ physically by the same distance along the continuum (30\%) but in the other direction. We show that, behaviorally, subjects are more likely to classify face pairs in the third paired presentation as different and that this effect is more pronounced for subjects who are more familiar with the faces. In functional magnetic resonance imaging (fMRI), inferior occipital gyrus (IOG) shows sensitivity to physical rather than to identity changes, whereas right fusiform gyrus (FFG) shows sensitivity to identity rather than to physical changes. Bilateral anterior temporal regions show sensitivity to identity change that varies with the subjects' pre-experimental familiarity with the faces. These findings provide neurobiological support for a hierarchical model of face perception.},
language = {eng},
number = {1},
journal = {Nat Neurosci},
author = {Rotshtein, Pia and Henson, Richard N A and Treves, Alessandro and Driver, Jon and Dolan, Raymond J},
year = {2005},
pmid = {15592463},
note = {Place: United States
ISBN: 1097-6256},
keywords = {Adult, Brain, Brain Mapping, Face, Female, Humans, Magnetic Resonance Imaging, Male, Occipital Lobe, Pattern Recognition, Visual, Temporal Lobe, research support, non-u.s. gov't},
pages = {107--113},
}View-independent coding of face identity in frontal and temporal cortices is modulated by familiarity: an event-related fMRI study. Pourtois, G., Schwartz, S., Seghier, M. L, Lazeyras, F., & Vuilleumier, P. Neuroimage, 24(4):1214–1224, 2005. Place: United States ISBN: 1053-8119
doi abstract bibtex
doi abstract bibtex
Face recognition is a unique visual skill enabling us to recognize a large number of person identities, despite many differences in the visual image from one exposure to another due to changes in viewpoint, illumination, or simply passage of time. Previous familiarity with a face may facilitate recognition when visual changes are important. Using event-related fMRI in 13 healthy observers, we studied the brain systems involved in extracting face identity independent of modifications in visual appearance during a repetition priming paradigm in which two different photographs of the same face (either famous or unfamiliar) were repeated at varying delays. We found that functionally defined face-selective areas in the lateral fusiform cortex showed no repetition effects for faces across changes in image views, irrespective of pre-existing familiarity, suggesting that face representations formed in this region do not generalize across different visual images, even for well-known faces. Repetition of different but easily recognizable views of an unfamiliar face produced selective repetition decreases in a medial portion of the right fusiform gyrus, whereas distinct views of a famous face produced repetition decreases in left middle temporal and left inferior frontal cortex selectively, but no decreases in fusiform cortex. These findings reveal that different views of the same familiar face may not be integrated within a single representation at initial perceptual stages subserved by the fusiform face areas, but rather involve later processing stages where more abstract identity information is accessed.
@article{pourtois_view-independent_2005,
title = {View-independent coding of face identity in frontal and temporal cortices is modulated by familiarity: an event-related {fMRI} study.},
volume = {24},
doi = {10.1016/j.neuroimage.2004.10.038},
abstract = {Face recognition is a unique visual skill enabling us to recognize a large number of person identities, despite many differences in the visual image from one exposure to another due to changes in viewpoint, illumination, or simply passage of time. Previous familiarity with a face may facilitate recognition when visual changes are important. Using event-related fMRI in 13 healthy observers, we studied the brain systems involved in extracting face identity independent of modifications in visual appearance during a repetition priming paradigm in which two different photographs of the same face (either famous or unfamiliar) were repeated at varying delays. We found that functionally defined face-selective areas in the lateral fusiform cortex showed no repetition effects for faces across changes in image views, irrespective of pre-existing familiarity, suggesting that face representations formed in this region do not generalize across different visual images, even for well-known faces. Repetition of different but easily recognizable views of an unfamiliar face produced selective repetition decreases in a medial portion of the right fusiform gyrus, whereas distinct views of a famous face produced repetition decreases in left middle temporal and left inferior frontal cortex selectively, but no decreases in fusiform cortex. These findings reveal that different views of the same familiar face may not be integrated within a single representation at initial perceptual stages subserved by the fusiform face areas, but rather involve later processing stages where more abstract identity information is accessed.},
language = {eng},
number = {4},
journal = {Neuroimage},
author = {Pourtois, Gilles and Schwartz, Sophie and Seghier, Mohamed L and Lazeyras, François and Vuilleumier, Patrik},
year = {2005},
pmid = {15670699},
note = {Place: United States
ISBN: 1053-8119},
keywords = {Adult, Cues, Famous Persons, Female, Frontal Lobe, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Photic Stimulation, Reaction Time, Recognition (Psychology), Sex Characteristics, Temporal Lobe, Visual Cortex, clinical trial, research support, non-u.s. gov't},
pages = {1214--1224},
}2004 (14)
Modelling the recent common ancestry of all living humans. Rohde, D., L., Olson, S., & Chang, J., T. Nature, 431(7008):562-566, 2004.
Paper abstract bibtex
Paper abstract bibtex If a common ancestor of all living humans is defined as an individual who is a genealogical ancestor of all present-day people, the most recent common ancestor (MRCA) for a randomly mating population would have lived in the very recent past. However, the random mating model ignores essential aspects of population substructure, such as the tendency of individuals to choose mates from the same social group, and the relative isolation of geographically separated groups. Here we show that recent common ancestors also emerge from two models incorporating substantial population substructure. One model, designed for simplicity and theoretical insight, yields explicit mathematical results through a probabilistic analysis. A more elaborate second model, designed to capture historical population dynamics in a more realistic way, is analysed computationally through Monte Carlo simulations. These analyses suggest that the genealogies of all living humans overlap in remarkable ways in the recent past. In particular, the MRCA of all present-day humans lived just a few thousand years ago in these models. Moreover, among all individuals living more than just a few thousand years earlier than the MRCA, each present-day human has exactly the same set of genealogical ancestors.
@article{
title = {Modelling the recent common ancestry of all living humans},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {*Computer Simulation,*Pedigree,*Phylogeny,Emigration and Immigration,Female,Geography,Humans,Male,Monte Carlo Method,Population Density,Population Dynamics,Reproduction,Research Support, U.S. Gov't, P.H.S.,Time Factors},
pages = {562-566},
volume = {431},
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source_type = {Journal Article},
notes = {<m:note>Journal Article</m:note>},
abstract = {If a common ancestor of all living humans is defined as an individual who is a genealogical ancestor of all present-day people, the most recent common ancestor (MRCA) for a randomly mating population would have lived in the very recent past. However, the random mating model ignores essential aspects of population substructure, such as the tendency of individuals to choose mates from the same social group, and the relative isolation of geographically separated groups. Here we show that recent common ancestors also emerge from two models incorporating substantial population substructure. One model, designed for simplicity and theoretical insight, yields explicit mathematical results through a probabilistic analysis. A more elaborate second model, designed to capture historical population dynamics in a more realistic way, is analysed computationally through Monte Carlo simulations. These analyses suggest that the genealogies of all living humans overlap in remarkable ways in the recent past. In particular, the MRCA of all present-day humans lived just a few thousand years ago in these models. Moreover, among all individuals living more than just a few thousand years earlier than the MRCA, each present-day human has exactly the same set of genealogical ancestors.},
bibtype = {article},
author = {Rohde, D L and Olson, S and Chang, J T},
journal = {Nature},
number = {7008}
}Clinical phenotype of families with longevity. Atzmon, G., Schechter, C., Greiner, W., Davidson, D., Rennert, G., & Barzilai, N. J Am Geriatr Soc, 52(2):274-277, 2004.
Paper Website abstract bibtex
Paper Website abstract bibtex OBJECTIVES: To determine whether offspring of centenarians acquired protection from age-related diseases. DESIGN: Case-control study. SETTING: The study was part of the Longevity Genes Project at Albert Einstein College of Medicine. PARTICIPANTS: Centenarians (n=145), offspring of centenarians (n=180), and spouses of the offspring of centenarians (n=75) as a control group. Two additional groups served as controls: age-matched Ashkenazi Jews, and an age-matched control group from the Third National Health and Nutrition Examination Survey. MEASUREMENTS: Self-reported family history of longevity; prevalence of hypertension, diabetes mellitus, heart attacks, and strokes; and objective measurements of body mass index and fat mass. RESULTS: Parents of centenarians (born in approximately 1870) had a markedly greater ( approximately sevenfold) "risk" for longevity (reaching ages 90-99), supporting the notion that genetics contributed to longevity in these families. The offspring of long-lived parents had significantly lower prevalence of hypertension (by 23%), diabetes mellitus (by 50%), heart attacks (by 60%), and strokes (no events reported) than several age-matched control groups. CONCLUSION: Offspring of centenarians may inherit significantly better health. The authors suggest that a cohort of these subjects and their spouses is ideal to study the phenotype and genotype of longevity and its interaction with the environment.
@article{
title = {Clinical phenotype of families with longevity},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {*Family Health,Aged,Aged, 80 and over,Cardiovascular Diseases/*epidemiology/genetics,Case-Control Studies,Chronic Disease/*epidemiology,European Continental Ancestry Group/statistics & n,Female,Humans,Israel/epidemiology,Jews/statistics & numerical data,Longevity/*genetics,Male,Matched-Pair Analysis,Middle Aged,Prevalence,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.,Risk,Sex Factors,Statistics, Nonparametric,United States/epidemiology},
pages = {274-277},
volume = {52},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14728640},
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abstract = {OBJECTIVES: To determine whether offspring of centenarians acquired protection from age-related diseases. DESIGN: Case-control study. SETTING: The study was part of the Longevity Genes Project at Albert Einstein College of Medicine. PARTICIPANTS: Centenarians (n=145), offspring of centenarians (n=180), and spouses of the offspring of centenarians (n=75) as a control group. Two additional groups served as controls: age-matched Ashkenazi Jews, and an age-matched control group from the Third National Health and Nutrition Examination Survey. MEASUREMENTS: Self-reported family history of longevity; prevalence of hypertension, diabetes mellitus, heart attacks, and strokes; and objective measurements of body mass index and fat mass. RESULTS: Parents of centenarians (born in approximately 1870) had a markedly greater ( approximately sevenfold) "risk" for longevity (reaching ages 90-99), supporting the notion that genetics contributed to longevity in these families. The offspring of long-lived parents had significantly lower prevalence of hypertension (by 23%), diabetes mellitus (by 50%), heart attacks (by 60%), and strokes (no events reported) than several age-matched control groups. CONCLUSION: Offspring of centenarians may inherit significantly better health. The authors suggest that a cohort of these subjects and their spouses is ideal to study the phenotype and genotype of longevity and its interaction with the environment.},
bibtype = {article},
author = {Atzmon, G and Schechter, C and Greiner, W and Davidson, D and Rennert, G and Barzilai, N},
journal = {J Am Geriatr Soc},
number = {2}
}Underlying principles of visual shape selectivity in posterior inferotemporal cortex. Brincat, S. L & Connor, C. E Nat Neurosci, 7(8):880–886, 2004. Place: United States ISBN: 1097-6256
doi abstract bibtex
doi abstract bibtex
Object perception depends on shape processing in the ventral visual pathway, which in monkeys culminates in inferotemporal cortex (IT). Here we provide a description of fundamental quantitative principles governing neural selectivity for complex shape in IT. By measuring responses to large, parametric sets of two-dimensional (2D) silhouette shapes, we found that neurons in posterior IT (Brodmann's areas TEO and posterior TE) integrate information about multiple contour elements (straight and curved edge fragments of the type represented in lower-level areas) using both linear and nonlinear mechanisms. This results in complex, distributed response patterns that cannot be characterized solely in terms of example stimuli. We explained these response patterns with tuning functions in multidimensional shape space and accurately predicted neural responses to the widely varying shapes in our stimulus set. Integration of contour element information in earlier stages of IT represents an important step in the transformation from low-level shape signals to complex object representation.
@article{brincat_underlying_2004,
title = {Underlying principles of visual shape selectivity in posterior inferotemporal cortex.},
volume = {7},
doi = {10.1038/nn1278},
abstract = {Object perception depends on shape processing in the ventral visual pathway, which in monkeys culminates in inferotemporal cortex (IT). Here we provide a description of fundamental quantitative principles governing neural selectivity for complex shape in IT. By measuring responses to large, parametric sets of two-dimensional (2D) silhouette shapes, we found that neurons in posterior IT (Brodmann's areas TEO and posterior TE) integrate information about multiple contour elements (straight and curved edge fragments of the type represented in lower-level areas) using both linear and nonlinear mechanisms. This results in complex, distributed response patterns that cannot be characterized solely in terms of example stimuli. We explained these response patterns with tuning functions in multidimensional shape space and accurately predicted neural responses to the widely varying shapes in our stimulus set. Integration of contour element information in earlier stages of IT represents an important step in the transformation from low-level shape signals to complex object representation.},
language = {eng},
number = {8},
journal = {Nat Neurosci},
author = {Brincat, Scott L and Connor, Charles E},
year = {2004},
pmid = {15235606},
note = {Place: United States
ISBN: 1097-6256},
keywords = {Action Potentials, Animals, Form Perception, Macaca mulatta, Models, Neurological, Neurons, Temporal Lobe, Visual Pathways, Visual Perception, research support, non-u.s. gov't, research support, u.s. gov't, p.h.s.},
pages = {880--886},
}Optimality principles in sensorimotor control. Todorov, E. Nat Neurosci, 7(9):907-15, 2004.
doi abstract bibtex
doi abstract bibtex
The sensorimotor system is a product of evolution, development, learning and adaptation-which work on different time scales to improve behavioral performance. Consequently, many theories of motor function are based on 'optimal performance': they quantify task goals as cost functions, and apply the sophisticated tools of optimal control theory to obtain detailed behavioral predictions. The resulting models, although not without limitations, have explained more empirical phenomena than any other class. Traditional emphasis has been on optimizing desired movement trajectories while ignoring sensory feedback. Recent work has redefined optimality in terms of feedback control laws, and focused on the mechanisms that generate behavior online. This approach has allowed researchers to fit previously unrelated concepts and observations into what may become a unified theoretical framework for interpreting motor function. At the heart of the framework is the relationship between high-level goals, and the real-time sensorimotor control strategies most suitable for accomplishing those goals.
@Article{Todorov2004,
author = {Emanuel Todorov},
journal = {Nat Neurosci},
title = {Optimality principles in sensorimotor control.},
year = {2004},
number = {9},
pages = {907-15},
volume = {7},
abstract = {The sensorimotor system is a product of evolution, development, learning
and adaptation-which work on different time scales to improve behavioral
performance. Consequently, many theories of motor function are based
on 'optimal performance': they quantify task goals as cost functions,
and apply the sophisticated tools of optimal control theory to obtain
detailed behavioral predictions. The resulting models, although not
without limitations, have explained more empirical phenomena than
any other class. Traditional emphasis has been on optimizing desired
movement trajectories while ignoring sensory feedback. Recent work
has redefined optimality in terms of feedback control laws, and focused
on the mechanisms that generate behavior online. This approach has
allowed researchers to fit previously unrelated concepts and observations
into what may become a unified theoretical framework for interpreting
motor function. At the heart of the framework is the relationship
between high-level goals, and the real-time sensorimotor control
strategies most suitable for accomplishing those goals.},
doi = {10.1038/nn1309},
keywords = {Adaptation, Afferent Pathways, Algorithms, Animals, Arm, Artifacts, Central Nervous System, Computer Simulation, Efferent Pathways, Extramural, Feedback, Humans, Linear Models, Models, Movement, N.I.H., Neurological, Normal Distribution, P.H.S., Physiological, Psychomotor Performance, Research Support, Stochastic Processes, U.S. Gov't, 15332089},
}The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology. Freimer, N. & Sabatti, C. Nat Genet, 36(10):1045-1051, 2004.
Paper abstract bibtex
Paper abstract bibtex Efforts to identify gene variants associated with susceptibility to common diseases use three approaches: pedigree and affected sib-pair linkage studies and association studies of population samples. The different aims of these study designs reflect their derivation from biological versus epidemiological traditions. Similar principles regarding determination of the evidence levels required to consider the results statistically significant apply to both linkage and association studies, however. Such determination requires explicit attention to the prior probability of particular findings, as well as appropriate correction for multiple comparisons. For most common diseases, increasing the sample size in a study is a crucial step in achieving statistically significant genetic mapping results. Recent studies suggest that the technology and statistical methodology will soon be available to make well-powered studies feasible using any of these approaches.
@article{
title = {The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {Chromosome Mapping,Epidemiologic Methods,Genetic Diseases, Inborn/epidemiology/*genetics,Humans,Linkage (Genetics),Pedigree,Phenotype,Research Support, U.S. Gov't, P.H.S.},
pages = {1045-1051},
volume = {36},
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source_type = {Journal Article},
notes = {<m:note>Journal Article<m:linebreak/>Review</m:note>},
abstract = {Efforts to identify gene variants associated with susceptibility to common diseases use three approaches: pedigree and affected sib-pair linkage studies and association studies of population samples. The different aims of these study designs reflect their derivation from biological versus epidemiological traditions. Similar principles regarding determination of the evidence levels required to consider the results statistically significant apply to both linkage and association studies, however. Such determination requires explicit attention to the prior probability of particular findings, as well as appropriate correction for multiple comparisons. For most common diseases, increasing the sample size in a study is a crucial step in achieving statistically significant genetic mapping results. Recent studies suggest that the technology and statistical methodology will soon be available to make well-powered studies feasible using any of these approaches.},
bibtype = {article},
author = {Freimer, N and Sabatti, C},
journal = {Nat Genet},
number = {10}
}Linkage disequilibrium in young genetically isolated Dutch population. Aulchenko, Y., S., Heutink, P., Mackay, I., Bertoli-Avella, A., M., Pullen, J., Vaessen, N., Rademaker, T., A., Sandkuijl, L., A., Cardon, L., Oostra, B., & van Duijn, C., M. Eur J Hum Genet, 12(7):527-534, 2004.
Paper Website abstract bibtex
Paper Website abstract bibtex The design and feasibility of genetic studies of complex diseases are critically dependent on the extent and distribution of linkage disequilibrium (LD) across the genome and between different populations. We have examined genomewide and region-specific LD in a young genetically isolated population identified in the Netherlands by genotyping approximately 800 Short Tandem Repeat markers distributed genomewide across 58 individuals. Several regions were analyzed further using a denser marker map. The permutation-corrected measure of LD was used for analysis. A significant (P<0.0004) relation between LD and genetic distance on a genomewide scale was found. Distance explained 4% of the total LD variation. For fine-mapping data, distance accounted for a larger proportion of LD variation (up to 39%). A notable similarity in the genomewide distribution of LD was revealed between this population and other young genetically isolated populations from Micronesia and Costa Rica. Our study population and experiment was simulated in silico to confirm our knowledge of the history of the population. High agreement was observed between results of analysis of simulated and empirical data. We conclude that our population shows a high level of LD similar to that demonstrated previously in other young genetic isolates. In Europe, there may be a large number of young genetically isolated populations that are similar in history to ours. In these populations, a similar degree of LD is expected and thus they may be effectively used for linkage or LD mapping.
@article{
title = {Linkage disequilibrium in young genetically isolated Dutch population},
type = {article},
year = {2004},
identifiers = {[object Object]},
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pages = {527-534},
volume = {12},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15054401},
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notes = {<m:note>1018-4813 (Print)<m:linebreak/>Journal Article</m:note>},
abstract = {The design and feasibility of genetic studies of complex diseases are critically dependent on the extent and distribution of linkage disequilibrium (LD) across the genome and between different populations. We have examined genomewide and region-specific LD in a young genetically isolated population identified in the Netherlands by genotyping approximately 800 Short Tandem Repeat markers distributed genomewide across 58 individuals. Several regions were analyzed further using a denser marker map. The permutation-corrected measure of LD was used for analysis. A significant (P<0.0004) relation between LD and genetic distance on a genomewide scale was found. Distance explained 4% of the total LD variation. For fine-mapping data, distance accounted for a larger proportion of LD variation (up to 39%). A notable similarity in the genomewide distribution of LD was revealed between this population and other young genetically isolated populations from Micronesia and Costa Rica. Our study population and experiment was simulated in silico to confirm our knowledge of the history of the population. High agreement was observed between results of analysis of simulated and empirical data. We conclude that our population shows a high level of LD similar to that demonstrated previously in other young genetic isolates. In Europe, there may be a large number of young genetically isolated populations that are similar in history to ours. In these populations, a similar degree of LD is expected and thus they may be effectively used for linkage or LD mapping.},
bibtype = {article},
author = {Aulchenko, Y S and Heutink, P and Mackay, I and Bertoli-Avella, A M and Pullen, J and Vaessen, N and Rademaker, T A and Sandkuijl, L A and Cardon, L and Oostra, B and van Duijn, C M},
journal = {Eur J Hum Genet},
number = {7}
}Origin and spread of the 1278insTATC mutation causing Tay-Sachs disease in Ashkenazi Jews: genetic drift as a robust and parsimonious hypothesis. Frisch, A., Colombo, R., Michaelovsky, E., Karpati, M., Goldman, B., & Peleg, L. Hum Genet, 114(4):366-376, 2004.
Paper Website abstract bibtex
Paper Website abstract bibtex The 1278insTATC is the most prevalent beta-hexosaminidase A ( HEXA) gene mutation causing Tay-Sachs disease (TSD), one of the four lysosomal storage diseases (LSDs) occurring at elevated frequencies among Ashkenazi Jews (AJs). To investigate the genetic history of this mutation in the AJ population, a conserved haplotype (D15S981:175-D15S131:240-D15S1050:284-D15S197:144-D15S188:418) was identified in 1278insTATC chromosomes from 55 unrelated AJ individuals (15 homozygotes and 40 heterozygotes for the TSD mutation), suggesting the occurrence of a common founder. When two methods were used for analysis of linkage disequilibrium (LD) between flanking polymorphic markers and the disease locus and for the study of the decay of LD over time, the estimated age of the insertion was found to be 40+/-12 generations (95% confidence interval: 30-50 generations), so that the most recent common ancestor of the mutation-bearing chromosomes would date to the 8th-9th century. This corresponds with the demographic expansion of AJs in central Europe, following the founding of the Ashkenaz settlement in the early Middle Ages. The results are consistent with the geographic distribution of the main TSD mutation, 1278insTATC being more common in central Europe, and with the coalescent times of mutations causing two other LSDs, Gaucher disease and mucolipidosis type IV. Evidence for the absence of a determinant positive selection (heterozygote advantage) over the mutation is provided by a comparison between the estimated age of 1278insTATC and the probability of the current AJ frequency of the mutant allele as a function of its age, calculated by use of a branching-process model. Therefore, the founder effect in a rapidly expanding population arising from a bottleneck provides a robust parsimonious hypothesis explaining the spread of 1278insTATC-linked TSD in AJ individuals.
@article{
title = {Origin and spread of the 1278insTATC mutation causing Tay-Sachs disease in Ashkenazi Jews: genetic drift as a robust and parsimonious hypothesis},
type = {article},
year = {2004},
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pages = {366-376},
volume = {114},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14727180},
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abstract = {The 1278insTATC is the most prevalent beta-hexosaminidase A ( HEXA) gene mutation causing Tay-Sachs disease (TSD), one of the four lysosomal storage diseases (LSDs) occurring at elevated frequencies among Ashkenazi Jews (AJs). To investigate the genetic history of this mutation in the AJ population, a conserved haplotype (D15S981:175-D15S131:240-D15S1050:284-D15S197:144-D15S188:418) was identified in 1278insTATC chromosomes from 55 unrelated AJ individuals (15 homozygotes and 40 heterozygotes for the TSD mutation), suggesting the occurrence of a common founder. When two methods were used for analysis of linkage disequilibrium (LD) between flanking polymorphic markers and the disease locus and for the study of the decay of LD over time, the estimated age of the insertion was found to be 40+/-12 generations (95% confidence interval: 30-50 generations), so that the most recent common ancestor of the mutation-bearing chromosomes would date to the 8th-9th century. This corresponds with the demographic expansion of AJs in central Europe, following the founding of the Ashkenaz settlement in the early Middle Ages. The results are consistent with the geographic distribution of the main TSD mutation, 1278insTATC being more common in central Europe, and with the coalescent times of mutations causing two other LSDs, Gaucher disease and mucolipidosis type IV. Evidence for the absence of a determinant positive selection (heterozygote advantage) over the mutation is provided by a comparison between the estimated age of 1278insTATC and the probability of the current AJ frequency of the mutant allele as a function of its age, calculated by use of a branching-process model. Therefore, the founder effect in a rapidly expanding population arising from a bottleneck provides a robust parsimonious hypothesis explaining the spread of 1278insTATC-linked TSD in AJ individuals.},
bibtype = {article},
author = {Frisch, A and Colombo, R and Michaelovsky, E and Karpati, M and Goldman, B and Peleg, L},
journal = {Hum Genet},
number = {4}
}Familial aggregation patterns in mathematical ability. Wijsman, E., M., Robinson, N., M., Ainsworth, K., H., Rosenthal, E., A., Holzman, T., & Raskind, W., H. Behav Genet, 34(1):51-62, 2004.
Paper Website abstract bibtex
Paper Website abstract bibtex Mathematical talent is an asset in modern society both at an individual and a societal level. Environmental factors such as quality of mathematics education undoubtedly affect an individual's performance, and there is some evidence that genetic factors also may play a role. The current study was performed to investigate the feasibility of undertaking genetics studies on mathematical ability. Because the etiology of low ability in mathematics is likely to be multifactorial and heterogeneous, we evaluated families ascertained through a proband with high mathematical performance in grade 7 on the SAT to eliminate, to some degree, adverse environmental factors. Families of sex-matched probands, selected for high verbal performance on the SAT, served as the comparison group. We evaluated a number of proxy measures for their usefulness in the study of clustering of mathematical talent. Given the difficulty of testing mathematics performance across developmental ages, especially with the added complexity of decreasing exposure to formal mathematics concepts post schooling, we also devised a semiquantitative scale that incorporated educational, occupational, and avocational information as a surrogate for an academic mathematics measure. Whereas several proxy measures showed no evidence of a genetic basis, we found that the semiquantitative scale of mathematical talent showed strong evidence of a genetic basis, with a differential response as a function of the performance measure used to select the proband. This observation suggests that there may be a genetic basis to specific mathematical talent, and that specific, as opposed to proxy, investigative measures that are designed to measure such talent in family members could be of benefit for this purpose.
@article{
title = {Familial aggregation patterns in mathematical ability},
type = {article},
year = {2004},
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pages = {51-62},
volume = {34},
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abstract = {Mathematical talent is an asset in modern society both at an individual and a societal level. Environmental factors such as quality of mathematics education undoubtedly affect an individual's performance, and there is some evidence that genetic factors also may play a role. The current study was performed to investigate the feasibility of undertaking genetics studies on mathematical ability. Because the etiology of low ability in mathematics is likely to be multifactorial and heterogeneous, we evaluated families ascertained through a proband with high mathematical performance in grade 7 on the SAT to eliminate, to some degree, adverse environmental factors. Families of sex-matched probands, selected for high verbal performance on the SAT, served as the comparison group. We evaluated a number of proxy measures for their usefulness in the study of clustering of mathematical talent. Given the difficulty of testing mathematics performance across developmental ages, especially with the added complexity of decreasing exposure to formal mathematics concepts post schooling, we also devised a semiquantitative scale that incorporated educational, occupational, and avocational information as a surrogate for an academic mathematics measure. Whereas several proxy measures showed no evidence of a genetic basis, we found that the semiquantitative scale of mathematical talent showed strong evidence of a genetic basis, with a differential response as a function of the performance measure used to select the proband. This observation suggests that there may be a genetic basis to specific mathematical talent, and that specific, as opposed to proxy, investigative measures that are designed to measure such talent in family members could be of benefit for this purpose.},
bibtype = {article},
author = {Wijsman, E M and Robinson, N M and Ainsworth, K H and Rosenthal, E A and Holzman, T and Raskind, W H},
journal = {Behav Genet},
number = {1}
}Similar network activity from disparate circuit parameters. Prinz, A. A, Bucher, D., & Marder, E. Nat Neurosci, 7(12):1345-52, 2004.
doi abstract bibtex
doi abstract bibtex
It is often assumed that cellular and synaptic properties need to be regulated to specific values to allow a neuronal network to function properly. To determine how tightly neuronal properties and synaptic strengths need to be tuned to produce a given network output, we simulated more than 20 million versions of a three-cell model of the pyloric network of the crustacean stomatogastric ganglion using different combinations of synapse strengths and neuron properties. We found that virtually indistinguishable network activity can arise from widely disparate sets of underlying mechanisms, suggesting that there could be considerable animal-to-animal variability in many of the parameters that control network activity, and that many different combinations of synaptic strengths and intrinsic membrane properties can be consistent with appropriate network performance.
@Article{Prinz2004,
author = {Astrid A Prinz and Dirk Bucher and Eve Marder},
journal = {Nat Neurosci},
title = {Similar network activity from disparate circuit parameters.},
year = {2004},
number = {12},
pages = {1345-52},
volume = {7},
abstract = {It is often assumed that cellular and synaptic properties need to
be regulated to specific values to allow a neuronal network to function
properly. To determine how tightly neuronal properties and synaptic
strengths need to be tuned to produce a given network output, we
simulated more than 20 million versions of a three-cell model of
the pyloric network of the crustacean stomatogastric ganglion using
different combinations of synapse strengths and neuron properties.
We found that virtually indistinguishable network activity can arise
from widely disparate sets of underlying mechanisms, suggesting that
there could be considerable animal-to-animal variability in many
of the parameters that control network activity, and that many different
combinations of synaptic strengths and intrinsic membrane properties
can be consistent with appropriate network performance.},
doi = {10.1038/nn1352},
keywords = {Action Potentials, Animals, Comparative Study, Crustacea, Nerve Net, Neurons, Research Support, Non-U.S. Gov't, U.S. Gov't, P.H.S., Synapses, 15643435},
}Integration of new genetic diseases into statewide newborn screening: New England experience. Comeau, A., M., Larson, C., & Eaton, R., B. Am J Med Genet C Semin Med Genet, 125(1):35-41, 2004.
Paper abstract bibtex
Paper abstract bibtex Using a data set of newborn screening specimens tested by the New England Newborn Screening Program (NENSP) between January 1999 and February 2003, we analyzed the number of infants with positive newborn screening results and determined how many positive screening results were due to a recent multiplex expansion of services in some of the states. We found that for the subset of the 4-year cohort for which there was a 233% increase in the number of disorders screened (from 9 to 30 disorders), there was a 31% increase in the number of affected infants identified by the screen. We project that if all states in the program expanded their services and if the incidence of disorders is similar across states, there would be an observed 45% increase in the number of infants detected by the screen and a 43% increase in the number of infants for whom the screening algorithm would require some contact with the infants' health care provider. Furthermore, of those requiring contact, we project a 300% increase in the number of screened-positive infants who would be referred to tertiary care centers for a diagnostic evaluation. Increased contact with the medical community from additions to newborn screening as demonstrated in this report emphasizes the need for an approach in which the newborn screening program assures coordinated communications between birth units, laboratory, primary health care providers, and specialists.
@article{
title = {Integration of new genetic diseases into statewide newborn screening: New England experience},
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pages = {35-41},
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abstract = {Using a data set of newborn screening specimens tested by the New England Newborn Screening Program (NENSP) between January 1999 and February 2003, we analyzed the number of infants with positive newborn screening results and determined how many positive screening results were due to a recent multiplex expansion of services in some of the states. We found that for the subset of the 4-year cohort for which there was a 233% increase in the number of disorders screened (from 9 to 30 disorders), there was a 31% increase in the number of affected infants identified by the screen. We project that if all states in the program expanded their services and if the incidence of disorders is similar across states, there would be an observed 45% increase in the number of infants detected by the screen and a 43% increase in the number of infants for whom the screening algorithm would require some contact with the infants' health care provider. Furthermore, of those requiring contact, we project a 300% increase in the number of screened-positive infants who would be referred to tertiary care centers for a diagnostic evaluation. Increased contact with the medical community from additions to newborn screening as demonstrated in this report emphasizes the need for an approach in which the newborn screening program assures coordinated communications between birth units, laboratory, primary health care providers, and specialists.},
bibtype = {article},
author = {Comeau, A M and Larson, C and Eaton, R B},
journal = {Am J Med Genet C Semin Med Genet},
number = {1}
}Genetic influences on life span and survival among elderly African-Americans, Caribbean Hispanics, and Caucasians. Lee, J., H., Flaquer, A., Costa, R., Andrews, H., Cross, P., Lantigua, R., Schupf, N., Tang, M., X., & Mayeux, R. Am J Med Genet A, 128(2):159-164, 2004.
Paper Website abstract bibtex
Paper Website abstract bibtex An investigation of the genetic influences on life span and survival was conducted among elderly African-Americans, Caribbean Hispanics, and Caucasians Medicare recipients (ages 65-104 years). Family history information on 13,161 parents and siblings was obtained. Heritability of life span varied by the age and by ethnic group being lowest for African-Americans. We recalculated the heritability coefficients for life span including only probands and their siblings, but the differences across ethnic groups persisted. In contrast the heritability of survival was more similar across ethnic groups but was similar to that for life span. Heritability coefficients for survival in probands and their siblings revealed little difference between ethnic groups and suggested that as much as 35% of the variation in survival may be genetically influenced. These results indicate that life span and survival are genetically influenced. Comparisons across generations and ethnic groups indicate that changes in environmental hygiene, social welfare, and health care systems are significant contributors to life span and survival, but genetic influences are also important. Identifying the genes associated with life span and survival will provide insight into how the genes interact with environment to influence aging in humans.
@article{
title = {Genetic influences on life span and survival among elderly African-Americans, Caribbean Hispanics, and Caucasians},
type = {article},
year = {2004},
identifiers = {[object Object]},
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pages = {159-164},
volume = {128},
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abstract = {An investigation of the genetic influences on life span and survival was conducted among elderly African-Americans, Caribbean Hispanics, and Caucasians Medicare recipients (ages 65-104 years). Family history information on 13,161 parents and siblings was obtained. Heritability of life span varied by the age and by ethnic group being lowest for African-Americans. We recalculated the heritability coefficients for life span including only probands and their siblings, but the differences across ethnic groups persisted. In contrast the heritability of survival was more similar across ethnic groups but was similar to that for life span. Heritability coefficients for survival in probands and their siblings revealed little difference between ethnic groups and suggested that as much as 35% of the variation in survival may be genetically influenced. These results indicate that life span and survival are genetically influenced. Comparisons across generations and ethnic groups indicate that changes in environmental hygiene, social welfare, and health care systems are significant contributors to life span and survival, but genetic influences are also important. Identifying the genes associated with life span and survival will provide insight into how the genes interact with environment to influence aging in humans.},
bibtype = {article},
author = {Lee, J H and Flaquer, A and Costa, R and Andrews, H and Cross, P and Lantigua, R and Schupf, N and Tang, M X and Mayeux, R},
journal = {Am J Med Genet A},
number = {2}
}Inherited predisposition to cancer: a historical overview. Lynch, H., T., Shaw, T., G., & Lynch, J., F. Am J Med Genet C Semin Med Genet, 129(1):5-22, 2004.
Paper abstract bibtex
Paper abstract bibtex The hereditary predisposition to cancer dates historically to interest piqued by physicians as well as family members wherein striking phenotypic features were shown to cluster in families, inclusive of the rather grotesque cutaneous findings in von Recklinghausen's neurofibromatosis, which date back to the sixteenth century. The search for the role of primary genetic factors was heralded by studies at the infrahuman level, particularly on laboratory mouse strains with strong susceptibility to carcinogen-induced cancer, and conversely, with resistance to the same carcinogens. These studies, developed in the 19th and 20th centuries, continue today. This article traces the historical aspects of hereditary cancer dealing with identification and ultimate molecular genetic confirmation of commonly occurring cancers, particularly of the colon in the case of familial adenomatous polyposis and its attenuated form, both due to the APC germline mutation; the Lynch syndrome due to mutations in mismatch repair genes, the most common of which were found to be MSH2, MLH1, and MSH6 germline mutations; the hereditary breast-ovarian cancer syndrome with BRCA1 and BRCA2 germline mutations; the Li-Fraumeni (SBLA) syndrome due to the p53 mutation; and the familial atypical multiple mole melanoma in association with pancreatic cancer due to the CDKN2A (p16) germline mutation. These and other hereditary cancer syndromes have been discussed in some detail relevant to their characterization, which, for many conditions, took place in the late 18th century and, in the more modern molecular genetic era, during the past two decades. Emphasis has been placed upon the manner in which improved cancer control will emanate from these discoveries. Copyright 2004 Wiley-Liss, Inc.
@article{
title = {Inherited predisposition to cancer: a historical overview},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {*Genetic Predisposition to Disease,Animals,Breast Neoplasms/genetics/history,Colorectal Neoplasms/genetics/history,Disease Models, Animal,Female,History, 16th Century,History, 17th Century,History, 18th Century,History, 19th Century,History, 20th Century,History, 21st Century,Humans,Melanoma/genetics/history,Mice,Multiple Endocrine Neoplasia/genetics/history,Neoplasms/genetics/*history,Neoplastic Syndromes, Hereditary/genetics/history,Neurofibromatoses/genetics/history,Ovarian Neoplasms/genetics/history,Pedigree,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.},
pages = {5-22},
volume = {129},
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source_type = {Journal Article},
notes = {<m:note>Historical Article<m:linebreak/>Journal Article</m:note>},
abstract = {The hereditary predisposition to cancer dates historically to interest piqued by physicians as well as family members wherein striking phenotypic features were shown to cluster in families, inclusive of the rather grotesque cutaneous findings in von Recklinghausen's neurofibromatosis, which date back to the sixteenth century. The search for the role of primary genetic factors was heralded by studies at the infrahuman level, particularly on laboratory mouse strains with strong susceptibility to carcinogen-induced cancer, and conversely, with resistance to the same carcinogens. These studies, developed in the 19th and 20th centuries, continue today. This article traces the historical aspects of hereditary cancer dealing with identification and ultimate molecular genetic confirmation of commonly occurring cancers, particularly of the colon in the case of familial adenomatous polyposis and its attenuated form, both due to the APC germline mutation; the Lynch syndrome due to mutations in mismatch repair genes, the most common of which were found to be MSH2, MLH1, and MSH6 germline mutations; the hereditary breast-ovarian cancer syndrome with BRCA1 and BRCA2 germline mutations; the Li-Fraumeni (SBLA) syndrome due to the p53 mutation; and the familial atypical multiple mole melanoma in association with pancreatic cancer due to the CDKN2A (p16) germline mutation. These and other hereditary cancer syndromes have been discussed in some detail relevant to their characterization, which, for many conditions, took place in the late 18th century and, in the more modern molecular genetic era, during the past two decades. Emphasis has been placed upon the manner in which improved cancer control will emanate from these discoveries. Copyright 2004 Wiley-Liss, Inc.},
bibtype = {article},
author = {Lynch, H T and Shaw, T G and Lynch, J F},
journal = {Am J Med Genet C Semin Med Genet},
number = {1}
}Object perception as Bayesian inference. Kersten, D, Mamassian, P, & Yuille, A Annu Rev Psychol, 55:271–304, 2004.
abstract bibtex
abstract bibtex
We perceive the shapes and material properties of objects quickly and reliably despite the complexity and objective ambiguities of natural images. Typical images are highly complex because they consist of many objects embedded in background clutter. Moreover, the image features of an object are extremely variable and ambiguous owing to the effects of projection, occlusion, background clutter, and illumination. The very success of everyday vision implies neural mechanisms, yet to be understood, that discount irrelevant information and organize ambiguous or noisy local image features into objects and surfaces. Recent work in Bayesian theories of visual perception has shown how complexity may be managed and ambiguity resolved through the task-dependent, probabilistic integration of prior object knowledge with image features.
@article{kersten_object_2004,
title = {Object perception as {Bayesian} inference},
volume = {55},
abstract = {We perceive the shapes and material properties of objects quickly and reliably despite the complexity and objective ambiguities of natural images. Typical images are highly complex because they consist of many objects embedded in background clutter. Moreover, the image features of an object are extremely variable and ambiguous owing to the effects of projection, occlusion, background clutter, and illumination. The very success of everyday vision implies neural mechanisms, yet to be understood, that discount irrelevant information and organize ambiguous or noisy local image features into objects and surfaces. Recent work in Bayesian theories of visual perception has shown how complexity may be managed and ambiguity resolved through the task-dependent, probabilistic integration of prior object knowledge with image features.},
journal = {Annu Rev Psychol},
author = {Kersten, D and Mamassian, P and Yuille, A},
year = {2004},
pmid = {14744217},
keywords = {*Bayes Theorem, *Decision Making, *Learning, *Psychological Theory, Humans, Psychophysics, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., Visual Perception/*physiology},
pages = {271--304},
}Genetic alterations in hereditary breast cancer. Cipollini, G., Tommasi, S., Paradiso, A., Aretini, P., Bonatti, F., Brunetti, I., Bruno, M., Lombardi, G., Schittulli, F., Sensi, E., Tancredi, M., Bevilacqua, G., & Caligo, M., A. Ann Oncol, 15 Suppl 1:I7-I13, 2004.
Website abstract bibtex
Website abstract bibtex Genetic linkage studies have led to the identification of highly penetrant genes as the possible cause of inherited cancer risk in many cancer-prone families. Most women with a family history of breast/ovarian cancer have tumors characterized by alterations in particular genes, mainly BRCA1 and BRCA2, but also CHK2, ATM, STK11 and others. This paper examines the BRCA1 and BRCA2 genes, focusing on the Italian pattern of mutations. The function of these two genes, classified as tumor suppressors, is linked with key metabolic mechanisms such as DNA damage repair, regulation of gene expression and cell cycle control. The pathological BRCA allelic variants may cause alteration of protein function, transcriptional activity and DNA repair; accumulation of the defects leads to widespread chromosome instability that may be directly responsible for cancer formation. In fact, mutations in BRCA1 and BRCA2, conferring a highly increased susceptibility to breast and ovarian cancer, do not lead to cancer by themselves. The current consensus is that these are 'caretaker' genes, which, when inactivated, allow other genetic defects to accumulate. The nature of these other molecular events may define the pathway through which BRCA1 and BRCA2 act. The BRCA mutation spectrum is complex, and the significance of most nucleotide alterations is difficult to understand. Moreover, the mutation pattern seems to be related to ethnicity. The Italian Consortium of Hereditary Breast and Ovarian Cancer has reviewed 1758 families; 23% have been found to be carriers of pathogenetic mutations in BRCA1 or BRCA2. Founder mutations have been described in geographically restricted areas of Italy; a regional founder effect has been demonstrated in Italy for the mutations BRCA1 5083del19 and BRCA2 8765delAG, and a probable new founder mutation has been characterized in Tuscany. The presence of founder mutations has practical implications for genetic testing.
@article{
title = {Genetic alterations in hereditary breast cancer},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {*Mutation,Adult,Age Factors,Aged,Aged, 80 and over,Alleles,BRCA1 Protein/*genetics,BRCA2 Protein/*genetics,Breast Neoplasms/epidemiology/*genetics,Female,Genotype,Humans,Italy/epidemiology,Middle Aged,Research Support, Non-U.S. Gov't},
pages = {I7-I13},
volume = {15 Suppl 1},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15280181},
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notes = {<m:note>0923-7534 (Print)<m:linebreak/>Journal Article</m:note>},
abstract = {Genetic linkage studies have led to the identification of highly penetrant genes as the possible cause of inherited cancer risk in many cancer-prone families. Most women with a family history of breast/ovarian cancer have tumors characterized by alterations in particular genes, mainly BRCA1 and BRCA2, but also CHK2, ATM, STK11 and others. This paper examines the BRCA1 and BRCA2 genes, focusing on the Italian pattern of mutations. The function of these two genes, classified as tumor suppressors, is linked with key metabolic mechanisms such as DNA damage repair, regulation of gene expression and cell cycle control. The pathological BRCA allelic variants may cause alteration of protein function, transcriptional activity and DNA repair; accumulation of the defects leads to widespread chromosome instability that may be directly responsible for cancer formation. In fact, mutations in BRCA1 and BRCA2, conferring a highly increased susceptibility to breast and ovarian cancer, do not lead to cancer by themselves. The current consensus is that these are 'caretaker' genes, which, when inactivated, allow other genetic defects to accumulate. The nature of these other molecular events may define the pathway through which BRCA1 and BRCA2 act. The BRCA mutation spectrum is complex, and the significance of most nucleotide alterations is difficult to understand. Moreover, the mutation pattern seems to be related to ethnicity. The Italian Consortium of Hereditary Breast and Ovarian Cancer has reviewed 1758 families; 23% have been found to be carriers of pathogenetic mutations in BRCA1 or BRCA2. Founder mutations have been described in geographically restricted areas of Italy; a regional founder effect has been demonstrated in Italy for the mutations BRCA1 5083del19 and BRCA2 8765delAG, and a probable new founder mutation has been characterized in Tuscany. The presence of founder mutations has practical implications for genetic testing.},
bibtype = {article},
author = {Cipollini, G and Tommasi, S and Paradiso, A and Aretini, P and Bonatti, F and Brunetti, I and Bruno, M and Lombardi, G and Schittulli, F and Sensi, E and Tancredi, M and Bevilacqua, G and Caligo, M A},
journal = {Ann Oncol}
}2003 (8)
The Newfoundland population: a unique resource for genetic investigation of complex diseases. Rahman, P., Jones, A., Curtis, J., Bartlett, S., Peddle, L., Fernandez, B., A., & Freimer, N., B. Hum Mol Genet, 12 Spec No:R167-72, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex The population of the province of Newfoundland and Labrador is genetically isolated. This isolation is evidenced by an overabundance of several monogenic disorders. The Newfoundland population, like that of other isolates, is now the focus of interest for identification of genes implicated in common diseases. However, the utility of such populations for this purpose remains unproven. In this paper, we review the current genetic architecture of the province, with respect to geographic isolation, homogeneity, founder effect, genetic drift and extended linkage disequilibrium. Based on these factors, we propose that the population of Newfoundland offers many advantages for genetic mapping of common diseases, compared with admixed populations, and even compared with other isolates.
@article{
title = {The Newfoundland population: a unique resource for genetic investigation of complex diseases},
type = {article},
year = {2003},
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keywords = {Founder Effect,Genetic Diseases, Inborn/*genetics,Humans,Linkage Disequilibrium,Newfoundland,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.},
pages = {R167-72},
volume = {12 Spec No},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12915452},
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notes = {<m:note>0964-6906 (Print)<m:linebreak/>Journal Article<m:linebreak/>Review</m:note>},
abstract = {The population of the province of Newfoundland and Labrador is genetically isolated. This isolation is evidenced by an overabundance of several monogenic disorders. The Newfoundland population, like that of other isolates, is now the focus of interest for identification of genes implicated in common diseases. However, the utility of such populations for this purpose remains unproven. In this paper, we review the current genetic architecture of the province, with respect to geographic isolation, homogeneity, founder effect, genetic drift and extended linkage disequilibrium. Based on these factors, we propose that the population of Newfoundland offers many advantages for genetic mapping of common diseases, compared with admixed populations, and even compared with other isolates.},
bibtype = {article},
author = {Rahman, P and Jones, A and Curtis, J and Bartlett, S and Peddle, L and Fernandez, B A and Freimer, N B},
journal = {Hum Mol Genet}
}Understanding the Determinants of Exceptional Longevity. Perls, T. & Terry, D. Ann Intern Med, 139(5 Pt 2):445-449, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex Centenarians represent an extreme of life expectancy. They achieve their exceptional longevity in part by lacking genetic variations linked to premature death. Pedigree studies have shown a substantial familial component in the ability to survive to extreme old age, and a recent study demonstrated a locus on chromosome 4 linked to exceptional longevity, indicating the likely existence of at least one longevity-enabling gene in humans. The children of centenarians have markedly reduced relative risks for age-related diseases, particularly heart disease, hypertension, and diabetes, and are a promising model for genetic and phenotypic studies of 1) aging slowly relative to the general population and 2) the delay of and perhaps escape from important age-related diseases. These studies and those of other mammals and lower organisms show great promise for the delineation of important environmental and genetic determinants of aging well.
@article{
title = {Understanding the Determinants of Exceptional Longevity},
type = {article},
year = {2003},
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keywords = {*Longevity,Animals,Genes,Humans,Life Expectancy,Non-U.S. Gov't,P.H.S.,Phenotype,Research Support,U.S. Gov't},
pages = {445-449},
volume = {139},
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notes = {<m:note> <m:bold>From Duplicate 2 ( </m:bold> <m:bold> </m:bold><m:bold><m:italic>Understanding the determinants of exceptional longevity</m:italic></m:bold><m:bold> </m:bold> <m:bold> - Perls, T; Terry, D )<m:linebreak/> </m:bold> <m:linebreak/>1539-3704<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/> <m:linebreak/> </m:note>},
abstract = {Centenarians represent an extreme of life expectancy. They achieve their exceptional longevity in part by lacking genetic variations linked to premature death. Pedigree studies have shown a substantial familial component in the ability to survive to extreme old age, and a recent study demonstrated a locus on chromosome 4 linked to exceptional longevity, indicating the likely existence of at least one longevity-enabling gene in humans. The children of centenarians have markedly reduced relative risks for age-related diseases, particularly heart disease, hypertension, and diabetes, and are a promising model for genetic and phenotypic studies of 1) aging slowly relative to the general population and 2) the delay of and perhaps escape from important age-related diseases. These studies and those of other mammals and lower organisms show great promise for the delineation of important environmental and genetic determinants of aging well.},
bibtype = {article},
author = {Perls, Thomas and Terry, Dellara},
journal = {Ann Intern Med},
number = {5 Pt 2}
}Predictors of mortality in 2,249 nonagenarians--the Danish 1905-Cohort Survey. Nybo, H., Petersen, H., C., Gaist, D., Jeune, B., Andersen, K., McGue, M., Vaupel, J., W., & Christensen, K. J Am Geriatr Soc, 51(10):1365-1373, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex OBJECTIVES: : To elucidate whether well-known predictions of mortality are reduced or even reversed, or whether mortality is a stochastic process in the oldest old. DESIGN: : A multidimensional survey of the Danish 1905 cohort conducted in 1998 with follow-up of vital status after 15 months. SETTING: : Denmark. PARTICIPANTS: : All Danes born in 1905, irrespective of physical and mental status were approached. Two thousand two hundred sixty-two persons of 3,600 participated in this survey. MEASUREMENTS: : Professional interviewers collected data concerning sociodemographic factors, smoking, alcohol consumption, body mass index, physical and cognitive performance, and health during a visit at the participant's residency. Cox regression models were used to evaluate predictors of mortality. RESULTS: : Five hundred seventy-nine (25.7%) of the 2,249 participants eligible for the analysis died during the 15 months follow-up. Multivariate analyses showed that marital status, education, smoking, obesity, consumption of alcohol, and number of self-reported diseases were not associated with mortality. Disability and cognitive impairment were significant risk factors in men and women. In addition poor self-rated health was associated with an increase in mortality in women. CONCLUSION: : In the oldest old, several known predictors of mortality, such as sociodemographic factors, smoking, and obesity, have lost their importance, but a high disability level, poor physical and cognitive performance, and self-rated health (women only), predict mortality, which shows that mortality in the oldest old is not a stochastic process.
@article{
title = {Predictors of mortality in 2,249 nonagenarians--the Danish 1905-Cohort Survey},
type = {article},
year = {2003},
identifiers = {[object Object]},
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pages = {1365-1373},
volume = {51},
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abstract = {OBJECTIVES: : To elucidate whether well-known predictions of mortality are reduced or even reversed, or whether mortality is a stochastic process in the oldest old. DESIGN: : A multidimensional survey of the Danish 1905 cohort conducted in 1998 with follow-up of vital status after 15 months. SETTING: : Denmark. PARTICIPANTS: : All Danes born in 1905, irrespective of physical and mental status were approached. Two thousand two hundred sixty-two persons of 3,600 participated in this survey. MEASUREMENTS: : Professional interviewers collected data concerning sociodemographic factors, smoking, alcohol consumption, body mass index, physical and cognitive performance, and health during a visit at the participant's residency. Cox regression models were used to evaluate predictors of mortality. RESULTS: : Five hundred seventy-nine (25.7%) of the 2,249 participants eligible for the analysis died during the 15 months follow-up. Multivariate analyses showed that marital status, education, smoking, obesity, consumption of alcohol, and number of self-reported diseases were not associated with mortality. Disability and cognitive impairment were significant risk factors in men and women. In addition poor self-rated health was associated with an increase in mortality in women. CONCLUSION: : In the oldest old, several known predictors of mortality, such as sociodemographic factors, smoking, and obesity, have lost their importance, but a high disability level, poor physical and cognitive performance, and self-rated health (women only), predict mortality, which shows that mortality in the oldest old is not a stochastic process.},
bibtype = {article},
author = {Nybo, H and Petersen, H C and Gaist, D and Jeune, B and Andersen, K and McGue, M and Vaupel, J W and Christensen, K},
journal = {J Am Geriatr Soc},
number = {10}
}The receptive fields of inferior temporal cortex neurons in natural scenes. Rolls, E. T, Aggelopoulos, N. C, & Zheng, F. J Neurosci, 23(1):339–348, 2003. Place: United States ISBN: 1529-2401
abstract bibtex
abstract bibtex
Inferior temporal cortex neurons have generally been found to have large visual receptive fields that typically include the fovea and extend throughout much of the visual field. However, a problem of such a large receptive field is that it does not easily support object selection by subsequent processing areas, in that all objects within such a large receptive field might activate inferior temporal cortex cells. To clarify this, we recorded from inferior temporal cortex neurons while macaques searched for objects in complex natural scenes or in plain backgrounds, as normally used. Inferior temporal cortex neuron receptive fields were much smaller in natural scenes (mean radius, 11 degrees) than in plain backgrounds (39 degrees). With two objects in a scene, one of which was a target for action (a touch), the firing rates were equally high during foveation of the effective stimulus when it was the target and when it was the distractor in both the plain and the complex scenes. With a plain background and two objects present, the receptive fields were much larger (24 degrees ) for the stimulus when it was the target than when it was the distractor (9 degrees ). This effect of object-based attention was much less evident in the complex scene, when the receptive fields were small both when the stimulus was a distractor and when it was a target. The results show that the temporal visual cortex provides an unambiguous representation in natural scenes by responding to the object shown at or close to the fixation point.
@article{rolls_receptive_2003,
title = {The receptive fields of inferior temporal cortex neurons in natural scenes.},
volume = {23},
abstract = {Inferior temporal cortex neurons have generally been found to have large visual receptive fields that typically include the fovea and extend throughout much of the visual field. However, a problem of such a large receptive field is that it does not easily support object selection by subsequent processing areas, in that all objects within such a large receptive field might activate inferior temporal cortex cells. To clarify this, we recorded from inferior temporal cortex neurons while macaques searched for objects in complex natural scenes or in plain backgrounds, as normally used. Inferior temporal cortex neuron receptive fields were much smaller in natural scenes (mean radius, 11 degrees) than in plain backgrounds (39 degrees). With two objects in a scene, one of which was a target for action (a touch), the firing rates were equally high during foveation of the effective stimulus when it was the target and when it was the distractor in both the plain and the complex scenes. With a plain background and two objects present, the receptive fields were much larger (24 degrees ) for the stimulus when it was the target than when it was the distractor (9 degrees ). This effect of object-based attention was much less evident in the complex scene, when the receptive fields were small both when the stimulus was a distractor and when it was a target. The results show that the temporal visual cortex provides an unambiguous representation in natural scenes by responding to the object shown at or close to the fixation point.},
language = {eng},
number = {1},
journal = {J Neurosci},
author = {Rolls, Edmund T and Aggelopoulos, Nicholas C and Zheng, Fashan},
year = {2003},
pmid = {12514233},
note = {Place: United States
ISBN: 1529-2401},
keywords = {Action Potentials, Animals, Kinetics, Macaca mulatta, Neurons, Visual Cortex, Visual Fields, Visual Perception, research support, non-u.s. gov't},
pages = {339--348},
}Haplotype-based identification of a microsomal transfer protein marker associated with the human lifespan. Geesaman, B., J., Benson, E., Brewster, S., J., Kunkel, L., M., Blanche, H., Thomas, G., Perls, T., T., Daly, M., J., & Puca, A., A. Proc Natl Acad Sci U S A, 100(24):14115-14120, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex We previously reported a genomewide linkage study for human longevity using 308 long-lived individuals (LLI) (centenarians or near-centenarians) in 137 sibships and identified statistically significant linkage within chromosome 4 near microsatellite D4S1564. This interval spans 12 million bp and contains approximately 50 putative genes. To identify the specific gene and gene variants impacting lifespan, we performed a haplotype-based fine-mapping study of the interval. The resulting genetic association study identified a haplotype marker within microsomal transfer protein as a modifier of human lifespan. This same variant was tested in a second cohort of LLI from France, and although the association was not replicated, there was evidence for statistical distortion in the form of Hardy-Weinberg disequilibrium. Microsomal transfer protein has been identified as the rate-limiting step in lipoprotein synthesis and may affect longevity by subtly modulating this pathway. This study provides proof of concept for the feasibility of using the genomes of LLI to identify genes impacting longevity.
@article{
title = {Haplotype-based identification of a microsomal transfer protein marker associated with the human lifespan},
type = {article},
year = {2003},
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keywords = {Adolescent,Adult,Aged,Aged, 80 and over,Alleles,Apolipoproteins E/genetics,Biological Markers,Carrier Proteins/*genetics/physiology,Case-Control Studies,Chromosomes, Human, Pair 4/genetics,Cohort Studies,Female,Haplotypes/*genetics,Humans,Linkage (Genetics),Longevity/*genetics/physiology,Male,Microsomes/metabolism,Middle Aged,Polymorphism, Single Nucleotide,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.},
pages = {14115-14120},
volume = {100},
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abstract = {We previously reported a genomewide linkage study for human longevity using 308 long-lived individuals (LLI) (centenarians or near-centenarians) in 137 sibships and identified statistically significant linkage within chromosome 4 near microsatellite D4S1564. This interval spans 12 million bp and contains approximately 50 putative genes. To identify the specific gene and gene variants impacting lifespan, we performed a haplotype-based fine-mapping study of the interval. The resulting genetic association study identified a haplotype marker within microsomal transfer protein as a modifier of human lifespan. This same variant was tested in a second cohort of LLI from France, and although the association was not replicated, there was evidence for statistical distortion in the form of Hardy-Weinberg disequilibrium. Microsomal transfer protein has been identified as the rate-limiting step in lipoprotein synthesis and may affect longevity by subtly modulating this pathway. This study provides proof of concept for the feasibility of using the genomes of LLI to identify genes impacting longevity.},
bibtype = {article},
author = {Geesaman, B J and Benson, E and Brewster, S J and Kunkel, L M and Blanche, H and Thomas, G and Perls, T T and Daly, M J and Puca, A A},
journal = {Proc Natl Acad Sci U S A},
number = {24}
}Y-chromosome evidence for differing ancient demographic histories in the Americas. Bortolini, M., C., Salzano, F., M., Thomas, M., G., Stuart, S., Nasanen, S., P., Bau, C., H., Hutz, M., H., Layrisse, Z., Petzl-Erler, M., L., Tsuneto, L., T., Hill, K., Hurtado, A., M., Castro-de-Guerra, D., Torres, M., M., Groot, H., Michalski, R., Nymadawa, P., Bedoya, G., Bradman, N., Labuda, D., & Ruiz-Linares, A. Am J Hum Genet, 73(3):524-539, 2003.
Paper abstract bibtex
Paper abstract bibtex To scrutinize the male ancestry of extant Native American populations, we examined eight biallelic and six microsatellite polymorphisms from the nonrecombining portion of the Y chromosome, in 438 individuals from 24 Native American populations (1 Na Dene and 23 South Amerinds) and in 404 Mongolians. One of the biallelic markers typed is a recently identified mutation (M242) characterizing a novel founder Native American haplogroup. The distribution, relatedness, and diversity of Y lineages in Native Americans indicate a differentiated male ancestry for populations from North and South America, strongly supporting a diverse demographic history for populations from these areas. These data are consistent with the occurrence of two major male migrations from southern/central Siberia to the Americas (with the second migration being restricted to North America) and a shared ancestry in central Asia for some of the initial migrants to Europe and the Americas. The microsatellite diversity and distribution of a Y lineage specific to South America (Q-M19) indicates that certain Amerind populations have been isolated since the initial colonization of the region, suggesting an early onset for tribalization of Native Americans. Age estimates based on Y-chromosome microsatellite diversity place the initial settlement of the American continent at approximately 14,000 years ago, in relative agreement with the age of well-established archaeological evidence.
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title = {Y-chromosome evidence for differing ancient demographic histories in the Americas},
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pages = {524-539},
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notes = {<m:note>Historical Article<m:linebreak/>Journal Article</m:note>},
abstract = {To scrutinize the male ancestry of extant Native American populations, we examined eight biallelic and six microsatellite polymorphisms from the nonrecombining portion of the Y chromosome, in 438 individuals from 24 Native American populations (1 Na Dene and 23 South Amerinds) and in 404 Mongolians. One of the biallelic markers typed is a recently identified mutation (M242) characterizing a novel founder Native American haplogroup. The distribution, relatedness, and diversity of Y lineages in Native Americans indicate a differentiated male ancestry for populations from North and South America, strongly supporting a diverse demographic history for populations from these areas. These data are consistent with the occurrence of two major male migrations from southern/central Siberia to the Americas (with the second migration being restricted to North America) and a shared ancestry in central Asia for some of the initial migrants to Europe and the Americas. The microsatellite diversity and distribution of a Y lineage specific to South America (Q-M19) indicates that certain Amerind populations have been isolated since the initial colonization of the region, suggesting an early onset for tribalization of Native Americans. Age estimates based on Y-chromosome microsatellite diversity place the initial settlement of the American continent at approximately 14,000 years ago, in relative agreement with the age of well-established archaeological evidence.},
bibtype = {article},
author = {Bortolini, M C and Salzano, F M and Thomas, M G and Stuart, S and Nasanen, S P and Bau, C H and Hutz, M H and Layrisse, Z and Petzl-Erler, M L and Tsuneto, L T and Hill, K and Hurtado, A M and Castro-de-Guerra, D and Torres, M M and Groot, H and Michalski, R and Nymadawa, P and Bedoya, G and Bradman, N and Labuda, D and Ruiz-Linares, A},
journal = {Am J Hum Genet},
number = {3}
}Genetics of exceptional longevity. Perls, T. & Terry, D. Exp Gerontol, 38(7):725-730, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex Centenarians exist at the extreme of life expectancy and are rare. A number of pedigree and molecular genetic studies indicate that a significant component of exceptional longevity is genetically influenced. Furthermore, the recent discovery of a genetic locus on chromosome 4 indicates the powerful potential of studying centenarians for genetic factors that significantly modulate aging and susceptibility to age-related diseases. These studies include siblings and children of centenarians. Siblings have a significantly increased propensity to achieve exceptional old age and have half the mortality risk of their birth cohort from young adulthood through extreme old age. The children of centenarians are emerging as a promising model for the genetic and phenotypic study of aging relatively slowly and the delay and perhaps escape of important age-related diseases.
@article{
title = {Genetics of exceptional longevity},
type = {article},
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pages = {725-730},
volume = {38},
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notes = {<m:note>0531-5565<m:linebreak/>Journal Article</m:note>},
abstract = {Centenarians exist at the extreme of life expectancy and are rare. A number of pedigree and molecular genetic studies indicate that a significant component of exceptional longevity is genetically influenced. Furthermore, the recent discovery of a genetic locus on chromosome 4 indicates the powerful potential of studying centenarians for genetic factors that significantly modulate aging and susceptibility to age-related diseases. These studies include siblings and children of centenarians. Siblings have a significantly increased propensity to achieve exceptional old age and have half the mortality risk of their birth cohort from young adulthood through extreme old age. The children of centenarians are emerging as a promising model for the genetic and phenotypic study of aging relatively slowly and the delay and perhaps escape of important age-related diseases.},
bibtype = {article},
author = {Perls, T and Terry, D},
journal = {Exp Gerontol},
number = {7}
}Locus-specific genetic diversity between human populations: an analysis of the literature. Garte, S. Am J Hum Biol, 15(6):814-823, 2003.
Paper Website abstract bibtex
Paper Website abstract bibtex The debate over classification of the human species according to racial or continental lines has involved reports on genetic differences in allele frequencies of a number of loci with important biomedical functions. Such differences are in contrast with the fact that, for human beings, intrapopulation genetic diversity is larger than that seen between populations. In an attempt to address the hypothesis that certain genes show high interpopulation diversity due to selective pressure, the literature was surveyed to quantify such diversity using Wrights Fst statistic. The gene-specific Fst values were then compared to pairwise population values of Fst taken over a large number of genes, which presumably reflect mostly neutral mechanisms of genetic diversity such as drift. The results showed that the majority of pairwise population values of Fst for over 30 genes of biomedical significance were either below or within the expected limits of Fst based on published values. These results do not support the idea that positive or diversifying natural selection plays an important role in increasing genetic diversity, even in genes that might be expected to be subject to selection pressure. Balancing selection, whereby the degree of genetic diversity is actually lower than that expected, appears to occur more frequently for these genes. The fact that allele frequency differences between populations might be "statistically significant" does not therefore necessarily imply a degree of genetic diversity greater than would be expected due to nonselective mechanisms.
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title = {Locus-specific genetic diversity between human populations: an analysis of the literature},
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keywords = {*Variation (Genetics),Chromosome Mapping,Gene Frequency,Genetics, Population/*methods,Humans,Research Support, U.S. Gov't, P.H.S.,Selection (Genetics)},
pages = {814-823},
volume = {15},
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abstract = {The debate over classification of the human species according to racial or continental lines has involved reports on genetic differences in allele frequencies of a number of loci with important biomedical functions. Such differences are in contrast with the fact that, for human beings, intrapopulation genetic diversity is larger than that seen between populations. In an attempt to address the hypothesis that certain genes show high interpopulation diversity due to selective pressure, the literature was surveyed to quantify such diversity using Wrights Fst statistic. The gene-specific Fst values were then compared to pairwise population values of Fst taken over a large number of genes, which presumably reflect mostly neutral mechanisms of genetic diversity such as drift. The results showed that the majority of pairwise population values of Fst for over 30 genes of biomedical significance were either below or within the expected limits of Fst based on published values. These results do not support the idea that positive or diversifying natural selection plays an important role in increasing genetic diversity, even in genes that might be expected to be subject to selection pressure. Balancing selection, whereby the degree of genetic diversity is actually lower than that expected, appears to occur more frequently for these genes. The fact that allele frequency differences between populations might be "statistically significant" does not therefore necessarily imply a degree of genetic diversity greater than would be expected due to nonselective mechanisms.},
bibtype = {article},
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journal = {Am J Hum Biol},
number = {6}
}2002 (7)
Building an Asynchronous Web-Based Tool for Machine Learning Classification. Weber, G., Vinterbo, S., & Ohno-Machado, L. JAMIA, Suppl. S:869–73, 2002.
abstract bibtex
abstract bibtex
Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.
@article{Weber2002,
title = {Building an Asynchronous Web-Based Tool for Machine Learning Classification.},
author = {Weber, Griffin and Vinterbo, Staal and {Ohno-Machado}, Lucila},
year = {2002},
journal = {JAMIA},
volume = {Suppl. S},
pages = {869--73},
abstract = {Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.},
copyright = {All rights reserved},
pii = {D020001919},
pubmedid = {12463949},
keywords = {12463949,Algorithms,Anonymous Testing,Artificial Intelligence,Carcinoma,Child,Comparative Study,Computerized,Confidentiality,Databases,Diagnosis,Differential,Disclosure,DNA,Gene Expression,Gene Expression Profiling,Gene Expression Regulation,Genetic Markers,Humans,Internet,Logistic Models,Lung Neoplasms,Medical Records Systems,Multivariate Analysis,Neoplasm,Neoplasms,Neoplastic,Neural Networks (Computer),Non-U.S. Gov't,Oligonucleotide Array Sequence Analysis,P.H.S.,Privacy,Research Support,Rhabdomyosarcoma,Sarcoma,Small Cell,Software,U.S. Gov't},
file = {/Users/staal/Documents/Zotero/storage/26TPF5RW/amia02-weber.pdf;/Users/staal/Documents/Zotero/storage/FRPABBPG/amia02-weber.pdf;/Users/staal/Documents/Zotero/storage/GME7HZA7/amia02-weber.pdf}
}Comparing Imperfect Measurements with the Bland-Altman Technique: Application in Gene Expression Analysis. Ohno-Machado, L., Vinterbo, S., Dreiseitl, S., Jenssen, T., & Kuo, W. JAMIA, Suppl. S:572–6, 2002.
abstract bibtex
abstract bibtex
Several problems in medicine and biology involve the comparison of two measurements made on the same set of cases. The problem differs from a calibration problem because no gold standard can be identified. Testing the null hypothesis of no relationship using measures of association is not optimal since the measurements are made on the same cases, and therefore correlation coefficients will tend to be significant. The descriptive Bland-Altman method can be used in exploratory analysis of this problem, allowing the visualization of gross systematic differences between the two sets of measurements. We utilize the method on three sets of matched observations and demonstrate its usefulness in detecting systematic variations between two measurement technologies to assess gene expression.
@article{Ohno-Machado2002,
title = {Comparing Imperfect Measurements with the {{Bland-Altman}} Technique: Application in Gene Expression Analysis.},
author = {{Ohno-Machado}, Lucila and Vinterbo, Staal and Dreiseitl, Stephen and Jenssen, Tor-Kristian and Kuo, Winston},
year = {2002},
journal = {JAMIA},
volume = {Suppl. S},
pages = {572--6},
abstract = {Several problems in medicine and biology involve the comparison of two measurements made on the same set of cases. The problem differs from a calibration problem because no gold standard can be identified. Testing the null hypothesis of no relationship using measures of association is not optimal since the measurements are made on the same cases, and therefore correlation coefficients will tend to be significant. The descriptive Bland-Altman method can be used in exploratory analysis of this problem, allowing the visualization of gross systematic differences between the two sets of measurements. We utilize the method on three sets of matched observations and demonstrate its usefulness in detecting systematic variations between two measurement technologies to assess gene expression.},
copyright = {All rights reserved},
pii = {1833},
pubmedid = {12463888},
keywords = {12463888,Algorithms,Anonymous Testing,Artificial Intelligence,Bias (Epidemiology),Carcinoma,Child,Comparative Study,Computational Biology,Computerized,Confidentiality,Data Interpretation,Databases,Diagnosis,Differential,Disclosure,DNA,Gene Expression,Gene Expression Profiling,Gene Expression Regulation,Genetic Markers,Humans,Internet,Logistic Models,Lung Neoplasms,Medical Records Systems,Messenger,Multivariate Analysis,Neoplasm,Neoplasms,Neoplastic,Neural Networks (Computer),Non-U.S. Gov't,Oligonucleotide Array Sequence Analysis,P.H.S.,Privacy,Research Support,Rhabdomyosarcoma,RNA,Sarcoma,Small Cell,Software,Statistical,U.S. Gov't}
}Do children of long-lived parents age more successfully?. Frederiksen, H., McGue, M., Jeune, B., Gaist, D., Nybo, H., Skytthe, A., Vaupel, J., W., & Christensen, K. Epidemiology, 13(3):334-339, 2002.
Website abstract bibtex
Website abstract bibtex BACKGROUND: Long-lived individuals are rare and may be selected in part for the genetic factors that promote successful aging. The children of long-lived parents may therefore age more successfully than the children of short-lived parents. METHODS: We used three major cross-sectional population-based surveys to study the association of parental longevity with successful aging in offspring. The measures of aging were hand-grip strength, cognitive performance (Mini Mental State Examination and a cognitive composite score), self-reported diseases, and self-rated health. RESULTS: For every additional 10 years the parents lived, their children's grip strength increased by 0.32 kg (95% CI = 0.00-0.63), Mini Mental State Examination score by 0.20 points (95% CI = 0.03-0.37), and cognitive composite score by 0.24 points (95% CI = 0.07-0.40). A 10-year increment of parental life was associated with a reduction by approximately 0.20 in the adjusted odds ratio for their children having each of the following conditions: diabetes; hypertension; ischemic heart disease; heart failure; stroke; or fair, poor, or very poor self-rated health. Almost all the effects were seen solely in the cohort of 70+-year-olds, but not among middle-aged or nonagenarian subjects. CONCLUSIONS: Parental life span is positively associated with the children's physical and cognitive functioning and avoidance of some of the common chronic diseases. However, the effects are small and are seen among offspring who are elderly, but not among the middle-aged or the oldest old.
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pages = {334-339},
volume = {13},
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abstract = {BACKGROUND: Long-lived individuals are rare and may be selected in part for the genetic factors that promote successful aging. The children of long-lived parents may therefore age more successfully than the children of short-lived parents. METHODS: We used three major cross-sectional population-based surveys to study the association of parental longevity with successful aging in offspring. The measures of aging were hand-grip strength, cognitive performance (Mini Mental State Examination and a cognitive composite score), self-reported diseases, and self-rated health. RESULTS: For every additional 10 years the parents lived, their children's grip strength increased by 0.32 kg (95% CI = 0.00-0.63), Mini Mental State Examination score by 0.20 points (95% CI = 0.03-0.37), and cognitive composite score by 0.24 points (95% CI = 0.07-0.40). A 10-year increment of parental life was associated with a reduction by approximately 0.20 in the adjusted odds ratio for their children having each of the following conditions: diabetes; hypertension; ischemic heart disease; heart failure; stroke; or fair, poor, or very poor self-rated health. Almost all the effects were seen solely in the cohort of 70+-year-olds, but not among middle-aged or nonagenarian subjects. CONCLUSIONS: Parental life span is positively associated with the children's physical and cognitive functioning and avoidance of some of the common chronic diseases. However, the effects are small and are seen among offspring who are elderly, but not among the middle-aged or the oldest old.},
bibtype = {article},
author = {Frederiksen, H and McGue, M and Jeune, B and Gaist, D and Nybo, H and Skytthe, A and Vaupel, J W and Christensen, K},
journal = {Epidemiology},
number = {3}
}Markers that discriminate between European and African ancestry show limited variation within Africa. Collins-Schramm, H., E., Kittles, R., A., Operario, D., J., Weber, J., L., Criswell, L., A., Cooper, R., S., & Seldin, M., F. Hum Genet, 111(6):566-569, 2002.
Paper abstract bibtex
Paper abstract bibtex Markers informative for ancestry are necessary for admixture mapping and improving case-control association analyses. In particular, African Americans are an admixed population for which genetic studies require accurately evaluating admixture. This will require markers that can be used in African Americans to determine if a given genomic region is of European or African ancestry. This report shows that, despite studies indicating high intra-African sequence variation, markers with large inter-ethnic differences have only small variations in allele distribution among divergent African populations and should be valuable for evaluating admixture in complex disease genetic studies.
@article{
title = {Markers that discriminate between European and African ancestry show limited variation within Africa},
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abstract = {Markers informative for ancestry are necessary for admixture mapping and improving case-control association analyses. In particular, African Americans are an admixed population for which genetic studies require accurately evaluating admixture. This will require markers that can be used in African Americans to determine if a given genomic region is of European or African ancestry. This report shows that, despite studies indicating high intra-African sequence variation, markers with large inter-ethnic differences have only small variations in allele distribution among divergent African populations and should be valuable for evaluating admixture in complex disease genetic studies.},
bibtype = {article},
author = {Collins-Schramm, H E and Kittles, R A and Operario, D J and Weber, J L and Criswell, L A and Cooper, R S and Seldin, M F},
journal = {Hum Genet},
number = {6}
}CARD15 genetic variation in a Quebec population: prevalence, genotype-phenotype relationship, and haplotype structure. Vermeire, S., Wild, G., Kocher, K., Cousineau, J., Dufresne, L., Bitton, A., Langelier, D., Pare, P., Lapointe, G., Cohen, A., Daly, M., J., & Rioux, J., D. Am J Hum Genet, 71(1):74-83, 2002.
Paper Website abstract bibtex
Paper Website abstract bibtex The caspase recruitment domain gene (CARD15) was recently identified as the underlying gene associated with the IBD1 locus that confers susceptibility to Crohn disease (CD). CARD15 is related to the NOD1/Apaf-1 family of apoptosis regulators, and three sequence variants (Arg702Trp, Gly908Arg, and Leu1007fsinsC) in the gene were demonstrated to be associated with CD. We collected a cohort of 231 patients with CD and 71 healthy control individuals from the Canadian province of Quebec, to determine the prevalence of these sequence variants in an independent population. Clinical records of all patients were systematically reviewed, and detailed phenotypic information was obtained. All patient DNA samples were genotyped for the three variants, thus enabling an analysis of genotype-phenotype correlations. In this cohort, 45.0% of patients with CD carried at least one variant in the CARD15 gene, compared with 9.0% of control individuals (P<10-7). Allele frequencies of Arg702Trp, Gly908Arg, and Leu1007fsinsC were 12.9%, 5.2%, and 10.3% in patients with CD, compared with 4.2%, 0.7%, and 0.7% in control individuals, respectively. Importantly, CARD15 mutants were seen with equal frequency in patients with familial and sporadic CD. Analysis of the relationship between genotype and phenotype convincingly demonstrates that CARD15 variants are significantly associated with ileal disease involvement, as opposed to strictly colonic disease (P<.001). Moreover, we were able to determine the haplotype structure surrounding this disease gene by genotyping 45 single-nucleotide polymorphisms (SNPs) in a 177-kb region that contained the CARD15 gene. This structure helps clarify the history of these causal mutations. Finally, this analysis shows that CARD15 involvement with CD is detectable by use of publicly available SNPs alone.
@article{
title = {CARD15 genetic variation in a Quebec population: prevalence, genotype-phenotype relationship, and haplotype structure},
type = {article},
year = {2002},
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pages = {74-83},
volume = {71},
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abstract = {The caspase recruitment domain gene (CARD15) was recently identified as the underlying gene associated with the IBD1 locus that confers susceptibility to Crohn disease (CD). CARD15 is related to the NOD1/Apaf-1 family of apoptosis regulators, and three sequence variants (Arg702Trp, Gly908Arg, and Leu1007fsinsC) in the gene were demonstrated to be associated with CD. We collected a cohort of 231 patients with CD and 71 healthy control individuals from the Canadian province of Quebec, to determine the prevalence of these sequence variants in an independent population. Clinical records of all patients were systematically reviewed, and detailed phenotypic information was obtained. All patient DNA samples were genotyped for the three variants, thus enabling an analysis of genotype-phenotype correlations. In this cohort, 45.0% of patients with CD carried at least one variant in the CARD15 gene, compared with 9.0% of control individuals (P<10-7). Allele frequencies of Arg702Trp, Gly908Arg, and Leu1007fsinsC were 12.9%, 5.2%, and 10.3% in patients with CD, compared with 4.2%, 0.7%, and 0.7% in control individuals, respectively. Importantly, CARD15 mutants were seen with equal frequency in patients with familial and sporadic CD. Analysis of the relationship between genotype and phenotype convincingly demonstrates that CARD15 variants are significantly associated with ileal disease involvement, as opposed to strictly colonic disease (P<.001). Moreover, we were able to determine the haplotype structure surrounding this disease gene by genotyping 45 single-nucleotide polymorphisms (SNPs) in a 177-kb region that contained the CARD15 gene. This structure helps clarify the history of these causal mutations. Finally, this analysis shows that CARD15 involvement with CD is detectable by use of publicly available SNPs alone.},
bibtype = {article},
author = {Vermeire, S and Wild, G and Kocher, K and Cousineau, J and Dufresne, L and Bitton, A and Langelier, D and Pare, P and Lapointe, G and Cohen, A and Daly, M J and Rioux, J D},
journal = {Am J Hum Genet},
number = {1}
}Genomics. New mapping project splits the community. Couzin, J. Science, 296(5572):1391-1393, 2002.
Paper bibtex
Paper bibtex @article{
title = {Genomics. New mapping project splits the community},
type = {article},
year = {2002},
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keywords = {*Chromosome Mapping/economics,*Genome, Human,*Genomics,*Haplotypes,Costs and Cost Analysis,Databases, Nucleic Acid,Financing, Government,Genetic Predisposition to Disease,Genotype,Human,Mutation,National Institutes of Health (U.S.),Polymorphism, Single Nucleotide,Racial Stocks/genetics,Research Support,United States},
pages = {1391-1393},
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source_type = {Journal Article},
notes = {<m:note>News</m:note>},
bibtype = {article},
author = {Couzin, J},
journal = {Science},
number = {5572}
}AGEID: a database of aging genes and interventions. Kaeberlein, M., Jegalian, B., & McVey, M. Mech Ageing Dev, 123(8):1115-1119, 2002.
Paper Website abstract bibtex
Paper Website abstract bibtex The aging genes/interventions database (AGEID) is a database of experimental results related to aging. AGEID is available as part of the science of aging knowledge environment on the World Wide Web at http://sageke.sciencemag.org/cgi/genesdb. The goal of AGEID is to catalog, in one location, every published experiment where life span has been measured in any organism. AGEID also includes information on genes that influence the incidence of age-associated disorders such as Alzheimer's disease and Parkinson's disease. AGEID gene/intervention reports are formatted pages containing the organism and strain background in which the particular experiment was performed, the type of genetic or environmental perturbation, the effect on life span, a description of the gene function and its role in longevity, protein homologs, and references. The use of this database by researchers who study aging should facilitate easy comparison of the genes and interventions that affect life span in different organisms.
@article{
title = {AGEID: a database of aging genes and interventions},
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identifiers = {[object Object]},
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pages = {1115-1119},
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abstract = {The aging genes/interventions database (AGEID) is a database of experimental results related to aging. AGEID is available as part of the science of aging knowledge environment on the World Wide Web at http://sageke.sciencemag.org/cgi/genesdb. The goal of AGEID is to catalog, in one location, every published experiment where life span has been measured in any organism. AGEID also includes information on genes that influence the incidence of age-associated disorders such as Alzheimer's disease and Parkinson's disease. AGEID gene/intervention reports are formatted pages containing the organism and strain background in which the particular experiment was performed, the type of genetic or environmental perturbation, the effect on life span, a description of the gene function and its role in longevity, protein homologs, and references. The use of this database by researchers who study aging should facilitate easy comparison of the genes and interventions that affect life span in different organisms.},
bibtype = {article},
author = {Kaeberlein, M and Jegalian, B and McVey, M},
journal = {Mech Ageing Dev},
number = {8}
}2001 (11)
Replication studies in longevity: puzzling findings in Danish centenarians at the 3'APOB-VNTR locus. Varcasia, O., Garasto, S., Rizza, T., Andersen-Ranberg, K., Jeune, B., Bathum, L., Andreev, K., Tan, Q., Yashin, A., I., Bonafe, M., Franceschi, C., & De Benedictis, G. Ann Hum Genet, 65(Pt 4):371-376, 2001.
Website abstract bibtex
Website abstract bibtex In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20-64-year-old subjects. However, when Danish and Italian data were compared, a significant difference (p = 0.0004) was found between the frequencies of Small alleles in youths, which disappeared in centenarians (p = 0.290). Furthermore, the demographic-genetic approach revealed in Danes a significant gene-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history.
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title = {Replication studies in longevity: puzzling findings in Danish centenarians at the 3'APOB-VNTR locus},
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pages = {371-376},
volume = {65},
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abstract = {In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20-64-year-old subjects. However, when Danish and Italian data were compared, a significant difference (p = 0.0004) was found between the frequencies of Small alleles in youths, which disappeared in centenarians (p = 0.290). Furthermore, the demographic-genetic approach revealed in Danes a significant gene-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history.},
bibtype = {article},
author = {Varcasia, O and Garasto, S and Rizza, T and Andersen-Ranberg, K and Jeune, B and Bathum, L and Andreev, K and Tan, Q and Yashin, A I and Bonafe, M and Franceschi, C and De Benedictis, G},
journal = {Ann Hum Genet},
number = {Pt 4}
}Objects and attention: The state of the art. Scholl, B. J. Cognition, 80(1-2):1-46, 2001.
abstract bibtex
abstract bibtex
What are the units of attention? In addition to standard models holding that attention can select spatial regions and visual features, recent work suggests that in some cases attention can directly select discrete objects. This paper reviews the state of the art with regard to such 'object-based' attention, and explores how objects of attention relate to locations, reference frames, perceptual groups, surfaces, parts, and features. Also discussed are the dynamic aspects of objecthood, including the question of how attended objects are individuated in time, and the possibility of attending to simple dynamic motions and events. The final sections of this review generalize these issues beyond vision science, to other modalities and fields such as auditory objects of attention and the infant's 'object concept'.
@Article{Scholl2001b,
author = {B. J. Scholl},
journal = {Cognition},
title = {Objects and attention: {T}he state of the art.},
year = {2001},
number = {1-2},
pages = {1-46},
volume = {80},
abstract = {What are the units of attention? In addition to standard models holding
that attention can select spatial regions and visual features, recent
work suggests that in some cases attention can directly select discrete
objects. This paper reviews the state of the art with regard to such
'object-based' attention, and explores how objects of attention relate
to locations, reference frames, perceptual groups, surfaces, parts,
and features. Also discussed are the dynamic aspects of objecthood,
including the question of how attended objects are individuated in
time, and the possibility of attending to simple dynamic motions
and events. The final sections of this review generalize these issues
beyond vision science, to other modalities and fields such as auditory
objects of attention and the infant's 'object concept'.},
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}Understanding human disease mutations through the use of interspecific genetic variation. Miller, M., P. & Kumar, S. Hum Mol Genet, 10(21):2319-2328, 2001.
Paper Website abstract bibtex
Paper Website abstract bibtex Data on replacement mutations in genes of disease patients exist in a variety of online resources. In addition, genome sequencing projects and individual gene sequencing efforts have led to the identification of disease gene homologs in diverse metazoan species. The availability of these two types of information provides unique opportunities to investigate factors that are important in the development of genetically based disease by contrasting long and short-term molecular evolutionary patterns. Therefore, we conducted an analysis of disease-associated human genetic variation for seven disease genes: the cystic fibrosis transmembrane conductance regulator, glucose-6-phosphate dehydrogenase, the neural cell adhesion molecule L1, phenylalanine hydroxylase, paired box 6, the X-linked retinoschisis gene and TSC2/tuberin. Our analyses indicate that disease mutations show definite patterns when examined from an evolutionary perspective. Human replacement mutations resulting in disease are overabundant at amino acid positions most conserved throughout the long-term history of metazoans. In contrast, human polymorphic replacement mutations and silent mutations are randomly distributed across sites with respect to the level of conservation of amino acid sites within genes. Furthermore, disease-causing amino acid changes are of types usually not observed among species. Using Grantham's chemical difference matrix, we find that amino acid changes observed in disease patients are far more radical than the variation found among species and in non-diseased humans. Overall, our results demonstrate the usefulness of evolutionary analyses for understanding patterns of human disease mutations and underscore the biomedical significance of sequence data currently being generated from various model organism genome sequencing projects.
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title = {Understanding human disease mutations through the use of interspecific genetic variation},
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pages = {2319-2328},
volume = {10},
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notes = {<m:note>0964-6906 (Print)<m:linebreak/>Journal Article</m:note>},
abstract = {Data on replacement mutations in genes of disease patients exist in a variety of online resources. In addition, genome sequencing projects and individual gene sequencing efforts have led to the identification of disease gene homologs in diverse metazoan species. The availability of these two types of information provides unique opportunities to investigate factors that are important in the development of genetically based disease by contrasting long and short-term molecular evolutionary patterns. Therefore, we conducted an analysis of disease-associated human genetic variation for seven disease genes: the cystic fibrosis transmembrane conductance regulator, glucose-6-phosphate dehydrogenase, the neural cell adhesion molecule L1, phenylalanine hydroxylase, paired box 6, the X-linked retinoschisis gene and TSC2/tuberin. Our analyses indicate that disease mutations show definite patterns when examined from an evolutionary perspective. Human replacement mutations resulting in disease are overabundant at amino acid positions most conserved throughout the long-term history of metazoans. In contrast, human polymorphic replacement mutations and silent mutations are randomly distributed across sites with respect to the level of conservation of amino acid sites within genes. Furthermore, disease-causing amino acid changes are of types usually not observed among species. Using Grantham's chemical difference matrix, we find that amino acid changes observed in disease patients are far more radical than the variation found among species and in non-diseased humans. Overall, our results demonstrate the usefulness of evolutionary analyses for understanding patterns of human disease mutations and underscore the biomedical significance of sequence data currently being generated from various model organism genome sequencing projects.},
bibtype = {article},
author = {Miller, M P and Kumar, S},
journal = {Hum Mol Genet},
number = {21}
}Increase of homozygosity in centenarians revealed by a new inter-Alu PCR technique. Bonafe, M., Cardelli, M., Marchegiani, F., Cavallone, L., Giovagnetti, S., Olivieri, F., Lisa, R., Pieri, C., & Franceschi, C. Exp Gerontol, 36(7):1063-1073, 2001.
Paper Website abstract bibtex
Paper Website abstract bibtex In the present study a novel inter-Alu PCR technique that allows one to detect inter-individual differences in the genomic regions flanked by Alu repetitive sequences was developed. Two primers complementary to sequences present in different Alu repeats and marked with two different fluorochromes were used in the same PCR reaction, and the PCR products were separated and analyzed by capillary electrophoresis using an automatic sequencer. The method is highly reliable, and three patterns of peaks (QM376-400, QM780-790 and QM480) appeared to be representative for germ-line polymorphisms, as suggested by the results obtained in nine couples of monozygotic twins and four three-generation families. The frequency of these polymorphic peaks was studied in two different age groups (100 young subjects and 69 centenarians). In two out of the three regions (QM376-400 and QM480) a significant increase in homozygote genotypes frequency was observed in centenarians. These counterintuitive results suggest that increased homozygosity contributes to human longevity. This novel inter-Alu PCR approach could represent a valuable tool to identify longevity-associated DNA sequences interspersed throughout human genome, without making any a priori assumption about their nature and function.
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abstract = {In the present study a novel inter-Alu PCR technique that allows one to detect inter-individual differences in the genomic regions flanked by Alu repetitive sequences was developed. Two primers complementary to sequences present in different Alu repeats and marked with two different fluorochromes were used in the same PCR reaction, and the PCR products were separated and analyzed by capillary electrophoresis using an automatic sequencer. The method is highly reliable, and three patterns of peaks (QM376-400, QM780-790 and QM480) appeared to be representative for germ-line polymorphisms, as suggested by the results obtained in nine couples of monozygotic twins and four three-generation families. The frequency of these polymorphic peaks was studied in two different age groups (100 young subjects and 69 centenarians). In two out of the three regions (QM376-400 and QM480) a significant increase in homozygote genotypes frequency was observed in centenarians. These counterintuitive results suggest that increased homozygosity contributes to human longevity. This novel inter-Alu PCR approach could represent a valuable tool to identify longevity-associated DNA sequences interspersed throughout human genome, without making any a priori assumption about their nature and function.},
bibtype = {article},
author = {Bonafe, M and Cardelli, M and Marchegiani, F and Cavallone, L and Giovagnetti, S and Olivieri, F and Lisa, R and Pieri, C and Franceschi, C},
journal = {Exp Gerontol},
number = {7}
}Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas. Jensen-Seaman, M., I., Deinard, A., S., & Kidd, K., K. J Hered, 92(6):475-480, 2001.
Paper Website abstract bibtex
Paper Website abstract bibtex In order to fully understand human evolutionary history through the use of molecular data, it is essential to include our closest relatives as a comparison. We provide here estimates of nucleotide diversity and effective population size of modern African ape species using data from several independent noncoding nuclear loci, and use these estimates to make predictions about the nature of the ancestral population that eventually gave rise to the living species of African apes, including humans. Chimpanzees, bonobos, and gorillas possess two to three times more nucleotide diversity than modern humans. We hypothesize that the last common ancestor (LCA) of these species had an effective population size more similar to modern apes than modern humans. In addition, estimated dates for the divergence of the Homo, Pan, and Gorilla lineages suggest that the LCA may have had stronger geographic structuring to its mtDNA than its nuclear DNA, perhaps indicative of strong female philopatry or a dispersal system analogous to gorillas, where females disperse only short distances from their natal group. Synthesizing different classes of data, and the inferences drawn from them, allows us to predict some of the genetic and demographic properties of the LCA of humans, chimpanzees, and gorillas.
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title = {Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas},
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abstract = {In order to fully understand human evolutionary history through the use of molecular data, it is essential to include our closest relatives as a comparison. We provide here estimates of nucleotide diversity and effective population size of modern African ape species using data from several independent noncoding nuclear loci, and use these estimates to make predictions about the nature of the ancestral population that eventually gave rise to the living species of African apes, including humans. Chimpanzees, bonobos, and gorillas possess two to three times more nucleotide diversity than modern humans. We hypothesize that the last common ancestor (LCA) of these species had an effective population size more similar to modern apes than modern humans. In addition, estimated dates for the divergence of the Homo, Pan, and Gorilla lineages suggest that the LCA may have had stronger geographic structuring to its mtDNA than its nuclear DNA, perhaps indicative of strong female philopatry or a dispersal system analogous to gorillas, where females disperse only short distances from their natal group. Synthesizing different classes of data, and the inferences drawn from them, allows us to predict some of the genetic and demographic properties of the LCA of humans, chimpanzees, and gorillas.},
bibtype = {article},
author = {Jensen-Seaman, M I and Deinard, A S and Kidd, K K},
journal = {J Hered},
number = {6}
}Arteriel Pressure, Left Ventricular Mass, and Aldosterone in Essential Hypertension. El-gharbawy, A., H., Nadig, V., S., Kotchen, J., M., Grim, C., E., Sagar, K., B., Kaldunski, M., Hamet, P., Pausova, Z., Gaudet, D., Gossard, F., & Kotchen, T., A. Hypertension, 37(3):845-850, 2001.
Paper abstract bibtex
Paper abstract bibtex The purpose of the present study was to evaluate the relationship of aldosterone to blood pressure and left ventricular size in black American (n=109) and white French Canadian (n=73) patients with essential hypertension. Measurements were obtained with patients off antihypertensive medications and included 24-hour blood pressure monitoring, plasma renin activity and aldosterone, and an echocardiogram. Compared with the French Canadians, the black Americans had higher body mass indexes, higher systolic blood pressures, attenuated nighttime reduction of blood pressure, and lower serum potassium concentrations (P:<0.01 for each). Left ventricular mass index, posterior wall thickness, interventricular septal thickness, and relative wall thickness were also greater (P:<0.01 for each) in the black American patients. Supine and standing plasma renin activity was lower (P:<0.01 and P:<0.05, respectively) in the black Americans, whereas supine plasma aldosterone concentrations did not differ, and standing plasma aldosterone was greater (P:<0.05) in the black Americans (9.2+/-0.7 ng/dL) than in the French Canadians (7.3+/-0.6 ng/dL). In the black Americans, supine plasma aldosterone was positively correlated with nighttime systolic (r=0.30; P:<0.01) and diastolic (r=0.39; P:<0.001) blood pressures and inversely correlated with the nocturnal decline of systolic (r=-0.29; P:<0.01) and diastolic (r=-0.37; P:<0.001) blood pressures. In the black Americans, standing plasma aldosterone was positively correlated with left ventricular mass index (r=0.36; P:<0.001), posterior wall thickness (r=0.33; P:<0.01), and interventricular septal thickness (r=0.26; P:<0.05). When the black American patients were divided into obese and nonobese groups, significant correlations between plasma aldosterone and both blood pressure and cardiac mass were observed only in the obese. In the French Canadians, overall, plasma aldosterone did not correlate with either blood pressure or any measures of heart size. However, among obese French Canadians, supine plasma aldosterone correlated with nighttime diastolic (r=0.53, P:<0.02) and systolic (r=0.44, P:<0.01) blood pressures but not with cardiac mass. These results are consistent with the hypothesis that aldosterone contributes to elevated arterial pressure in obese black American and obese white French Canadian patients with essential hypertension and to the attenuated nocturnal decline of blood pressure and left ventricular hypertrophy in obese, hypertensive black Americans.
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notes = {<m:note> <m:bold>From Duplicate 1 ( </m:bold> <m:bold> </m:bold><m:bold><m:italic>Arterial pressure, left ventricular mass, and aldosterone in essential hypertension</m:italic></m:bold><m:bold> </m:bold> <m:bold> - El-Gharbawy, A H; Nadig, V S; Kotchen, J M; Grim, C E; Sagar, K B; Kaldunski, M; Hamet, P; Pausova, Z; Gaudet, D; Gossard, F; Kotchen, T A )<m:linebreak/> </m:bold> <m:linebreak/>Journal Article<m:linebreak/> <m:linebreak/> </m:note>},
abstract = {The purpose of the present study was to evaluate the relationship of aldosterone to blood pressure and left ventricular size in black American (n=109) and white French Canadian (n=73) patients with essential hypertension. Measurements were obtained with patients off antihypertensive medications and included 24-hour blood pressure monitoring, plasma renin activity and aldosterone, and an echocardiogram. Compared with the French Canadians, the black Americans had higher body mass indexes, higher systolic blood pressures, attenuated nighttime reduction of blood pressure, and lower serum potassium concentrations (P:<0.01 for each). Left ventricular mass index, posterior wall thickness, interventricular septal thickness, and relative wall thickness were also greater (P:<0.01 for each) in the black American patients. Supine and standing plasma renin activity was lower (P:<0.01 and P:<0.05, respectively) in the black Americans, whereas supine plasma aldosterone concentrations did not differ, and standing plasma aldosterone was greater (P:<0.05) in the black Americans (9.2+/-0.7 ng/dL) than in the French Canadians (7.3+/-0.6 ng/dL). In the black Americans, supine plasma aldosterone was positively correlated with nighttime systolic (r=0.30; P:<0.01) and diastolic (r=0.39; P:<0.001) blood pressures and inversely correlated with the nocturnal decline of systolic (r=-0.29; P:<0.01) and diastolic (r=-0.37; P:<0.001) blood pressures. In the black Americans, standing plasma aldosterone was positively correlated with left ventricular mass index (r=0.36; P:<0.001), posterior wall thickness (r=0.33; P:<0.01), and interventricular septal thickness (r=0.26; P:<0.05). When the black American patients were divided into obese and nonobese groups, significant correlations between plasma aldosterone and both blood pressure and cardiac mass were observed only in the obese. In the French Canadians, overall, plasma aldosterone did not correlate with either blood pressure or any measures of heart size. However, among obese French Canadians, supine plasma aldosterone correlated with nighttime diastolic (r=0.53, P:<0.02) and systolic (r=0.44, P:<0.01) blood pressures but not with cardiac mass. These results are consistent with the hypothesis that aldosterone contributes to elevated arterial pressure in obese black American and obese white French Canadian patients with essential hypertension and to the attenuated nocturnal decline of blood pressure and left ventricular hypertrophy in obese, hypertensive black Americans.},
bibtype = {article},
author = {El-gharbawy, Areeg H and Nadig, Vishwanatha S and Kotchen, Jane Morley and Grim, Clarence E and Sagar, Kiran B and Kaldunski, Mary and Hamet, Pavel and Pausova, Zdenka and Gaudet, Daniel and Gossard, Francis and Kotchen, Theodore A},
journal = {Hypertension},
number = {3}
}Searching for human longevity genes: the future history of gerontology in the post-genomic era. Barzilai, N. & Shuldiner, A., R. J Gerontol A Biol Sci Med Sci, 56(2):M83-7, 2001.
Website abstract bibtex
Website abstract bibtex Over the last 30 years, a number of genetic and environmental factors that lead to decreased length of life have been identified. Unfortunately, much less progress has been achieved in identifying genes associated with longevity that protect from common diseases or slow the aging process. Recent compelling evidence supports a role for important genetic and environmental interactions on longevity in lower organisms. Although less is known in humans, commonality in molecular and biological processes, evolutionary arguments, and epidemiological data would strongly suggest that similar mechanisms also apply. The completion of the Human Genome Project and the rapid innovations in technology will make possible the identification of human longevity-assurance genes. This article reviews such evidence, its implications for the identification of human longevity-assurance genes, and the significance of finding longevity genes to human health and disease.
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title = {Searching for human longevity genes: the future history of gerontology in the post-genomic era},
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pages = {M83-7},
volume = {56},
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abstract = {Over the last 30 years, a number of genetic and environmental factors that lead to decreased length of life have been identified. Unfortunately, much less progress has been achieved in identifying genes associated with longevity that protect from common diseases or slow the aging process. Recent compelling evidence supports a role for important genetic and environmental interactions on longevity in lower organisms. Although less is known in humans, commonality in molecular and biological processes, evolutionary arguments, and epidemiological data would strongly suggest that similar mechanisms also apply. The completion of the Human Genome Project and the rapid innovations in technology will make possible the identification of human longevity-assurance genes. This article reviews such evidence, its implications for the identification of human longevity-assurance genes, and the significance of finding longevity genes to human health and disease.},
bibtype = {article},
author = {Barzilai, N and Shuldiner, A R},
journal = {J Gerontol A Biol Sci Med Sci},
number = {2}
}Measuring the genetic influence in modulating the human life span: gene-environment interaction and the sex-specific genetic effect. Tan, Q., De Benedictis, G., Yashi, A., I., Bonafe, M., DeLuca, M., Valensin, S., Vaupel, J., W., & Franceschi, C. Biogerontology, 2(3):141-153, 2001.
Paper Website abstract bibtex
Paper Website abstract bibtex New approaches are needed to explore the different ways in which genes affect the human life span. One needs to assess the genetic effects themselves, as well as gene-environment interactions and sex dependency. In this paper, we present a new model that combines both genotypic and demographic information in the estimation of the genetic influence on life spans. Based on Cox's proportional hazard assumption, the model measures the risks for each gene as well as for gene-environment and gene-sex interactions, while controlling for confounding factors. A two-step MLE is introduced to obtain a non-parametric form of the baseline hazard function. The model is applied to genotypic data from Italian centenarian studies to estimate relative risks of candidate genes, risks due to interactions and initial frequencies of different genes in the population. Results from models that either do or do not take into consideration individual heterogeneity are compared. It is shown that ignoring the existence of heterogeneity can lead to a systematic underestimation of genetic effects and effects due to interactions.
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pages = {141-153},
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notes = {<m:note>1389-5729<m:linebreak/>Journal Article</m:note>},
abstract = {New approaches are needed to explore the different ways in which genes affect the human life span. One needs to assess the genetic effects themselves, as well as gene-environment interactions and sex dependency. In this paper, we present a new model that combines both genotypic and demographic information in the estimation of the genetic influence on life spans. Based on Cox's proportional hazard assumption, the model measures the risks for each gene as well as for gene-environment and gene-sex interactions, while controlling for confounding factors. A two-step MLE is introduced to obtain a non-parametric form of the baseline hazard function. The model is applied to genotypic data from Italian centenarian studies to estimate relative risks of candidate genes, risks due to interactions and initial frequencies of different genes in the population. Results from models that either do or do not take into consideration individual heterogeneity are compared. It is shown that ignoring the existence of heterogeneity can lead to a systematic underestimation of genetic effects and effects due to interactions.},
bibtype = {article},
author = {Tan, Q and De Benedictis, G and Yashi, A I and Bonafe, M and DeLuca, M and Valensin, S and Vaupel, J W and Franceschi, C},
journal = {Biogerontology},
number = {3}
}Y chromosome binary markers to study the high prevalence of males in Sardinian centenarians and the genetic structure of the Sardinian population. Passarino, G., Underhill, P., A., Cavalli-Sforza, L., L., Semino, O., Pes, G., M., Carru, C., Ferrucci, L., Bonafe, M., Franceschi, C., Deiana, L., Baggio, G., & De Benedictis, G. Hum Hered, 52(3):136-139, 2001.
Website abstract bibtex
Website abstract bibtex We have analyzed a sample of 40 centenarians and 116 young controls from Sardinia, with a set of new Y chromosome binary markers, to evaluate if Y chromosome genes are involved in the high prevalence of males among centenarian Sardinians (1/2 vs. 1/4 in other populations studied). The results indicate that none of the seven lineages that account for >97% of the Y chromosome diversity in Sardinia provide an advantage with respect to the extreme longevity. However, our results, although based on the male-specific Y chromosome polymorphisms, give a clear profile of the pattern of genetic variability in Sardinia. Indeed they indicate that the Sardinian population had two main founder populations that have evolved in isolation for at least the last 5,000 years. These findings set the stage for future studies on longevity and other complex traits in Sardinia.
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title = {Y chromosome binary markers to study the high prevalence of males in Sardinian centenarians and the genetic structure of the Sardinian population},
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pages = {136-139},
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abstract = {We have analyzed a sample of 40 centenarians and 116 young controls from Sardinia, with a set of new Y chromosome binary markers, to evaluate if Y chromosome genes are involved in the high prevalence of males among centenarian Sardinians (1/2 vs. 1/4 in other populations studied). The results indicate that none of the seven lineages that account for >97% of the Y chromosome diversity in Sardinia provide an advantage with respect to the extreme longevity. However, our results, although based on the male-specific Y chromosome polymorphisms, give a clear profile of the pattern of genetic variability in Sardinia. Indeed they indicate that the Sardinian population had two main founder populations that have evolved in isolation for at least the last 5,000 years. These findings set the stage for future studies on longevity and other complex traits in Sardinia.},
bibtype = {article},
author = {Passarino, G and Underhill, P A and Cavalli-Sforza, L L and Semino, O and Pes, G M and Carru, C and Ferrucci, L and Bonafe, M and Franceschi, C and Deiana, L and Baggio, G and De Benedictis, G},
journal = {Hum Hered},
number = {3}
}Positive and negative selection on the human genome. Fay, J., C., Wyckoff, G., J., & Wu, C., I. Genetics, 158(3):1227-1234, 2001.
Paper abstract bibtex
Paper abstract bibtex The distinction between deleterious, neutral, and adaptive mutations is a fundamental problem in the study of molecular evolution. Two significant quantities are the fraction of DNA variation in natural populations that is deleterious and destined to be eliminated and the fraction of fixed differences between species driven by positive Darwinian selection. We estimate these quantities using the large number of human genes for which there are polymorphism and divergence data. The fraction of amino acid mutations that is neutral is estimated to be 0.20 from the ratio of common amino acid (A) to synonymous (S) single nucleotide polymorphisms (SNPs) at frequencies of > or =15%. Among the 80% of amino acid mutations that are deleterious at least 20% of them are only slightly deleterious and often attain frequencies of 1-10%. We estimate that these slightly deleterious mutations comprise at least 3% of amino acid SNPs in the average individual or at least 300 per diploid genome. This estimate is not sensitive to human population history. The A/S ratio of fixed differences is greater than that of common SNPs and suggests that a large fraction of protein divergence is adaptive and driven by positive Darwinian selection.
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title = {Positive and negative selection on the human genome},
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year = {2001},
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pages = {1227-1234},
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notes = {<m:note>Journal Article</m:note>},
abstract = {The distinction between deleterious, neutral, and adaptive mutations is a fundamental problem in the study of molecular evolution. Two significant quantities are the fraction of DNA variation in natural populations that is deleterious and destined to be eliminated and the fraction of fixed differences between species driven by positive Darwinian selection. We estimate these quantities using the large number of human genes for which there are polymorphism and divergence data. The fraction of amino acid mutations that is neutral is estimated to be 0.20 from the ratio of common amino acid (A) to synonymous (S) single nucleotide polymorphisms (SNPs) at frequencies of > or =15%. Among the 80% of amino acid mutations that are deleterious at least 20% of them are only slightly deleterious and often attain frequencies of 1-10%. We estimate that these slightly deleterious mutations comprise at least 3% of amino acid SNPs in the average individual or at least 300 per diploid genome. This estimate is not sensitive to human population history. The A/S ratio of fixed differences is greater than that of common SNPs and suggests that a large fraction of protein divergence is adaptive and driven by positive Darwinian selection.},
bibtype = {article},
author = {Fay, J C and Wyckoff, G J and Wu, C I},
journal = {Genetics},
number = {3}
}A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4. Puca, A., A., Daly, M., J., Brewster, S., J., Matise, T., C., Barrett, J., Shea-Drinkwater, M., Kang, S., Joyce, E., Nicoli, J., Benson, E., Kunkel, L., M., & Perls, T. Proc Natl Acad Sci U S A, 98(18):10505-10508, 2001.
Paper Website abstract bibtex
Paper Website abstract bibtex Substantial evidence supports the familial aggregation of exceptional longevity. The existence of rare families demonstrating clustering for this phenotype suggests that a genetic etiology may be an important component. Previous attempts at localizing loci predisposing for exceptional longevity have been limited to association studies of candidate gene polymorphisms. In this study, a genome-wide scan for such predisposing loci was conducted by using 308 individuals belonging to 137 sibships demonstrating exceptional longevity. By using nonparametric analysis, significant evidence for linkage was noted for chromosome 4 at D4S1564 with a MLS of 3.65 (P = 0.044). The analysis was corroborated by a parametric analysis (P = 0.052). These linkage results indicate the likelihood that there exists a gene, or genes, that exerts a substantial influence on the ability to achieve exceptional old age. Identification of the genes in humans that allow certain individuals to live to extreme old age should lead to insights on cellular pathways that are important to the aging process.
@article{
title = {A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4},
type = {article},
year = {2001},
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keywords = {*Linkage (Genetics),Aged,Aged, 80 and over,Aging/genetics,Chromosomes, Human, Pair 4/*genetics,Female,Genome, Human,Humans,Lod Score,Longevity/*genetics,Male,Nuclear Family,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.},
pages = {10505-10508},
volume = {98},
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abstract = {Substantial evidence supports the familial aggregation of exceptional longevity. The existence of rare families demonstrating clustering for this phenotype suggests that a genetic etiology may be an important component. Previous attempts at localizing loci predisposing for exceptional longevity have been limited to association studies of candidate gene polymorphisms. In this study, a genome-wide scan for such predisposing loci was conducted by using 308 individuals belonging to 137 sibships demonstrating exceptional longevity. By using nonparametric analysis, significant evidence for linkage was noted for chromosome 4 at D4S1564 with a MLS of 3.65 (P = 0.044). The analysis was corroborated by a parametric analysis (P = 0.052). These linkage results indicate the likelihood that there exists a gene, or genes, that exerts a substantial influence on the ability to achieve exceptional old age. Identification of the genes in humans that allow certain individuals to live to extreme old age should lead to insights on cellular pathways that are important to the aging process.},
bibtype = {article},
author = {Puca, A A and Daly, M J and Brewster, S J and Matise, T C and Barrett, J and Shea-Drinkwater, M and Kang, S and Joyce, E and Nicoli, J and Benson, E and Kunkel, L M and Perls, T},
journal = {Proc Natl Acad Sci U S A},
number = {18}
}2000 (2)
Development and testing of a clinical tool measuring self-management of heart failure. Riegel, B., Carlson, B., & Glaser, D. Heart Lung, 29(1):4–15, 2000.
abstract bibtex
abstract bibtex
BACKGROUND: Self-management is a primary goal of treatment for heart failure. Yet no measure of self-management in this patient group currently exists. OBJECTIVES: To develop a clinically useful measure of the abilities of patients with heart failure to manage their disease. Self-management in this context was defined as a cognitive decision-making process undertaken in response to signs and symptoms of heart failure. A panel of experts agreed that the process involved 4 distinct stages: recognizing a change, evaluating the change, implementing a treatment strategy, and evaluating the treatment. The tool was developed to reflect this process. METHODS: Face validity of the process model was assessed in a sample of 25 patients with heart failure and used to develop a 65-item tool with 6 subscales. The subscales measure the 4 stages as well as the patients' ease in evaluating the signs and symptoms and their self-efficacy. The tool was pilot tested with 2 samples of patients with heart failure (N = 17; N = 129). Psychometrics of the final tool were then tested in a sample of 127 patients with heart failure. RESULTS: Face and content validity of the tool were demonstrated adequately through this study. Internal consistency scores of the 6 subscales of the Self-Management of Heart Failure instrument ranged from 0.79 (ease of evaluating treatment) to 0.92 (evaluating the change). Reliability could not be calculated for 1 subscale (evaluating the treatment) because of missing data that resulted from patients skipping sections because they had not experienced a symptom. CONCLUSION: Clinicians interested in evaluating the self-management abilities of their patients with heart failure are encouraged to use this tool and to contribute to additional testing
@article{riegel_development_2000,
title = {Development and testing of a clinical tool measuring self-management of heart failure.},
volume = {29},
issn = {0147-9563},
abstract = {BACKGROUND: Self-management is a primary goal of treatment for heart failure. Yet no measure of self-management in this patient group currently exists. OBJECTIVES: To develop a clinically useful measure of the abilities of patients with heart failure to manage their disease. Self-management in this context was defined as a cognitive decision-making process undertaken in response to signs and symptoms of heart failure. A panel of experts agreed that the process involved 4 distinct stages: recognizing a change, evaluating the change, implementing a treatment strategy, and evaluating the treatment. The tool was developed to reflect this process. METHODS: Face validity of the process model was assessed in a sample of 25 patients with heart failure and used to develop a 65-item tool with 6 subscales. The subscales measure the 4 stages as well as the patients' ease in evaluating the signs and symptoms and their self-efficacy. The tool was pilot tested with 2 samples of patients with heart failure (N = 17; N = 129). Psychometrics of the final tool were then tested in a sample of 127 patients with heart failure. RESULTS: Face and content validity of the tool were demonstrated adequately through this study. Internal consistency scores of the 6 subscales of the Self-Management of Heart Failure instrument ranged from 0.79 (ease of evaluating treatment) to 0.92 (evaluating the change). Reliability could not be calculated for 1 subscale (evaluating the treatment) because of missing data that resulted from patients skipping sections because they had not experienced a symptom. CONCLUSION: Clinicians interested in evaluating the self-management abilities of their patients with heart failure are encouraged to use this tool and to contribute to additional testing},
number = {1},
journal = {Heart Lung},
author = {Riegel, B. and Carlson, B. and Glaser, D.},
year = {2000},
keywords = {3D proceso validación, Aged, Evaluation Studies as Topic, Female, Heart Failure, Humans, Male, Middle Aged, Pilot Projects, Psychometrics, Reproducibility of Results, Self Care, content validity, non-u.s. gov't, research support, validity, validity \& reliability},
pages = {4--15}
}Genetic nature of individual frailty: comparison of two approaches. Begun, A., Z., Iachine, I., A., & Yashin, A., I. Twin Res, 3(1):51-57, 2000.
Website abstract bibtex
Website abstract bibtex The traditional frailty models used in genetic analysis of bivariate survival data assume that individual frailty (and longevity) is influenced by thousands of genes, and that the contribution of each separate gene is small. This assumption, however, does not have a solid biological basis. It may just happen that one or a small number of genes makes a major contribution to determining the human life span. To answer the questions about the nature of the genetic influence on life span using survival data, models are needed that specify the influence of major genes on individual frailty and longevity. The goal of this paper is to test the nature of genetic influences on individual frailty and longevity using survival data on Danish twins. We use a new bivariate survival model with one major gene influencing life span to analyse survival data on MZ (monozygotic) and DZ (dizygotic) twins. The analysis shows that two radically different classes of model provide an equally good fit to the data. However, the asymptotic behaviour of some conditional statistics is different in models from different classes. Because of the limited sample size of bivariate survival data we cannot draw reliable conclusions about the nature of genetic effects on life span. Additional information about tails of bivariate distribution or risk factors may help to solve this problem.
@article{
title = {Genetic nature of individual frailty: comparison of two approaches},
type = {article},
year = {2000},
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pages = {51-57},
volume = {3},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10808241},
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abstract = {The traditional frailty models used in genetic analysis of bivariate survival data assume that individual frailty (and longevity) is influenced by thousands of genes, and that the contribution of each separate gene is small. This assumption, however, does not have a solid biological basis. It may just happen that one or a small number of genes makes a major contribution to determining the human life span. To answer the questions about the nature of the genetic influence on life span using survival data, models are needed that specify the influence of major genes on individual frailty and longevity. The goal of this paper is to test the nature of genetic influences on individual frailty and longevity using survival data on Danish twins. We use a new bivariate survival model with one major gene influencing life span to analyse survival data on MZ (monozygotic) and DZ (dizygotic) twins. The analysis shows that two radically different classes of model provide an equally good fit to the data. However, the asymptotic behaviour of some conditional statistics is different in models from different classes. Because of the limited sample size of bivariate survival data we cannot draw reliable conclusions about the nature of genetic effects on life span. Additional information about tails of bivariate distribution or risk factors may help to solve this problem.},
bibtype = {article},
author = {Begun, A Z and Iachine, I A and Yashin, A I},
journal = {Twin Res},
number = {1}
}1999 (2)
Genetic factors in susceptibility to death: a comparative analysis of bivariate survival models. Yashin, A., I., Begun, A., Z., & Iachine, I., A. J Epidemiol Biostat, 4(1):53-60, 1999.
Website abstract bibtex
Website abstract bibtex BACKGROUND: Molecular epidemiological studies of aging and longevity are focused on evaluating the effects of single genes on susceptibility to disease and death. The effects of all genetic factors on susceptibility can be evaluated from the analysis of survival data on related individuals. METHOD: The analyses of survival data on Danish monozygotic (MZ) and dizygotic (DZ) twins are performed using gamma, inverse Gaussian and three-parameter correlated frailty models. The semiparametric representations of the respective models are used to obtain maximum likelihood estimates of model parameters. The results are compared using the likelihood ratio test. RESULTS: The survival of Danish MZ and DZ twins can be characterised by the same marginal hazards and identical univariate frailty distributions for any of the three frailty models. In all three cases the genetic influence on frailty is statistically significant. CONCLUSION: All three models can be used to study genetic effects on susceptibility. The gamma and inverse Gaussian frailty models fit the Danish twin data equally well. Our analyses show that for the Danish twin data these two models are preferable to the three-parameter model.
@article{
title = {Genetic factors in susceptibility to death: a comparative analysis of bivariate survival models},
type = {article},
year = {1999},
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pages = {53-60},
volume = {4},
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notes = {<m:note>1359-5229<m:linebreak/>Journal Article<m:linebreak/>Twin Study</m:note>},
abstract = {BACKGROUND: Molecular epidemiological studies of aging and longevity are focused on evaluating the effects of single genes on susceptibility to disease and death. The effects of all genetic factors on susceptibility can be evaluated from the analysis of survival data on related individuals. METHOD: The analyses of survival data on Danish monozygotic (MZ) and dizygotic (DZ) twins are performed using gamma, inverse Gaussian and three-parameter correlated frailty models. The semiparametric representations of the respective models are used to obtain maximum likelihood estimates of model parameters. The results are compared using the likelihood ratio test. RESULTS: The survival of Danish MZ and DZ twins can be characterised by the same marginal hazards and identical univariate frailty distributions for any of the three frailty models. In all three cases the genetic influence on frailty is statistically significant. CONCLUSION: All three models can be used to study genetic effects on susceptibility. The gamma and inverse Gaussian frailty models fit the Danish twin data equally well. Our analyses show that for the Danish twin data these two models are preferable to the three-parameter model.},
bibtype = {article},
author = {Yashin, A I and Begun, A Z and Iachine, I A},
journal = {J Epidemiol Biostat},
number = {1}
}Dynamic paradigms for human mortality and aging. Manton, K., G. J Gerontol A Biol Sci Med Sci, 54(6):B247-54, 1999.
Website abstract bibtex
Website abstract bibtex Hazard models are often applied to mortality data of humans and other species so that the parameter estimates made for those models can be used to make inferences about the biology, and comparative biology, of aging processes. Enough longitudinal data on physiological and functional changes in humans now exist to know that the age trajectory of the physiological state of individuals is multidimensional, stochastic, and plastic. Thus, to fully assess the biological significance of existing longitudinal data on human aging and mortality processes, multivariate stochastic process models must be developed that are biologically detailed and valid. This requires assessing genetic mechanisms controlling human longevity and rates of aging, developing models of how those traits may have evolved, and developing statistical methods for identifying gene environment interactions. This article examines the theoretical basis for such models and the biological rationale of their parametric structure. Several examples are given.
@article{
title = {Dynamic paradigms for human mortality and aging},
type = {article},
year = {1999},
identifiers = {[object Object]},
keywords = {*Aging/immunology/physiology,*Longevity,*Models, Biological,*Models, Statistical,Aged,Aged, 80 and over,Cytochrome P-450 Enzyme System/metabolism,Heat-Shock Proteins/metabolism,Humans,Life Expectancy,Middle Aged,Mortality,Nonlinear Dynamics,Research Support, U.S. Gov't, P.H.S.,Stochastic Processes},
pages = {B247-54},
volume = {54},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10411010},
id = {c24194cd-c364-356a-8720-ab36c5382190},
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notes = {<m:note>1079-5006<m:linebreak/>Journal Article</m:note>},
abstract = {Hazard models are often applied to mortality data of humans and other species so that the parameter estimates made for those models can be used to make inferences about the biology, and comparative biology, of aging processes. Enough longitudinal data on physiological and functional changes in humans now exist to know that the age trajectory of the physiological state of individuals is multidimensional, stochastic, and plastic. Thus, to fully assess the biological significance of existing longitudinal data on human aging and mortality processes, multivariate stochastic process models must be developed that are biologically detailed and valid. This requires assessing genetic mechanisms controlling human longevity and rates of aging, developing models of how those traits may have evolved, and developing statistical methods for identifying gene environment interactions. This article examines the theoretical basis for such models and the biological rationale of their parametric structure. Several examples are given.},
bibtype = {article},
author = {Manton, K G},
journal = {J Gerontol A Biol Sci Med Sci},
number = {6}
}1998 (4)
How heritable is individual susceptibility to death? The results of an analysis of survival data on Danish, Swedish and Finnish twins. Iachine, I., A., Holm, N., V., Harris, J., R., Begun, A., Z., Iachina, M., K., Laitinen, M., Kaprio, J., & Yashin, A., I. Twin Res, 1(4):196-205, 1998.
Website abstract bibtex
Website abstract bibtex Molecular epidemiological studies confirm a substantial contribution of individual genes to variability in susceptibility to disease and death for humans. To evaluate the contribution of all genes to susceptibility and to estimate individual survival characteristics, survival data on related individuals (eg twins or other relatives) are needed. Correlated gamma-frailty models of bivariate survival are used in a joint analysis of survival data on more than 31,000 pairs of Danish, Swedish and Finnish male and female twins using the maximum likelihood method. Additive decomposition of frailty into genetic and environmental components is used to estimate heritability in frailty. The estimate of the standard deviation of frailty from the pooled data is about 1.5. The hypothesis that variance in frailty and correlations of frailty for twins are similar in the data from all three countries is accepted. The estimate of narrow-sense heritability in frailty is about 0.5. The age trajectories of individual hazards are evaluated for all three populations of twins and both sexes. The results of our analysis confirm the presence of genetic influences on individual frailty and longevity. They also suggest that the mechanism of these genetic influences may be similar for the three Scandinavian countries. Furthermore, results indicate that the increase in individual hazard with age is more rapid than predicted by traditional demographic life tables.
@article{
title = {How heritable is individual susceptibility to death? The results of an analysis of survival data on Danish, Swedish and Finnish twins},
type = {article},
year = {1998},
identifiers = {[object Object]},
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pages = {196-205},
volume = {1},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10100811},
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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}
}Mitochondrial aging: open questions. Beckman, K., B. & Ames, B., N. Ann N Y Acad Sci, 854:118-127, 1998.
Website abstract bibtex
Website abstract bibtex Interest in the role of mitochondria in aging has intensified in recent years. This focus on mitochondria originated in part from the free radical theory of aging, which argues that oxidative damage plays a key role in degenerative senescence. Among the numerous mechanisms known to generate oxidants, leakage of the superoxide anion and hydrogen peroxide from the mitochondrial electron transport chain are of particular interest, due to the correlation between species-specific metabolic rate ("rate of living") and life span. Phenomenological studies of mitochondrial function long ago noted a decline in mitochondrial function with age, and on-going research continues to add to this body of knowledge. The extranuclear somatic mutation theory of aging proposes that the accumulation of mutations in the mitochondrial genome may be responsible in part for the mitochondrial phenomenology of aging. Recent studies of mitochondrial DNA (mtDNA) deletions have shown that they increase with age in humans and other mammals. Currently, there exist numerous important and fundamental questions surrounding mitochondria and aging. Among these are (1) How important are mitochondrial oxidants in determining overall cellular oxidative stress? (2) What are the mechanisms of mitochondrial oxidant generation? (3) How are lesions and mutations in mtDNA formed? (4) How important are mtDNA lesions and mutations in causing mitochondrial dysfunction? (5) How are mitochondria regulated, and how does this regulation change during aging? (6) What are the dynamics of mitochondrial turnover? (7) What is the relationship between mitochondrial damage and lipofuscinogenesis? (8) What are the relationships among mitochondria, apopotosis, and aging? and (9) How can mitochondrial function (ATP generation and the establishment of a membrane potential) and dysfunction (oxidant generation) be modulated and degenerative senescence thereby treated?
@article{
title = {Mitochondrial aging: open questions},
type = {article},
year = {1998},
identifiers = {[object Object]},
keywords = {Aging/*physiology,Animals,Antioxidants/metabolism,DNA, Mitochondrial/genetics,Humans,Life Expectancy,Longevity,Mammals,Mitochondria/*metabolism,Mutation,Oxidants/metabolism,Oxidative Phosphorylation,Research Support, U.S. Gov't, P.H.S.},
pages = {118-127},
volume = {854},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9928425},
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notes = {<m:note>0077-8923<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
abstract = {Interest in the role of mitochondria in aging has intensified in recent years. This focus on mitochondria originated in part from the free radical theory of aging, which argues that oxidative damage plays a key role in degenerative senescence. Among the numerous mechanisms known to generate oxidants, leakage of the superoxide anion and hydrogen peroxide from the mitochondrial electron transport chain are of particular interest, due to the correlation between species-specific metabolic rate ("rate of living") and life span. Phenomenological studies of mitochondrial function long ago noted a decline in mitochondrial function with age, and on-going research continues to add to this body of knowledge. The extranuclear somatic mutation theory of aging proposes that the accumulation of mutations in the mitochondrial genome may be responsible in part for the mitochondrial phenomenology of aging. Recent studies of mitochondrial DNA (mtDNA) deletions have shown that they increase with age in humans and other mammals. Currently, there exist numerous important and fundamental questions surrounding mitochondria and aging. Among these are (1) How important are mitochondrial oxidants in determining overall cellular oxidative stress? (2) What are the mechanisms of mitochondrial oxidant generation? (3) How are lesions and mutations in mtDNA formed? (4) How important are mtDNA lesions and mutations in causing mitochondrial dysfunction? (5) How are mitochondria regulated, and how does this regulation change during aging? (6) What are the dynamics of mitochondrial turnover? (7) What is the relationship between mitochondrial damage and lipofuscinogenesis? (8) What are the relationships among mitochondria, apopotosis, and aging? and (9) How can mitochondrial function (ATP generation and the establishment of a membrane potential) and dysfunction (oxidant generation) be modulated and degenerative senescence thereby treated?},
bibtype = {article},
author = {Beckman, K B and Ames, B N},
journal = {Ann N Y Acad Sci}
}A genome scan for loci influencing total serum immunoglobulin levels: possible linkage of IgA to the chromosome 13 atopy locus. Wiltshire, S., Bhattacharyya, S., Faux, J., A., Leaves, N., I., Daniels, S., E., Moffatt, M., F., James, A., Musk, A., W., & Cookson, W., O. Hum Mol Genet, 7(1):27-31, 1998.
Website abstract bibtex
Website abstract bibtex Immunoglobulins play an essential part in the immune system, and immunoglobulin deficiencies can have profound medical consequences. The genetic control and regulation of the immunoglobulin response is therefore of interest. Previous investigations have identified a number of loci influencing total and specific IgE levels. In this study, 80 nuclear families have been examined for linkage of total serum IgA, IgG and IgM levels to a genome-wide panel of microsatellite markers. Potential quantitative trait loci influencing IgA levels have been identified on chromosomes 10 and 13, and possible loci influencing IgG levels were found on chromosomes 3 and 13. No significant linkages to IgM levels were found. The linkage of IgA on chromosome 13 was to a marker previously linked to IgE responses (atopy). Linkage to IgG was in the same region but to a more distal marker. None of the factors known to influence immunoglobulin expression map to the loci identified in the present study. These loci are therefore likely to contain previously unrecognized components of the immunoregulatory system.
@article{
title = {A genome scan for loci influencing total serum immunoglobulin levels: possible linkage of IgA to the chromosome 13 atopy locus},
type = {article},
year = {1998},
identifiers = {[object Object]},
keywords = {*Chromosomes, Human, Pair 13,*Genes, Immunoglobulin,*Genome, Human,Humans,Immunoglobulin A/*genetics,Linkage (Genetics),Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.},
pages = {27-31},
volume = {7},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9384600},
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abstract = {Immunoglobulins play an essential part in the immune system, and immunoglobulin deficiencies can have profound medical consequences. The genetic control and regulation of the immunoglobulin response is therefore of interest. Previous investigations have identified a number of loci influencing total and specific IgE levels. In this study, 80 nuclear families have been examined for linkage of total serum IgA, IgG and IgM levels to a genome-wide panel of microsatellite markers. Potential quantitative trait loci influencing IgA levels have been identified on chromosomes 10 and 13, and possible loci influencing IgG levels were found on chromosomes 3 and 13. No significant linkages to IgM levels were found. The linkage of IgA on chromosome 13 was to a marker previously linked to IgE responses (atopy). Linkage to IgG was in the same region but to a more distal marker. None of the factors known to influence immunoglobulin expression map to the loci identified in the present study. These loci are therefore likely to contain previously unrecognized components of the immunoregulatory system.},
bibtype = {article},
author = {Wiltshire, S and Bhattacharyya, S and Faux, J A and Leaves, N I and Daniels, S E and Moffatt, M F and James, A and Musk, A W and Cookson, W O},
journal = {Hum Mol Genet},
number = {1}
}Surgical treatment of intrahepatic portosystemic shunts in 45 dogs. White, R., N., Burton, C., A., & McEvoy, F., J. The Veterinary record, 142(14):358-365, 4, 1998.
abstract bibtex
abstract bibtex
The surgical attenuation of an intrahepatic portosystemic shunt in 45 dogs is described. Twenty-nine (64 per cent) had left divisional shunts consistent with a patent ductus venosus (PDV), 15 (33 per cent) had central divisional shunts and one had a right divisional shunt. In the dogs with a PDV, the shunt vessel could be most easily manipulated at a posthepatic site, whereas in those with central and right divisional shunts the manipulation could be more easily made intrahepatically but sometimes involved demanding intravascular surgical techniques. Eight dogs (18 per cent) died during the surgery or shortly afterwards. Of the 37 dogs surviving longer term, 28 (76 per cent) became clinically normal and required no medication or diet control. In a further three animals the shunt was ligated completely only during a second surgical procedure. The remaining six dogs were euthanased because of clinical signs of encephalopathy which were either surgically or medically uncontrollable.
@article{
title = {Surgical treatment of intrahepatic portosystemic shunts in 45 dogs},
type = {article},
year = {1998},
identifiers = {[object Object]},
keywords = {Abnormalities/surgery/veterinary,Animals,Dog Diseases/surgery,Dogs,Female,Hepatic Veins/abnormalities,Male,Portal System/abnormalities,Portal Vein/abnormalities,Prognosis,Research Support, Non-U.S. Gov't,Surgery, Veterinary/methods,Suture Techniques/veterinary,Treatment Outcome},
pages = {358-365},
volume = {142},
month = {4},
day = {4},
city = {Department of Small Animal Medicine and Surgery, Royal Veterinary College, University of London, Hatfield, Hertfordshire.},
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abstract = {The surgical attenuation of an intrahepatic portosystemic shunt in 45 dogs is described. Twenty-nine (64 per cent) had left divisional shunts consistent with a patent ductus venosus (PDV), 15 (33 per cent) had central divisional shunts and one had a right divisional shunt. In the dogs with a PDV, the shunt vessel could be most easily manipulated at a posthepatic site, whereas in those with central and right divisional shunts the manipulation could be more easily made intrahepatically but sometimes involved demanding intravascular surgical techniques. Eight dogs (18 per cent) died during the surgery or shortly afterwards. Of the 37 dogs surviving longer term, 28 (76 per cent) became clinically normal and required no medication or diet control. In a further three animals the shunt was ligated completely only during a second surgical procedure. The remaining six dogs were euthanased because of clinical signs of encephalopathy which were either surgically or medically uncontrollable.},
bibtype = {article},
author = {White, R N and Burton, C A and McEvoy, F J},
journal = {The Veterinary record},
number = {14}
}1997 (3)
Neural mechanisms of spatial selective attention in areas V1, V2, and V4 of macaque visual cortex. Luck, S J, Chelazzi, L, Hillyard, S A, & Desimone, R J Neurophysiol, 77(1):24–42, 1997. Place: UNITED STATES ISBN: 0022-3077
abstract bibtex
abstract bibtex
Many neurons in extrastriate visual cortex have large receptive fields, and this may lead to significant computational problems whenever multiple stimuli fall within a single field. Previous studies have suggested that when multiple stimuli fall within a cell's receptive field, they compete for the cell's response in a manner that can be biased in favor of attended stimuli. In the present study we examined this role of attention in areas V1, V2, and V4 of macaque monkeys with the use of a behavioral paradigm in which attention was directed to one of two stimulus locations. When two stimuli were presented simultaneously inside the cell's receptive field (which could be accomplished only in areas V2 and V4), we found that the cell's response was strongly influenced by which of the two stimuli was attended. The size of this attention effect was reduced when the attended and ignored stimuli were presented sequentially rather than simultaneously. In addition, the effects became very weak and inconsistent in these areas when only one of the two stimuli was located inside the receptive field. Attention thus modulated sensory responses primarily when two or more simultaneous stimuli competed for access to a neuron's receptive field. As in areas V2 and V4, attention did not modulate sensory responses in area V1 when only a single stimulus was inside the receptive field. In addition, the small receptive fields in this area precluded the simultaneous presentation of attended and ignored stimuli inside the receptive field, making it impossible to determine whether attention effects would be observed under the conditions that led to consistent attention effects in areas V2 and V4. Spontaneous firing rates in areas V2 and V4 were found to be 30-40% higher when attention was directed inside rather than outside the receptive field, even when no stimulus was present in the receptive field. Spontaneous firing rates also varied according to the particular location within the receptive field that was attended. These shifts in spontaneous activity may reflect a top-down signal that biases responses in favor of stimuli at the attended location.
@article{luck_neural_1997,
title = {Neural mechanisms of spatial selective attention in areas {V1}, {V2}, and {V4} of macaque visual cortex.},
volume = {77},
abstract = {Many neurons in extrastriate visual cortex have large receptive fields, and this may lead to significant computational problems whenever multiple stimuli fall within a single field. Previous studies have suggested that when multiple stimuli fall within a cell's receptive field, they compete for the cell's response in a manner that can be biased in favor of attended stimuli. In the present study we examined this role of attention in areas V1, V2, and V4 of macaque monkeys with the use of a behavioral paradigm in which attention was directed to one of two stimulus locations. When two stimuli were presented simultaneously inside the cell's receptive field (which could be accomplished only in areas V2 and V4), we found that the cell's response was strongly influenced by which of the two stimuli was attended. The size of this attention effect was reduced when the attended and ignored stimuli were presented sequentially rather than simultaneously. In addition, the effects became very weak and inconsistent in these areas when only one of the two stimuli was located inside the receptive field. Attention thus modulated sensory responses primarily when two or more simultaneous stimuli competed for access to a neuron's receptive field. As in areas V2 and V4, attention did not modulate sensory responses in area V1 when only a single stimulus was inside the receptive field. In addition, the small receptive fields in this area precluded the simultaneous presentation of attended and ignored stimuli inside the receptive field, making it impossible to determine whether attention effects would be observed under the conditions that led to consistent attention effects in areas V2 and V4. Spontaneous firing rates in areas V2 and V4 were found to be 30-40\% higher when attention was directed inside rather than outside the receptive field, even when no stimulus was present in the receptive field. Spontaneous firing rates also varied according to the particular location within the receptive field that was attended. These shifts in spontaneous activity may reflect a top-down signal that biases responses in favor of stimuli at the attended location.},
language = {eng},
number = {1},
journal = {J Neurophysiol},
author = {Luck, S J and Chelazzi, L and Hillyard, S A and Desimone, R},
year = {1997},
pmid = {9120566},
note = {Place: UNITED STATES
ISBN: 0022-3077},
keywords = {Animals, Attention, Cues, Electrodes, Implanted, Evoked Potentials, Visual, Eye Movements, Macaca mulatta, Male, Neurons, Photic Stimulation, Psychomotor Performance, Space Perception, Visual Cortex, research support, non-u.s. gov't, research support, u.s. gov't, non-p.h.s., research support, u.s. gov't, p.h.s.},
pages = {24--42},
}Genetics of aging. Finch, C., E. & Tanzi, R., E. Science, 278(5337):407-411, 1997.
Website abstract bibtex
Website abstract bibtex The role of genetics in determining life-span is complex and paradoxical. Although the heritability of life-span is relatively minor, some genetic variants significantly modify senescence of mammals and invertebrates, with both positive and negative impacts on age-related disorders and life-spans. In certain examples, the gene variants alter metabolic pathways, which could thereby mediate interactions with nutritional and other environmental factors that influence life-span. Given the relatively minor effect and variable penetrance of genetic risk factors that appear to affect survival and health at advanced ages, life-style and other environmental influences may profoundly modify outcomes of aging.
@article{
title = {Genetics of aging},
type = {article},
year = {1997},
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keywords = {Aging/*genetics,Alzheimer Disease/genetics,Animals,Apoptosis/genetics,Gene Expression,Humans,Longevity/*genetics,Mutation,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.,Risk Factors,Variation (Genetics)},
pages = {407-411},
volume = {278},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9334291},
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notes = {<m:note>0036-8075<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
abstract = {The role of genetics in determining life-span is complex and paradoxical. Although the heritability of life-span is relatively minor, some genetic variants significantly modify senescence of mammals and invertebrates, with both positive and negative impacts on age-related disorders and life-spans. In certain examples, the gene variants alter metabolic pathways, which could thereby mediate interactions with nutritional and other environmental factors that influence life-span. Given the relatively minor effect and variable penetrance of genetic risk factors that appear to affect survival and health at advanced ages, life-style and other environmental influences may profoundly modify outcomes of aging.},
bibtype = {article},
author = {Finch, C E and Tanzi, R E},
journal = {Science},
number = {5337}
}Atopic dermatitis and birth factors: historical follow up by record linkage. Olesen, A., B., Ellingsen, A., R., Olesen, H., Juul, S., & Thestrup-Pedersen, K. Bmj, 314(7086):1003-1008, 1997.
Website abstract bibtex
Website abstract bibtex OBJECTIVE: To study if factors at birth are associated with later development of atopic dermatitis. DESIGN: Historical follow up by record linkage from Danish medical birth register. Children were followed up for 5.5 to 8.5 years. Second historical follow up study comprising questionnaire to mothers of singleborn children 6.5 to 9.5 years after birth. SETTING: Private dermatology clinics and dermatology and paediatric departments in the municipality of Aarhus, Denmark. SUBJECTS: 7862 singletons born in hospital between 1 January 1984 and 31 December 1986 to mothers living in the municipality of Aarhus. Questionnaires sent to 985 mothers. MAIN OUTCOME MEASURES: Gestational age, birth weight, parity, and age of mother at the time of birth. Atopy in children diagnosed by specialists in dermatology and physicians. Family size; diagnosis of atopic dermatitis, allergic rhinitis, and asthma; family predisposition; and mothers' smoking habits during pregnancy determined from questionnaires. RESULTS: Of 7862 children, 403 were diagnosed as having atopic dermatitis by a specialist; the cumulative incidence at age 7 was 5.6%. High gestational age and low parity were associated with an increased risk of atopic dermatitis. Among 985 children atopic dermatitis had been diagnosed by any physician in 184; the cumulative incidence at age 7 was 18.7%. High birth weight, high gestational age, and family history of atopy were associated with increased risk of atopic dermatitis. CONCLUSION: In both studies the incidence of atopic dermatitis was associated with high gestational age and in one with high birth weight also. The causes for these associations are at present unknown but may indicate that even during gestation factors associated with atopic dermatitis influence maturation.
@article{
title = {Atopic dermatitis and birth factors: historical follow up by record linkage},
type = {article},
year = {1997},
identifiers = {[object Object]},
keywords = {*Birth Weight,*Gestational Age,Adult,Age Factors,Child,Child, Preschool,Denmark/epidemiology,Dermatitis, Atopic/epidemiology/*etiology/genetics,Female,Follow-Up Studies,Humans,Incidence,Infant,Male,Maternal Age,Medical Record Linkage,Parity,Pedigree,Pregnancy,Research Support, Non-U.S. Gov't,Risk Factors},
pages = {1003-1008},
volume = {314},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9112844},
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abstract = {OBJECTIVE: To study if factors at birth are associated with later development of atopic dermatitis. DESIGN: Historical follow up by record linkage from Danish medical birth register. Children were followed up for 5.5 to 8.5 years. Second historical follow up study comprising questionnaire to mothers of singleborn children 6.5 to 9.5 years after birth. SETTING: Private dermatology clinics and dermatology and paediatric departments in the municipality of Aarhus, Denmark. SUBJECTS: 7862 singletons born in hospital between 1 January 1984 and 31 December 1986 to mothers living in the municipality of Aarhus. Questionnaires sent to 985 mothers. MAIN OUTCOME MEASURES: Gestational age, birth weight, parity, and age of mother at the time of birth. Atopy in children diagnosed by specialists in dermatology and physicians. Family size; diagnosis of atopic dermatitis, allergic rhinitis, and asthma; family predisposition; and mothers' smoking habits during pregnancy determined from questionnaires. RESULTS: Of 7862 children, 403 were diagnosed as having atopic dermatitis by a specialist; the cumulative incidence at age 7 was 5.6%. High gestational age and low parity were associated with an increased risk of atopic dermatitis. Among 985 children atopic dermatitis had been diagnosed by any physician in 184; the cumulative incidence at age 7 was 18.7%. High birth weight, high gestational age, and family history of atopy were associated with increased risk of atopic dermatitis. CONCLUSION: In both studies the incidence of atopic dermatitis was associated with high gestational age and in one with high birth weight also. The causes for these associations are at present unknown but may indicate that even during gestation factors associated with atopic dermatitis influence maturation.},
bibtype = {article},
author = {Olesen, A B and Ellingsen, A R and Olesen, H and Juul, S and Thestrup-Pedersen, K},
journal = {Bmj},
number = {7086}
}1996 (4)
Asthma on Tristan da Cunha: looking for the genetic link. The University of Toronto Genetics of Asthma Research Group. Zamel, N., McClean, P., A., Sandell, P., R., Siminovitch, K., A., & Slutsky, A., S. Am J Respir Crit Care Med, 153(6 Pt 1):1902-1906, 1996.
Website abstract bibtex
Website abstract bibtex Although asthma has a significant heritable component, the mode of inheritance remains controversial because of the complexity of the disease and the influence of environmental factors. Isolated, inbred populations serve to reduce variability, thus increasing the probability of gene localization. We studied the inbred population of the remote island of Tristan da Cunha to document asthma prevalence for the purpose of genetic linkage analysis. Medical histories and skin atopy were determined on 282 islanders, representing 97% of the population, and airway responsiveness was measured in 254; 226 by methacholine challenge (tidal breathing method) and 28 by bronchodilator response (400 micrograms salbutamol aerosol). Blood samples were collected from 275 islanders. Participants ranged in age from 3 to 94 yr. Asthma was defined as increased airway responsiveness (AR+: PC20 < 4 mg/ml or > or = 15% increase in FEV1 postbronchodilator) combined with a positive history (Hx+). Fifty-seven percent of the islanders had at least partial evidence of asthma (Hx+ and/or AR+) and 23% had a definitive diagnosis of asthma (AR+ with Hx+). Overall 47% of the population were atopic, atopy was proportionally higher in asthmatics (74%) than nonasthmatics (32%; p < 0.01). Analysis of the methacholine dose-response curves demonstrated that asthmatics were significantly (p < 0.01) more responsive than those with AR+ only, and nonasthmatics (AR-, Hx-) were more responsive than laboratory control subjects (p < 0.05), suggesting that these islanders may also carry an airway hyperresponsiveness gene. A frequency plot of the percent fall in FEV1 for all Hx- subjects compared with control data suggests a bimodal distribution consistent with a major gene mechanism for airway responsiveness. Genealogy mapping revealed that the islanders are direct descendants of the 15 original settlers, and historical records suggest at least two founders may have been asthmatic. The data confirm previous reports of a high asthma prevalence on Tristan and support the postulate that this prevalence is a result of gene enrichment occurring in isolated populations by virtue of extensive inbreeding and a probable founder effect.
@article{
title = {Asthma on Tristan da Cunha: looking for the genetic link. The University of Toronto Genetics of Asthma Research Group},
type = {article},
year = {1996},
identifiers = {[object Object]},
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pages = {1902-1906},
volume = {153},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8665053},
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abstract = {Although asthma has a significant heritable component, the mode of inheritance remains controversial because of the complexity of the disease and the influence of environmental factors. Isolated, inbred populations serve to reduce variability, thus increasing the probability of gene localization. We studied the inbred population of the remote island of Tristan da Cunha to document asthma prevalence for the purpose of genetic linkage analysis. Medical histories and skin atopy were determined on 282 islanders, representing 97% of the population, and airway responsiveness was measured in 254; 226 by methacholine challenge (tidal breathing method) and 28 by bronchodilator response (400 micrograms salbutamol aerosol). Blood samples were collected from 275 islanders. Participants ranged in age from 3 to 94 yr. Asthma was defined as increased airway responsiveness (AR+: PC20 < 4 mg/ml or > or = 15% increase in FEV1 postbronchodilator) combined with a positive history (Hx+). Fifty-seven percent of the islanders had at least partial evidence of asthma (Hx+ and/or AR+) and 23% had a definitive diagnosis of asthma (AR+ with Hx+). Overall 47% of the population were atopic, atopy was proportionally higher in asthmatics (74%) than nonasthmatics (32%; p < 0.01). Analysis of the methacholine dose-response curves demonstrated that asthmatics were significantly (p < 0.01) more responsive than those with AR+ only, and nonasthmatics (AR-, Hx-) were more responsive than laboratory control subjects (p < 0.05), suggesting that these islanders may also carry an airway hyperresponsiveness gene. A frequency plot of the percent fall in FEV1 for all Hx- subjects compared with control data suggests a bimodal distribution consistent with a major gene mechanism for airway responsiveness. Genealogy mapping revealed that the islanders are direct descendants of the 15 original settlers, and historical records suggest at least two founders may have been asthmatic. The data confirm previous reports of a high asthma prevalence on Tristan and support the postulate that this prevalence is a result of gene enrichment occurring in isolated populations by virtue of extensive inbreeding and a probable founder effect.},
bibtype = {article},
author = {Zamel, N and McClean, P A and Sandell, P R and Siminovitch, K A and Slutsky, A S},
journal = {Am J Respir Crit Care Med},
number = {6 Pt 1}
}Speed of processing in the human visual system. Thorpe, S, Fize, D, & Marlot, C Nature, 381(6582):520–522, 1996. Place: ENGLAND ISBN: 0028-0836
doi abstract bibtex
doi abstract bibtex
How long does it take for the human visual system to process a complex natural image? Subjectively, recognition of familiar objects and scenes appears to be virtually instantaneous, but measuring this processing time experimentally has proved difficult. Behavioural measures such as reaction times can be used, but these include not only visual processing but also the time required for response execution. However, event-related potentials (ERPs) can sometimes reveal signs of neural processing well before the motor output. Here we use a go/no-go categorization task in which subjects have to decide whether a previously unseen photograph, flashed on for just 20 ms, contains an animal. ERP analysis revealed a frontal negativity specific to no-go trials that develops roughly 150 ms after stimulus onset. We conclude that the visual processing needed to perform this highly demanding task can be achieved in under 150 ms.
@article{thorpe_speed_1996,
title = {Speed of processing in the human visual system.},
volume = {381},
doi = {10.1038/381520a0},
abstract = {How long does it take for the human visual system to process a complex natural image? Subjectively, recognition of familiar objects and scenes appears to be virtually instantaneous, but measuring this processing time experimentally has proved difficult. Behavioural measures such as reaction times can be used, but these include not only visual processing but also the time required for response execution. However, event-related potentials (ERPs) can sometimes reveal signs of neural processing well before the motor output. Here we use a go/no-go categorization task in which subjects have to decide whether a previously unseen photograph, flashed on for just 20 ms, contains an animal. ERP analysis revealed a frontal negativity specific to no-go trials that develops roughly 150 ms after stimulus onset. We conclude that the visual processing needed to perform this highly demanding task can be achieved in under 150 ms.},
language = {eng},
number = {6582},
journal = {Nature},
author = {Thorpe, S and Fize, D and Marlot, C},
year = {1996},
pmid = {8632824},
note = {Place: ENGLAND
ISBN: 0028-0836},
keywords = {Adult, Evoked Potentials, Visual, Female, Humans, Male, Middle Aged, Reaction Time, Vision, Ocular, research support, non-u.s. gov't},
pages = {520--522},
}Activity changes in early visual cortex reflect monkeys' percepts during binocular rivalry. Leopold, D. A. & Logothetis, N. K. Nature, 379(6565):549-53, 1996.
doi abstract bibtex
doi abstract bibtex
When the two eyes view dissimilar images, we experience binocular rivalry, in which one eye's view dominates for several seconds and is then replaced by that of the other eye. What causes these perceptual changes in the absence of any change in the stimulus? We showed previously that some neurons in monkey cortical area MT show changes in activity during motion rivalry that reflect the perceived direction of motion. To determine whether perception-related modulation of activity occurs in other visual cortical areas, we recorded from individual neurons in V1, V2 and V4 while monkeys reported the perceived orientation of rival gratings of two orthogonal orientations. Many cells, particularly in V4, showed patterns of activity that correlated with the perceptual dominance and suppression of one stimulus. The majority were orientation-selective and could be driven equally well from either eye. It has been previously suggested that binocular rivalry involves reciprocal inhibition between monocular neurons within V1 (for example, see ref. 4), but our results do not support this view; rather, we propose that binocular rivalry arises through interactions between binocular neurons at several levels in the visual pathways, and that similar mechanisms may underlie other multistable perceptual states that occur when viewing ambiguous images.
@Article{Leopold1996,
author = {D. A. Leopold and N. K. Logothetis},
journal = {Nature},
title = {Activity changes in early visual cortex reflect monkeys' percepts during binocular rivalry.},
year = {1996},
number = {6565},
pages = {549-53},
volume = {379},
abstract = {When the two eyes view dissimilar images, we experience binocular
rivalry, in which one eye's view dominates for several seconds and
is then replaced by that of the other eye. What causes these perceptual
changes in the absence of any change in the stimulus? We showed previously
that some neurons in monkey cortical area MT show changes in activity
during motion rivalry that reflect the perceived direction of motion.
To determine whether perception-related modulation of activity occurs
in other visual cortical areas, we recorded from individual neurons
in V1, V2 and V4 while monkeys reported the perceived orientation
of rival gratings of two orthogonal orientations. Many cells, particularly
in V4, showed patterns of activity that correlated with the perceptual
dominance and suppression of one stimulus. The majority were orientation-selective
and could be driven equally well from either eye. It has been previously
suggested that binocular rivalry involves reciprocal inhibition between
monocular neurons within V1 (for example, see ref. 4), but our results
do not support this view; rather, we propose that binocular rivalry
arises through interactions between binocular neurons at several
levels in the visual pathways, and that similar mechanisms may underlie
other multistable perceptual states that occur when viewing ambiguous
images.},
doi = {10.1038/379549a0},
keywords = {Animals, Binocular, Humans, Macaca mulatta, Neurons, Non-P.H.S., P.H.S., Research Support, U.S. Gov't, Vision, Visual Cortex, Visual Perception, 8596623},
}Genetic and aging epidemiology. The merging of two disciplines. Cauley, J., A., Dorman, J., S., & Ganguli, M. Neurol Clin, 14(2):467-475, 1996.
Website abstract bibtex
Website abstract bibtex For future research in aging epidemiology to be meaningful, it will have to integrate knowledge and skills from multiple areas, including the application of genetic and molecular epidemiologic techniques to the study of the elderly. This article begins with an overview of genetic and molecular epidemiology, followed by a discussion of several unique methodologic issues that need to be considered in the interpretation of genetic and molecular findings of epidemiologic studies of the elderly.
@article{
title = {Genetic and aging epidemiology. The merging of two disciplines},
type = {article},
year = {1996},
identifiers = {[object Object]},
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pages = {467-475},
volume = {14},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8827183},
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abstract = {For future research in aging epidemiology to be meaningful, it will have to integrate knowledge and skills from multiple areas, including the application of genetic and molecular epidemiologic techniques to the study of the elderly. This article begins with an overview of genetic and molecular epidemiology, followed by a discussion of several unique methodologic issues that need to be considered in the interpretation of genetic and molecular findings of epidemiologic studies of the elderly.},
bibtype = {article},
author = {Cauley, J A and Dorman, J S and Ganguli, M},
journal = {Neurol Clin},
number = {2}
}1995 (1)
Categorical effects in the perception of faces. Beale, J M & Keil, F C Cognition, 57(3):217–239, 1995.
abstract bibtex
abstract bibtex
These studies suggest categorical perception effects may be much more general than has commonly been believed and can occur in apparently similar ways at dramatically different levels of processing. To test the nature of individual face representations, a linear continuum of "morphed" faces was generated between individual exemplars of familiar faces. In separate categorization, discrimination and "better-likeness" tasks, subjects viewed pairs of faces from these continua. Subjects discriminate most accurately when face-pairs straddle apparent category boundaries; thus individual faces are perceived categorically. A high correlation is found between the familiarity of a face-pair and the magnitude of the categorization effect. Categorical perception therefore is not limited to low-level perceptual continua, but can occur at higher levels and may be acquired through experience as well.
@article{beale_categorical_1995,
title = {Categorical effects in the perception of faces},
volume = {57},
abstract = {These studies suggest categorical perception effects may be much more general than has commonly been believed and can occur in apparently similar ways at dramatically different levels of processing. To test the nature of individual face representations, a linear continuum of "morphed" faces was generated between individual exemplars of familiar faces. In separate categorization, discrimination and "better-likeness" tasks, subjects viewed pairs of faces from these continua. Subjects discriminate most accurately when face-pairs straddle apparent category boundaries; thus individual faces are perceived categorically. A high correlation is found between the familiarity of a face-pair and the magnitude of the categorization effect. Categorical perception therefore is not limited to low-level perceptual continua, but can occur at higher levels and may be acquired through experience as well.},
number = {3},
journal = {Cognition},
author = {Beale, J M and Keil, F C},
year = {1995},
pmid = {8556842},
keywords = {*Face, *Visual Perception, Facial Expression, Humans, Research Support, U.S. Gov't, P.H.S.},
pages = {217--239},
}1994 (2)
A model for the neuronal implementation of selective visual attention based on temporal correlation among neurons. Niebur, E & Koch, C J Comput Neurosci, 1(1-2):141–158, 1994. Place: UNITED STATES ISBN: 0929-5313
abstract bibtex
abstract bibtex
We propose a model for the neuronal implementation of selective visual attention based on temporal correlation among groups of neurons. Neurons in primary visual cortex respond to visual stimuli with a Poisson distributed spike train with an appropriate, stimulus-dependent mean firing rate. The spike trains of neurons whose receptive fields do not overlap with the "focus of attention" are distributed according to homogeneous (time-independent) Poisson process with no correlation between action potentials of different neurons. In contrast, spike trains of neurons with receptive fields within the focus of attention are distributed according to non-homogeneous (time-dependent) Poisson processes. Since the short-term average spike rates of all neurons with receptive fields in the focus of attention covary, correlations between these spike trains are introduced which are detected by inhibitory interneurons in V4. These cells, modeled as modified integrate-and-fire neurons, function as coincidence detectors and suppress the response of V4 cells associated with non-attended visual stimuli. The model reproduces quantitatively experimental data obtained in cortical area V4 of monkey by Moran and Desimone (1985).
@article{niebur_model_1994,
title = {A model for the neuronal implementation of selective visual attention based on temporal correlation among neurons.},
volume = {1},
abstract = {We propose a model for the neuronal implementation of selective visual attention based on temporal correlation among groups of neurons. Neurons in primary visual cortex respond to visual stimuli with a Poisson distributed spike train with an appropriate, stimulus-dependent mean firing rate. The spike trains of neurons whose receptive fields do not overlap with the "focus of attention" are distributed according to homogeneous (time-independent) Poisson process with no correlation between action potentials of different neurons. In contrast, spike trains of neurons with receptive fields within the focus of attention are distributed according to non-homogeneous (time-dependent) Poisson processes. Since the short-term average spike rates of all neurons with receptive fields in the focus of attention covary, correlations between these spike trains are introduced which are detected by inhibitory interneurons in V4. These cells, modeled as modified integrate-and-fire neurons, function as coincidence detectors and suppress the response of V4 cells associated with non-attended visual stimuli. The model reproduces quantitatively experimental data obtained in cortical area V4 of monkey by Moran and Desimone (1985).},
language = {eng},
number = {1-2},
journal = {J Comput Neurosci},
author = {Niebur, E and Koch, C},
year = {1994},
pmid = {8792229},
note = {Place: UNITED STATES
ISBN: 0929-5313},
keywords = {Animals, Macaca, Membrane Potentials, Neural Networks (Computer), Time Factors, Visual Pathways, research support, u.s. gov't, non-p.h.s.},
pages = {141--158},
}Measuring emotion: the Self-Assessment Manikin and the Semantic Differential. Bradley, M M & Lang, P J J Behav Ther Exp Psychiatry, 25(1):49–59, 1994. Place: UNITED STATES ISBN: 0005-7916
abstract bibtex
abstract bibtex
The Self-Assessment Manikin (SAM) is a non-verbal pictorial assessment technique that directly measures the pleasure, arousal, and dominance associated with a person's affective reaction to a wide variety of stimuli. In this experiment, we compare reports of affective experience obtained using SAM, which requires only three simple judgments, to the Semantic Differential scale devised by Mehrabian and Russell (An approach to environmental psychology, 1974) which requires 18 different ratings. Subjective reports were measured to a series of pictures that varied in both affective valence and intensity. Correlations across the two rating methods were high both for reports of experienced pleasure and felt arousal. Differences obtained in the dominance dimension of the two instruments suggest that SAM may better track the personal response to an affective stimulus. SAM is an inexpensive, easy method for quickly assessing reports of affective response in many contexts.
@article{bradley_measuring_1994,
title = {Measuring emotion: the {Self}-{Assessment} {Manikin} and the {Semantic} {Differential}.},
volume = {25},
abstract = {The Self-Assessment Manikin (SAM) is a non-verbal pictorial assessment technique that directly measures the pleasure, arousal, and dominance associated with a person's affective reaction to a wide variety of stimuli. In this experiment, we compare reports of affective experience obtained using SAM, which requires only three simple judgments, to the Semantic Differential scale devised by Mehrabian and Russell (An approach to environmental psychology, 1974) which requires 18 different ratings. Subjective reports were measured to a series of pictures that varied in both affective valence and intensity. Correlations across the two rating methods were high both for reports of experienced pleasure and felt arousal. Differences obtained in the dominance dimension of the two instruments suggest that SAM may better track the personal response to an affective stimulus. SAM is an inexpensive, easy method for quickly assessing reports of affective response in many contexts.},
language = {eng},
number = {1},
journal = {J Behav Ther Exp Psychiatry},
author = {Bradley, M M and Lang, P J},
year = {1994},
pmid = {7962581},
note = {Place: UNITED STATES
ISBN: 0005-7916},
keywords = {Adult, Affect, Arousal, Emotions, Factor Analysis, Statistical, Female, Humans, Internal-External Control, Male, MicroValence, Personality Inventory, Psychometrics, Semantic Differential, comparative study, research support, u.s. gov't, p.h.s.},
pages = {49--59},
}1993 (1)
Longevity is moderately heritable in a sample of Danish twins born 1870-1880. McGue, M., Vaupel, J., W., Holm, N., & Harvald, B. J Gerontol, 48(6):B237-44, 1993.
Website abstract bibtex
Website abstract bibtex The heritability of human longevity was investigated in a sample of 218 pairs of monozygotic (MZ) and 382 pairs of like-sex dizygotic (DZ) Danish twin pairs born 1870-1880. Twin similarity for age at death was significant for MZ twins but nonsignificant for DZ twins. The heritability (h2) of life span estimated from the best-fitting biometrical model was statistically significant but moderate in magnitude (h2 = .333 +/- .058). Heritability of longevity did not vary by gender, and the pattern of twin resemblance was more consistent with nonadditive as compared to additive genetic effects. In addition, evidence for a genetic association between premature and senescent deaths was observed. Although environmental factors accounted for a majority of the variance in life span, the relevant environmental factors appeared to be those that create differences rather than similarities among reared-together relatives. Findings are discussed in terms of their relevance for understanding the inheritance and evolution of human life span.
@article{
title = {Longevity is moderately heritable in a sample of Danish twins born 1870-1880},
type = {article},
year = {1993},
identifiers = {[object Object]},
keywords = {Aged,Female,Humans,Life Expectancy,Longevity/*genetics,Male,Research Support, U.S. Gov't, P.H.S.,Socioeconomic Factors,Twins/*genetics},
pages = {B237-44},
volume = {48},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8227991},
id = {a38c8e13-f0fc-321f-9c8b-f8ef7a7917ad},
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read = {false},
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confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0022-1422<m:linebreak/>Journal Article</m:note>},
abstract = {The heritability of human longevity was investigated in a sample of 218 pairs of monozygotic (MZ) and 382 pairs of like-sex dizygotic (DZ) Danish twin pairs born 1870-1880. Twin similarity for age at death was significant for MZ twins but nonsignificant for DZ twins. The heritability (h2) of life span estimated from the best-fitting biometrical model was statistically significant but moderate in magnitude (h2 = .333 +/- .058). Heritability of longevity did not vary by gender, and the pattern of twin resemblance was more consistent with nonadditive as compared to additive genetic effects. In addition, evidence for a genetic association between premature and senescent deaths was observed. Although environmental factors accounted for a majority of the variance in life span, the relevant environmental factors appeared to be those that create differences rather than similarities among reared-together relatives. Findings are discussed in terms of their relevance for understanding the inheritance and evolution of human life span.},
bibtype = {article},
author = {McGue, M and Vaupel, J W and Holm, N and Harvald, B},
journal = {J Gerontol},
number = {6}
}1991 (1)
Population genetics of vitamin D-dependent rickets in northeastern Quebec. De Braekeleer, M. & Larochelle, J. Ann Hum Genet, 55 ( Pt 4):283-290, 1991.
Website abstract bibtex
Website abstract bibtex Vitamin D-dependent rickets (VDD1) is an autosomal recessive disorder that was recognized in Saguenay-Lac-St-Jean (SLSJ) in 1970. The great majority of the VDD1 cases reported in the French Canadian population of Quebec originated from SLSJ, Charlevoix, and the Haute Cote Nord, all regions located in northeastern Quebec. The prevalence at birth in SLSJ was estimated at 1/2916 live borns, and the carrier rate was estimated at 1/27 inhabitants in the SLSJ region. The mean coefficient of inbreeding was not elevated in the VDD1 group of SLSJ compared with three matched control groups. The mean coefficient of kinship was 2.5 times higher in the VDD1 group than in the control groups. In the SLSJ region, the places of origin of the VDD1 children and their children did not show a clustered non-uniform distribution. Endogamy was not found to be higher in the VDD1 group than in control groups. The genealogical reconstruction showed all the obligate carriers of the VDD1 gene, but one, to be related to a small set of founders who settled in New France in the 17th century. All these results, as well as a strong linkage disequilibrium between RFLPs located on the long arm of chromosome 12 and the VDD1 locus, support the hypothesis of a founder effect for VDD1. They also suggest that a unique mutation accounts for most, if not all, of the cases known in northeastern Quebec.
@article{
title = {Population genetics of vitamin D-dependent rickets in northeastern Quebec},
type = {article},
year = {1991},
identifiers = {[object Object]},
keywords = {*Genetics, Population,Consanguinity,Female,Gene Frequency,Heterozygote,Humans,Male,Polymorphism, Restriction Fragment Length,Quebec,Research Support, Non-U.S. Gov't,Rickets/*genetics},
pages = {283-290},
volume = {55 ( Pt 4)},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1687883},
id = {6e968474-d174-3044-99c2-7ee58d8d5835},
created = {2017-06-19T13:45:30.172Z},
file_attached = {false},
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last_modified = {2017-06-19T13:45:30.270Z},
read = {false},
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authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0003-4800<m:linebreak/>Journal Article</m:note>},
abstract = {Vitamin D-dependent rickets (VDD1) is an autosomal recessive disorder that was recognized in Saguenay-Lac-St-Jean (SLSJ) in 1970. The great majority of the VDD1 cases reported in the French Canadian population of Quebec originated from SLSJ, Charlevoix, and the Haute Cote Nord, all regions located in northeastern Quebec. The prevalence at birth in SLSJ was estimated at 1/2916 live borns, and the carrier rate was estimated at 1/27 inhabitants in the SLSJ region. The mean coefficient of inbreeding was not elevated in the VDD1 group of SLSJ compared with three matched control groups. The mean coefficient of kinship was 2.5 times higher in the VDD1 group than in the control groups. In the SLSJ region, the places of origin of the VDD1 children and their children did not show a clustered non-uniform distribution. Endogamy was not found to be higher in the VDD1 group than in control groups. The genealogical reconstruction showed all the obligate carriers of the VDD1 gene, but one, to be related to a small set of founders who settled in New France in the 17th century. All these results, as well as a strong linkage disequilibrium between RFLPs located on the long arm of chromosome 12 and the VDD1 locus, support the hypothesis of a founder effect for VDD1. They also suggest that a unique mutation accounts for most, if not all, of the cases known in northeastern Quebec.},
bibtype = {article},
author = {De Braekeleer, M and Larochelle, J},
journal = {Ann Hum Genet}
}1990 (3)
Spectral properties of V4 neurons in the macaque. Schein, S J & Desimone, R J Neurosci, 10(10):3369–3389, 1990. Place: UNITED STATES ISBN: 0270-6474
abstract bibtex
abstract bibtex
Spectral properties of 129 cells in the V4 area of 5 macaque monkeys were studied quantitatively with narrow-band and broad-band colored lights. The large majority of cells exhibited some degree of wavelength sensitivity within their receptive fields. The half-bandwidth of the primary peak in the spectral-response curve was less than 50 nm for 72% of the cells; the mean half-bandwidth of these cells, 27 nm, is similar to that found for color-opponent ganglion cells and cells in the parvocellular dorsal lateral geniculate nucleus (dLGN). Contrast-response functions indicated that the narrow spectral tuning of these cells derived from cone opponent interactions. From comparison of receptive-field sizes, we suggest that a typical V4 neuron sums inputs that ultimately derive from several thousand ganglion or parvocellular dLGN cells. In spite of their wavelength sensitivity, most V4 cells had properties that would not fit some simple criteria for classification as "color selective." First, few cells showed overt signs of color opponency, namely, on-inhibition or off-excitation to spectrally opponent wavelengths. Second, about 30% of the cells in V4 had spectral-response curves with 2 peaks. (The wavelength distribution of these second peaks was almost identical to that of primary peaks, and combinations of peak wavelengths were fairly random.) Third, most cells responded to white light; overall, the response to white light was about 60% of that to the best narrow-band or broad-band colored light. Similarly, most V4 cells gave at least a small response to all or nearly all of the different broad-band colored lights we presented. Therefore, a given V4 cell is very likely to respond to most of the colored or white surfaces in natural scenes. These combinations of response properties probably explain the widely divergent percentages of "color" cells reported in previous studies of V4. The most unusual spectral property we found in V4 was a large, spectrally sensitive surround outside the "classical receptive field" of most cells. Although stimulation of the surround by itself did not cause any response, surround stimulation could completely suppress the response to even the optimally colored stimulus in the receptive field. In general, the optimal wavelengths for receptive-field excitation and surround suppression were the same or nearly so. Thus, "color contrast" may be computed in V4. In some cases, contrasting wavelengths in the surround caused moderate enhancement of response to a receptive-field stimulus.(ABSTRACT TRUNCATED AT 400 WORDS)
@article{schein_spectral_1990,
title = {Spectral properties of {V4} neurons in the macaque.},
volume = {10},
abstract = {Spectral properties of 129 cells in the V4 area of 5 macaque monkeys were studied quantitatively with narrow-band and broad-band colored lights. The large majority of cells exhibited some degree of wavelength sensitivity within their receptive fields. The half-bandwidth of the primary peak in the spectral-response curve was less than 50 nm for 72\% of the cells; the mean half-bandwidth of these cells, 27 nm, is similar to that found for color-opponent ganglion cells and cells in the parvocellular dorsal lateral geniculate nucleus (dLGN). Contrast-response functions indicated that the narrow spectral tuning of these cells derived from cone opponent interactions. From comparison of receptive-field sizes, we suggest that a typical V4 neuron sums inputs that ultimately derive from several thousand ganglion or parvocellular dLGN cells. In spite of their wavelength sensitivity, most V4 cells had properties that would not fit some simple criteria for classification as "color selective." First, few cells showed overt signs of color opponency, namely, on-inhibition or off-excitation to spectrally opponent wavelengths. Second, about 30\% of the cells in V4 had spectral-response curves with 2 peaks. (The wavelength distribution of these second peaks was almost identical to that of primary peaks, and combinations of peak wavelengths were fairly random.) Third, most cells responded to white light; overall, the response to white light was about 60\% of that to the best narrow-band or broad-band colored light. Similarly, most V4 cells gave at least a small response to all or nearly all of the different broad-band colored lights we presented. Therefore, a given V4 cell is very likely to respond to most of the colored or white surfaces in natural scenes. These combinations of response properties probably explain the widely divergent percentages of "color" cells reported in previous studies of V4. The most unusual spectral property we found in V4 was a large, spectrally sensitive surround outside the "classical receptive field" of most cells. Although stimulation of the surround by itself did not cause any response, surround stimulation could completely suppress the response to even the optimally colored stimulus in the receptive field. In general, the optimal wavelengths for receptive-field excitation and surround suppression were the same or nearly so. Thus, "color contrast" may be computed in V4. In some cases, contrasting wavelengths in the surround caused moderate enhancement of response to a receptive-field stimulus.(ABSTRACT TRUNCATED AT 400 WORDS)},
language = {eng},
number = {10},
journal = {J Neurosci},
author = {Schein, S J and Desimone, R},
year = {1990},
pmid = {2213146},
note = {Place: UNITED STATES
ISBN: 0270-6474},
keywords = {Animals, Cerebral Cortex, Color Perception, Macaca fascicularis, Neurons, Photic Stimulation, Spectrophotometry, Visual Cortex, research support, non-u.s. gov't, research support, u.s. gov't, p.h.s.},
pages = {3369--3389},
}Positron emission tomographic measurements of pulvinar activity during an attention task. LaBerge, D. & Buchsbaum, M. Journal of Neuroscience, 10(2):613–619, 1990.
Paper doi abstract bibtex
Paper doi abstract bibtex Positron emission tomographic scans were recorded from human subjects following an object-identification task, one version of which required attentional selection and the other version of which did not. In one experimental session, the attention-demanding displays were presented in the left visual field and the nonattention displays were presented in the right visual field. In a second session, the sides of the displays were reversed. Analysis of the scans indicated that, averaged across the 2 sessions, the pulvinar showed greater glucose uptake when it was contralateral to the display of the selective attention task than when it was contralateral to the display of the nonattention task. The pattern of the data indicated that the degree of the attention task effect on pulvinar glucose uptake may differ between the hemispheres. In view of known connections between the pulvinar and cortical areas that mediate object identification, the present finding suggests that the pulvinar operates interactively with these cortical structures when an identification process demands selective attention.
@article{laberge_positron_1990,
title = {Positron emission tomographic measurements of pulvinar activity during an attention task},
volume = {10},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2303863},
doi = {10/grrsr8},
abstract = {Positron emission tomographic scans were recorded from human subjects following an object-identification task, one version of which required attentional selection and the other version of which did not. In one experimental session, the attention-demanding displays were presented in the left visual field and the nonattention displays were presented in the right visual field. In a second session, the sides of the displays were reversed. Analysis of the scans indicated that, averaged across the 2 sessions, the pulvinar showed greater glucose uptake when it was contralateral to the display of the selective attention task than when it was contralateral to the display of the nonattention task. The pattern of the data indicated that the degree of the attention task effect on pulvinar glucose uptake may differ between the hemispheres. In view of known connections between the pulvinar and cortical areas that mediate object identification, the present finding suggests that the pulvinar operates interactively with these cortical structures when an identification process demands selective attention.},
number = {2},
journal = {Journal of Neuroscience},
author = {LaBerge, D. and Buchsbaum, M.S.},
year = {1990},
keywords = {\#nosource, *Tomography, Emission-Computed, Adult, Attention/*physiology, Behavior/physiology, Female, Glucose/metabolism, Humans, Magnetic Resonance Imaging, Occipital Lobe/metabolism, Reaction Time, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Thalamic Nuclei/*physiology/radionuclide imaging, Thalamus/metabolism},
pages = {613--619},
}The attention system of the human brain. Posner, M. & Petersen, S. Annu Rev Neurosci, 13:25–42, 1990.
Paper doi bibtex
Paper doi bibtex @article{posner_attention_1990,
title = {The attention system of the human brain},
volume = {13},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2183676},
doi = {10/b486gb},
journal = {Annu Rev Neurosci},
author = {Posner, M.I. and Petersen, S.E.},
year = {1990},
keywords = {\#nosource, Attention/*physiology, Brain/*physiology, Humans, Laterality/*physiology, Pattern Recognition, Visual/physiology, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.},
pages = {25--42},
}1989 (1)
Origin and diffusion of the myotonic dystrophy gene in the Saguenay region (Quebec). Bouchard, G., Roy, R., Declos, M., Mathieu, J., & Kouladjian, K. Can J Neurol Sci, 16(1):119-122, 1989.
Website abstract bibtex
Website abstract bibtex A very high prevalence (approximately 1/475 in 1985) of myotonic dystrophy (Steinert disease) is observed in the Saguenay region, which is located in the north-east part of the Province of Quebec. For various reasons, however, the literature on the subject generally associates a high degree of selective disadvantage with this gene, which seems to contradict the Saguenay data. Using a computerized regional population register, we have reconstituted patients' genealogies and family biographies. We have thus been able to study the origin of the gene and to compare the demographic behavior of patients and controls. On the whole, patients seem to be very little disadvantaged compared to controls, in terms of reproduction as well as of geographical and occupational mobility.
@article{
title = {Origin and diffusion of the myotonic dystrophy gene in the Saguenay region (Quebec)},
type = {article},
year = {1989},
identifiers = {[object Object]},
keywords = {Female,Humans,Male,Myotonic Dystrophy/epidemiology/*genetics,Non-U.S. Gov't,Quebec,Research Support},
pages = {119-122},
volume = {16},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2924205},
id = {e09e9b8b-cecd-3bd3-8d03-44ef0e80b5cd},
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read = {false},
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authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0317-1671<m:linebreak/>Journal Article</m:note>},
abstract = {A very high prevalence (approximately 1/475 in 1985) of myotonic dystrophy (Steinert disease) is observed in the Saguenay region, which is located in the north-east part of the Province of Quebec. For various reasons, however, the literature on the subject generally associates a high degree of selective disadvantage with this gene, which seems to contradict the Saguenay data. Using a computerized regional population register, we have reconstituted patients' genealogies and family biographies. We have thus been able to study the origin of the gene and to compare the demographic behavior of patients and controls. On the whole, patients seem to be very little disadvantaged compared to controls, in terms of reproduction as well as of geographical and occupational mobility.},
bibtype = {article},
author = {Bouchard, Gérard and Roy, R and Declos, M and Mathieu, J and Kouladjian, K},
journal = {Can J Neurol Sci},
number = {1}
}1987 (1)
Visual properties of neurons in area V4 of the macaque: sensitivity to stimulus form. Desimone, R & Schein, S J J Neurophysiol, 57(3):835–868, 1987. Place: UNITED STATES ISBN: 0022-3077
abstract bibtex
abstract bibtex
Area V4, a visuotopically organized area in prestriate cortex of the macaque, is the major source of visual input to the inferior temporal cortex, known to be crucial for object recognition. To examine the selectivity of cells in V4 for stimulus form, we quantitatively measured the responses of 322 cells to bars varying in length, width, orientation, and polarity of contrast, and sinusoidal gratings varying in spatial frequency, phase, orientation, and overall size. All of the cells recorded in V4 were located on the lower portion of the prelunate gyrus. Receptive fields were located almost exclusively within the representation of the central 5 degrees of the lower visual field, and receptive field size, in linear dimension, was 4-7 times greater than that in the corresponding representation of striate cortex (V1). Nearly all receptive fields consisted of overlapping dark and light zones, like "classic" complex fields in V1, but the relative strengths of the dark and light zones often differed. A few cells responded exclusively to light or dark stimuli. Many cells in V4 were selective for stimulus orientation, and a few were selective for direction of motion as well. Although the median orientation bandwidth of the orientation-selective cells (52 degrees) was wider than that reported for oriented cells in V1, approximately 8% of the oriented cells had bandwidths of less than 30 degrees, which is nearly as narrow as the most narrowly tuned cells in V1. The proportion of cells selective for direction of motion (13%) was not markedly different from that reported in V1. The large majority of V4 cells were tuned to the length and width of bars, and the "shape" of the optimal bar varied from cell to cell, as has been reported for cells in the dorsolateral visual area (DL) of the owl monkey, a possible homologue of V4 in the macaque. Preferred lengths and widths varied independently from approximately 0.05 to 6 degrees, with the smallest preferred bars about the size of the smallest receptive fields in V1 and the largest preferred bars larger than any fields in V1. The relationship between the size of the optimal bar and the size of the receptive field varied from cell to cell. Some cells, for example, responded best to bars much narrower or shorter than the field, whereas other cells responded best to bars that filled (but did not extend beyond) the excitatory field in the length, width, or both dimensions.(ABSTRACT TRUNCATED AT 400 WORDS)
@article{desimone_visual_1987,
title = {Visual properties of neurons in area {V4} of the macaque: sensitivity to stimulus form.},
volume = {57},
abstract = {Area V4, a visuotopically organized area in prestriate cortex of the macaque, is the major source of visual input to the inferior temporal cortex, known to be crucial for object recognition. To examine the selectivity of cells in V4 for stimulus form, we quantitatively measured the responses of 322 cells to bars varying in length, width, orientation, and polarity of contrast, and sinusoidal gratings varying in spatial frequency, phase, orientation, and overall size. All of the cells recorded in V4 were located on the lower portion of the prelunate gyrus. Receptive fields were located almost exclusively within the representation of the central 5 degrees of the lower visual field, and receptive field size, in linear dimension, was 4-7 times greater than that in the corresponding representation of striate cortex (V1). Nearly all receptive fields consisted of overlapping dark and light zones, like "classic" complex fields in V1, but the relative strengths of the dark and light zones often differed. A few cells responded exclusively to light or dark stimuli. Many cells in V4 were selective for stimulus orientation, and a few were selective for direction of motion as well. Although the median orientation bandwidth of the orientation-selective cells (52 degrees) was wider than that reported for oriented cells in V1, approximately 8\% of the oriented cells had bandwidths of less than 30 degrees, which is nearly as narrow as the most narrowly tuned cells in V1. The proportion of cells selective for direction of motion (13\%) was not markedly different from that reported in V1. The large majority of V4 cells were tuned to the length and width of bars, and the "shape" of the optimal bar varied from cell to cell, as has been reported for cells in the dorsolateral visual area (DL) of the owl monkey, a possible homologue of V4 in the macaque. Preferred lengths and widths varied independently from approximately 0.05 to 6 degrees, with the smallest preferred bars about the size of the smallest receptive fields in V1 and the largest preferred bars larger than any fields in V1. The relationship between the size of the optimal bar and the size of the receptive field varied from cell to cell. Some cells, for example, responded best to bars much narrower or shorter than the field, whereas other cells responded best to bars that filled (but did not extend beyond) the excitatory field in the length, width, or both dimensions.(ABSTRACT TRUNCATED AT 400 WORDS)},
language = {eng},
number = {3},
journal = {J Neurophysiol},
author = {Desimone, R and Schein, S J},
year = {1987},
pmid = {3559704},
note = {Place: UNITED STATES
ISBN: 0022-3077},
keywords = {Animals, Brain Mapping, Macaca fascicularis, Occipital Lobe, Orientation, Psychophysics, Space Perception, Visual Cortex, Visual Fields, Visual Perception, comparative study, research support, non-u.s. gov't},
pages = {835--868},
}1986 (1)
Both striate cortex and superior colliculus contribute to visual properties of neurons in superior temporal polysensory area of macaque monkey. Bruce, C J, Desimone, R, & Gross, C G J Neurophysiol, 55(5):1057–1075, 1986. Place: UNITED STATES ISBN: 0022-3077
abstract bibtex
abstract bibtex
Although the tectofugal system projects to the primate cerebral cortex by way of the pulvinar, previous studies have failed to find any physiological evidence that the superior colliculus influences visual activity in the cortex. We studied the relative contributions of the tectofugal and geniculostriate systems to the visual properties of neurons in the superior temporal polysensory area (STP) by comparing the effects of unilateral removal of striate cortex, the superior colliculus, or of both structures. In the intact monkey, STP neurons have large, bilateral receptive fields. Complete unilateral removal of striate cortex did not eliminate visual responses of STP neurons in the contralateral visual hemifield; rather, nearly half the cells still responded to visual stimuli in the hemifield contralateral to the lesion. Thus the visual properties of STP neurons are not completely dependent on the geniculostriate system. Unilateral striate lesions did affect the response properties of STP neurons in three ways. Whereas most STP neurons in the intact monkey respond similarly to stimuli in the two visual hemifields, responses to stimuli in the hemifield contralateral to the striate lesion were usually weaker than responses in the ipsilateral hemifield. Whereas the responses of many STP neurons in the intact monkey were selective for the direction of stimulus motion or for stimulus form, responses in the hemifield contralateral to the striate lesion were not selective for either motion or form. Whereas the median receptive field in the intact monkey extended 80 degrees into the contralateral visual field, the receptive fields of cells with responses in the contralateral field that survived the striate lesions had a median border that extended only 50 degrees into the contralateral visual field. Removal of both striate cortex and the superior colliculus in the same hemisphere abolished the responses of STP neurons to visual stimuli in the hemifield contralateral to the combined lesion. Nearly 80% of the cells still responded to visual stimuli in the hemifield ipsilateral to the lesion. Unilateral removal of the superior colliculus alone had only small effects on visual responses in STP. Receptive-field size and visual response strength were slightly reduced in the hemifield contralateral to the collicular lesion. As in the intact monkey, selectivity for stimulus motion or form were similar in the two visual hemifields. We conclude that both striate cortex and the superior colliculus contribute to the visual responses of STP neurons. Striate cortex is crucial for the movement and stimulus specificity of neurons in STP.(ABSTRACT TRUNCATED AT 400 WORDS)
@article{bruce_both_1986,
title = {Both striate cortex and superior colliculus contribute to visual properties of neurons in superior temporal polysensory area of macaque monkey.},
volume = {55},
abstract = {Although the tectofugal system projects to the primate cerebral cortex by way of the pulvinar, previous studies have failed to find any physiological evidence that the superior colliculus influences visual activity in the cortex. We studied the relative contributions of the tectofugal and geniculostriate systems to the visual properties of neurons in the superior temporal polysensory area (STP) by comparing the effects of unilateral removal of striate cortex, the superior colliculus, or of both structures. In the intact monkey, STP neurons have large, bilateral receptive fields. Complete unilateral removal of striate cortex did not eliminate visual responses of STP neurons in the contralateral visual hemifield; rather, nearly half the cells still responded to visual stimuli in the hemifield contralateral to the lesion. Thus the visual properties of STP neurons are not completely dependent on the geniculostriate system. Unilateral striate lesions did affect the response properties of STP neurons in three ways. Whereas most STP neurons in the intact monkey respond similarly to stimuli in the two visual hemifields, responses to stimuli in the hemifield contralateral to the striate lesion were usually weaker than responses in the ipsilateral hemifield. Whereas the responses of many STP neurons in the intact monkey were selective for the direction of stimulus motion or for stimulus form, responses in the hemifield contralateral to the striate lesion were not selective for either motion or form. Whereas the median receptive field in the intact monkey extended 80 degrees into the contralateral visual field, the receptive fields of cells with responses in the contralateral field that survived the striate lesions had a median border that extended only 50 degrees into the contralateral visual field. Removal of both striate cortex and the superior colliculus in the same hemisphere abolished the responses of STP neurons to visual stimuli in the hemifield contralateral to the combined lesion. Nearly 80\% of the cells still responded to visual stimuli in the hemifield ipsilateral to the lesion. Unilateral removal of the superior colliculus alone had only small effects on visual responses in STP. Receptive-field size and visual response strength were slightly reduced in the hemifield contralateral to the collicular lesion. As in the intact monkey, selectivity for stimulus motion or form were similar in the two visual hemifields. We conclude that both striate cortex and the superior colliculus contribute to the visual responses of STP neurons. Striate cortex is crucial for the movement and stimulus specificity of neurons in STP.(ABSTRACT TRUNCATED AT 400 WORDS)},
language = {eng},
number = {5},
journal = {J Neurophysiol},
author = {Bruce, C J and Desimone, R and Gross, C G},
year = {1986},
pmid = {3711967},
note = {Place: UNITED STATES
ISBN: 0022-3077},
keywords = {Animals, Cerebral Cortex, Evoked Potentials, Visual, Functional Laterality, Macaca fascicularis, Male, Nerve Crush, Neurons, Spatial Behavior, Superior Colliculi, Temporal Lobe, Visual Cortex, Visual Pathways, Visual Perception, research support, u.s. gov't, non-p.h.s., research support, u.s. gov't, p.h.s.},
pages = {1057--1075},
}1985 (1)
Genealogical studies in families with oral clefts and reference families. Nordstrom, S. Hereditas, 103(2):211-219, 1985.
Website bibtex
Website bibtex @article{
title = {Genealogical studies in families with oral clefts and reference families},
type = {article},
year = {1985},
identifiers = {[object Object]},
keywords = {Aged,Child,Cleft Lip/epidemiology/*genetics,Cleft Palate/epidemiology/*genetics,Demography,Female,Humans,Male,Middle Aged,Research Support, Non-U.S. Gov't,Sweden},
pages = {211-219},
volume = {103},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=4086322},
id = {1533231e-73e6-37ae-8f72-247abea6986a},
created = {2017-06-19T13:46:05.288Z},
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last_modified = {2017-06-19T13:46:05.401Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0018-0661<m:linebreak/>Journal Article</m:note>},
bibtype = {article},
author = {Nordstrom, S},
journal = {Hereditas},
number = {2}
}1982 (1)
On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex. Georgopoulos, A. P., Kalaska, J. F., Caminiti, R., & Massey, J. T. J Neurosci, 2(11):1527-37, 1982.
abstract bibtex
abstract bibtex
The activity of single cells in the motor cortex was recorded while monkeys made arm movements in eight directions (at 45 degrees intervals) in a two-dimensional apparatus. These movements started from the same point and were of the same amplitude. The activity of 606 cells related to proximal arm movements was examined in the task; 323 of the 606 cells were active in that task and were studied in detail. The frequency of discharge of 241 of the 323 cells (74.6%) varied in an orderly fashion with the direction of movement. Discharge was most intense with movements in a preferred direction and was reduced gradually when movements were made in directions farther and farther away from the preferred one. This resulted in a bell-shaped directional tuning curve. These relations were observed for cell discharge during the reaction time, the movement time, and the period that preceded the earliest changes in the electromyographic activity (approximately 80 msec before movement onset). In about 75% of the 241 directionally tuned cells, the frequency of discharge, D, was a sinusoidal function of the direction of movement, theta: D = b0 + b1 sin theta + b2cos theta, or, in terms of the preferred direction, theta 0: D = b0 + c1cos (theta - theta0), where b0, b1, b2, and c1 are regression coefficients. Preferred directions differed for different cells so that the tuning curves partially overlapped. The orderly variation of cell discharge with the direction of movement and the fact that cells related to only one of the eight directions of movement tested were rarely observed indicate that movements in a particular direction are not subserved by motor cortical cells uniquely related to that movement. It is suggested, instead, that a movement trajectory in a desired direction might be generated by the cooperation of cells with overlapping tuning curves. The nature of this hypothetical population code for movement direction remains to be elucidated.
@Article{Georgopoulos1982,
author = {A. P. Georgopoulos and J. F. Kalaska and R. Caminiti and J. T. Massey},
journal = {J Neurosci},
title = {On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex.},
year = {1982},
number = {11},
pages = {1527-37},
volume = {2},
abstract = {The activity of single cells in the motor cortex was recorded while
monkeys made arm movements in eight directions (at 45 degrees intervals)
in a two-dimensional apparatus. These movements started from the
same point and were of the same amplitude. The activity of 606 cells
related to proximal arm movements was examined in the task; 323 of
the 606 cells were active in that task and were studied in detail.
The frequency of discharge of 241 of the 323 cells (74.6\%) varied
in an orderly fashion with the direction of movement. Discharge was
most intense with movements in a preferred direction and was reduced
gradually when movements were made in directions farther and farther
away from the preferred one. This resulted in a bell-shaped directional
tuning curve. These relations were observed for cell discharge during
the reaction time, the movement time, and the period that preceded
the earliest changes in the electromyographic activity (approximately
80 msec before movement onset). In about 75\% of the 241 directionally
tuned cells, the frequency of discharge, D, was a sinusoidal function
of the direction of movement, theta: D = b0 + b1 sin theta + b2cos
theta, or, in terms of the preferred direction, theta 0: D = b0 +
c1cos (theta - theta0), where b0, b1, b2, and c1 are regression coefficients.
Preferred directions differed for different cells so that the tuning
curves partially overlapped. The orderly variation of cell discharge
with the direction of movement and the fact that cells related to
only one of the eight directions of movement tested were rarely observed
indicate that movements in a particular direction are not subserved
by motor cortical cells uniquely related to that movement. It is
suggested, instead, that a movement trajectory in a desired direction
might be generated by the cooperation of cells with overlapping tuning
curves. The nature of this hypothetical population code for movement
direction remains to be elucidated.},
keywords = {Animals, Arm, Biomechanics, Electromyography, Macaca mulatta, Male, Motor Cortex, Movement, Neurons, P.H.S., Research Support, U.S. Gov't, 7143039},
}1981 (1)
A longevity study of twins in the Mormon genealogy. Carmelli, D. & Andersen, S. Prog Clin Biol Res, 69 Pt C:187-200, 1981.
Website bibtex
Website bibtex @article{
title = {A longevity study of twins in the Mormon genealogy},
type = {article},
year = {1981},
identifiers = {[object Object]},
keywords = {*Longevity,*Twins,Actuarial Analysis,Age Factors,Christianity,Female,Genealogy and Heraldry,Humans,Infant,Infant Mortality,Male,Pregnancy,Research Support, U.S. Gov't, P.H.S.,Retrospective Studies,Sex Factors},
pages = {187-200},
volume = {69 Pt C},
websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7198241},
id = {5a9ff0f5-0bfd-3de1-a44a-50318b9f3ab8},
created = {2017-06-19T13:43:59.126Z},
file_attached = {false},
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group_id = {b2078731-0913-33b9-8902-a53629a24e83},
last_modified = {2017-06-19T13:43:59.250Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
source_type = {Journal Article},
notes = {<m:note>0361-7742<m:linebreak/>Journal Article</m:note>},
bibtype = {article},
author = {Carmelli, D and Andersen, S},
journal = {Prog Clin Biol Res}
}