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Carson C. Chow

Bio: Carson C. Chow is a academic researcher from National Institutes of Health. The author has contributed to research in topic(s): Population & Spiking neural network. The author has an hindex of 53, co-authored 192 publication(s) receiving 18836 citation(s). Previous affiliations of Carson C. Chow include University of Pittsburgh & Massachusetts Institute of Technology.

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Papers
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Open accessJournal ArticleDOI: 10.1186/S13742-015-0047-8
25 Feb 2015-GigaScience
Abstract: Background: PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1’s primary data format. Findings: To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O √ n -time/constant-space Hardy-Weinberg equilibrium and Fisher’s exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). Conclusions: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

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4,519 Citations


Open accessJournal ArticleDOI: 10.1186/S13742-015-0047-8
17 Oct 2014-arXiv: Genomics
Abstract: PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

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Topics: Codebase (51%)

3,513 Citations


Open accessJournal ArticleDOI: 10.1016/S0140-6736(11)60812-X
Kevin D. Hall1, Gary Sacks2, Dhruva Chandramohan1, Carson C. Chow1  +3 moreInstitutions (4)
27 Aug 2011-The Lancet
Abstract: Obesity interventions can result in weight loss, but accurate prediction of the bodyweight time course requires properly accounting for dynamic energy imbalances. In this report, we describe a mathematical modelling approach to adult human metabolism that simulates energy expenditure adaptations during weight loss. We also present a web-based simulator for prediction of weight change dynamics. We show that the bodyweight response to a change of energy intake is slow, with half times of about 1 year. Furthermore, adults with greater adiposity have a larger expected weight loss for the same change of energy intake, and to reach their steady-state weight will take longer than it would for those with less initial body fat. Using a population-averaged model, we calculated the energy-balance dynamics corresponding to the development of the US adult obesity epidemic. A small persistent average daily energy imbalance gap between intake and expenditure of about 30 kJ per day underlies the observed average weight gain. However, energy intake must have risen to keep pace with increased expenditure associated with increased weight. The average increase of energy intake needed to sustain the increased weight (the maintenance energy gap) has amounted to about 0·9 MJ per day and quantifies the public health challenge to reverse the obesity epidemic.

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Topics: Weight change (63%), Weight loss (55%)

832 Citations


Journal ArticleDOI: 10.1038/376236A0
20 Jul 1995-Nature
Abstract: STOCHASTIC resonance1‡-4 (SR) is a phenomenon wherein the response of a nonlinear system to a weak periodic input signal is optimized by the presence of a particular, non-zero level of noise5 ‡-7. SR has been proposed as a means for improving signal detection in a wide variety of systems, including superconducting quantum interference devices8, and may be used in some natural systems such as sensory neurons9‡-15. But for SR to be effective in a singleunit system (such as a sensory neuron or a single ion channel), the optimal intensity of the noise must be adjusted as the nature of the signal to be detected changes15. This has been thought to impose a limitation on the practical and natural uses of SR. Here we show that the ability of a summing network of excitable units to detect a range of weak (sub-threshold) signals (either periodic or aperiodic) can be optimized by a fixed level of noise, irrespective of the nature of the input signal. We also show that this noise does not significantly degrade the ability of the network to detect suprathreshold signals. Thus, large nonlinear networks do not suffer from the limitations of SR in single units, and might be able to use a single noise level, such as that provided by the intrinsic noise of the individual components, to enhance the system's sensitivity to weak inputs. This suggests a functional role for neuronal noise14,16‡-18 in sensory systems.

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Topics: Stochastic resonance (64%), Noise (signal processing) (59%), Signal (53%) ...read more

707 Citations


Open accessJournal ArticleDOI: 10.1371/JOURNAL.PONE.0007940
25 Nov 2009-PLOS ONE
Abstract: Food waste contributes to excess consumption of freshwater and fossil fuels which, along with methane and CO(2) emissions from decomposing food, impacts global climate change. Here, we calculate the energy content of nationwide food waste from the difference between the US food supply and the food consumed by the population. The latter was estimated using a validated mathematical model of metabolism relating body weight to the amount of food eaten. We found that US per capita food waste has progressively increased by approximately 50% since 1974 reaching more than 1400 kcal per person per day or 150 trillion kcal per year. Food waste now accounts for more than one quarter of the total freshwater consumption and approximately 300 million barrels of oil per year.

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Topics: Waste disposal (61%), Food waste (59%), Population (52%) ...read more

584 Citations


Cited by
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Journal ArticleDOI: 10.1038/30918
Duncan J. Watts1, Steven H. Strogatz1Institutions (1)
04 Jun 1998-Nature
Abstract: Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation. The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.

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Topics: Complex network (67%), Evolving networks (65%), Network motif (62%) ...read more

35,972 Citations


Open access
28 Jul 2005-
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

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18,940 Citations


Journal ArticleDOI: 10.1001/JAMA.1986.03370210189033
06 Jun 1986-JAMA
Abstract: I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

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7,364 Citations


Open accessJournal ArticleDOI: 10.1186/S13742-015-0047-8
25 Feb 2015-GigaScience
Abstract: Background: PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1’s primary data format. Findings: To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O √ n -time/constant-space Hardy-Weinberg equilibrium and Fisher’s exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). Conclusions: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

...read more

4,519 Citations


Open accessBook
György Buzsáki1Institutions (1)
01 Jan 2006-
Abstract: Prelude. Cycle 1. Introduction. Cycle 2. Structure defines function. Cycle 3. Diversity of cortical functions is provided by inhibition. Cycle 4. Windows on the brain. Cycle 5. A system of rhythms: from simple to complex dynamics. Cycle 6. Synchronization by oscillation. Cycle 7. The brain's default state: self-organized oscillations in rest and sleep. Cycle 8. Perturbation of the default patterns by experience. Cycle 9. The gamma buzz: gluing by oscillations in the waking brain. Cycle 10. Perceptions and actions are brain state-dependent. Cycle 11. Oscillations in the "other cortex:" navigation in real and memory space. Cycle 12. Coupling of systems by oscillations. Cycle 13. The tough problem. References.

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3,806 Citations


Performance
Metrics

Author's H-index: 53

No. of papers from the Author in previous years
YearPapers
202112
20209
20198
20189
20172
20165

Top Attributes

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Author's top 5 most impactful journals

arXiv: Neurons and Cognition

9 papers, 152 citations

bioRxiv

9 papers, 29 citations

Physical Review E

7 papers, 939 citations

eLife

6 papers, 200 citations

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