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PLoS Computational Biology

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https://www.readbyqxmd.com/read/29145389/the-use-of-ambient-humidity-conditions-to-improve-influenza-forecast
#1
Jeffrey Shaman, Sasikiran Kandula, Wan Yang, Alicia Karspeck
Laboratory and epidemiological evidence indicate that ambient humidity modulates the survival and transmission of influenza. Here we explore whether the inclusion of humidity forcing in mathematical models describing influenza transmission improves the accuracy of forecasts generated with those models. We generate retrospective forecasts for 95 cities over 10 seasons in the United States and assess both forecast accuracy and error. Overall, we find that humidity forcing improves forecast performance (at 1-4 lead weeks, 3...
November 16, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29140991/a-bayesian-method-for-detecting-pairwise-associations-in-compositional-data
#2
Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower
Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix...
November 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29140973/a-coupled-oscillator-model-of-olfactory-bulb-gamma-oscillations
#3
Guoshi Li, Thomas A Cleland
The olfactory bulb transforms not only the information content of the primary sensory representation, but also its underlying coding metric. High-variance, slow-timescale primary odor representations are transformed by bulbar circuitry into secondary representations based on principal neuron spike patterns that are tightly regulated in time. This emergent fast timescale for signaling is reflected in gamma-band local field potentials, presumably serving to efficiently integrate olfactory sensory information into the temporally regulated information networks of the central nervous system...
November 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29136638/a-free-boundary-model-of-a-motile-cell-explains-turning-behavior
#4
Masoud Nickaeen, Igor L Novak, Stephanie Pulford, Aaron Rumack, Jamie Brandon, Boris M Slepchenko, Alex Mogilner
To understand shapes and movements of cells undergoing lamellipodial motility, we systematically explore minimal free-boundary models of actin-myosin contractility consisting of the force-balance and myosin transport equations. The models account for isotropic contraction proportional to myosin density, viscous stresses in the actin network, and constant-strength viscous-like adhesion. The contraction generates a spatially graded centripetal actin flow, which in turn reinforces the contraction via myosin redistribution and causes retraction of the lamellipodial boundary...
November 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131825/a-model-based-clustering-method-to-detect-infectious-disease-transmission-outbreaks-from-sequence-variation
#5
Rosemary M McCloskey, Art F Y Poon
Clustering infections by genetic similarity is a popular technique for identifying potential outbreaks of infectious disease, in part because sequences are now routinely collected for clinical management of many infections. A diverse number of nonparametric clustering methods have been developed for this purpose. These methods are generally intuitive, rapid to compute, and readily scale with large data sets. However, we have found that nonparametric clustering methods can be biased towards identifying clusters of diagnosis-where individuals are sampled sooner post-infection-rather than the clusters of rapid transmission that are meant to be potential foci for public health efforts...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131824/predictive-model-identifies-key-network-regulators-of-cardiomyocyte-mechano-signaling
#6
Philip M Tan, Kyle S Buchholz, Jeffrey H Omens, Andrew D McCulloch, Jeffrey J Saucerman
Mechanical strain is a potent stimulus for growth and remodeling in cells. Although many pathways have been implicated in stretch-induced remodeling, the control structures by which signals from distinct mechano-sensors are integrated to modulate hypertrophy and gene expression in cardiomyocytes remain unclear. Here, we constructed and validated a predictive computational model of the cardiac mechano-signaling network in order to elucidate the mechanisms underlying signal integration. The model identifies calcium, actin, Ras, Raf1, PI3K, and JAK as key regulators of cardiac mechano-signaling and characterizes crosstalk logic imparting differential control of transcription by AT1R, integrins, and calcium channels...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131821/improving-virtual-screening-of-g-protein-coupled-receptors-via-ligand-directed-modeling
#7
Thomas Coudrat, John Simms, Arthur Christopoulos, Denise Wootten, Patrick M Sexton
G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131818/electrical-stimulus-artifact-cancellation-and-neural-spike-detection-on-large-multi-electrode-arrays
#8
Gonzalo E Mena, Lauren E Grosberg, Sasidhar Madugula, PaweĊ‚ Hottowy, Alan Litke, John Cunningham, E J Chichilnisky, Liam Paninski
Simultaneous electrical stimulation and recording using multi-electrode arrays can provide a valuable technique for studying circuit connectivity and engineering neural interfaces. However, interpreting these measurements is challenging because the spike sorting process (identifying and segregating action potentials arising from different neurons) is greatly complicated by electrical stimulation artifacts across the array, which can exhibit complex and nonlinear waveforms, and overlap temporarily with evoked spikes...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131817/characterizing-steady-states-of-genome-scale-metabolic-networks-in-continuous-cell-cultures
#9
Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet
In the continuous mode of cell culture, a constant flow carrying fresh media replaces culture fluid, cells, nutrients and secreted metabolites. Here we present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct accumulation. We provide a method to determine the steady states of this system that is tractable for metabolic networks of arbitrary complexity...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131816/automated-visualization-of-rule-based-models
#10
John Arul Prakash Sekar, Jose-Juan Tapia, James R Faeder
Frameworks such as BioNetGen, Kappa and Simmune use "reaction rules" to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions between rules scale poorly with model size...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29125844/significant-associations-between-driver-gene-mutations-and-dna-methylation-alterations-across-many-cancer-types
#11
Yun-Ching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski
Recent evidence shows that mutations in several driver genes can cause aberrant methylation patterns, a hallmark of cancer. In light of these findings, we hypothesized that the landscapes of tumor genomes and epigenomes are tightly interconnected. We measured this relationship using principal component analyses and methylation-mutation associations applied at the nucleotide level and with respect to genome-wide trends. We found that a few mutated driver genes were associated with genome-wide patterns of aberrant hypomethylation or CpG island hypermethylation in specific cancer types...
November 10, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29125840/are-there-physicochemical-differences-between-allosteric-and-competitive-ligands
#12
Richard D Smith, Jing Lu, Heather A Carlson
Previous studies have compared the physicochemical properties of allosteric compounds to non-allosteric compounds. Those studies have found that allosteric compounds tend to be smaller, more rigid, more hydrophobic, and more drug-like than non-allosteric compounds. However, previous studies have not properly corrected for the fact that some protein targets have much more data than other systems. This generates concern regarding the possible skew that can be introduced by the inherent bias in the available data...
November 10, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29121651/a-modeling-study-of-budding-yeast-colony-formation-and-its-relationship-to-budding-pattern-and-aging
#13
Yanli Wang, Wing-Cheong Lo, Ching-Shan Chou
Budding yeast, which undergoes polarized growth during budding and mating, has been a useful model system to study cell polarization. Bud sites are selected differently in haploid and diploid yeast cells: haploid cells bud in an axial manner, while diploid cells bud in a bipolar manner. While previous studies have been focused on the molecular details of the bud site selection and polarity establishment, not much is known about how different budding patterns give rise to different functions at the population level...
November 9, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29112973/reading-wild-minds-a-computational-assay-of-theory-of-mind-sophistication-across-seven-primate-species
#14
Marie Devaine, Aurore San-Galli, Cinzia Trapanese, Giulia Bardino, Christelle Hano, Michel Saint Jalme, Sebastien Bouret, Shelly Masi, Jean Daunizeau
Theory of Mind (ToM), i.e. the ability to understand others' mental states, endows humans with highly adaptive social skills such as teaching or deceiving. Candidate evolutionary explanations have been proposed for the unique sophistication of human ToM among primates. For example, the Machiavellian intelligence hypothesis states that the increasing complexity of social networks may have induced a demand for sophisticated ToM. This type of scenario ignores neurocognitive constraints that may eventually be crucial limiting factors for ToM evolution...
November 7, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29112954/metabolic-dynamics-restricted-by-conserved-carriers-jamming-and-feedback
#15
Tetsuhiro S Hatakeyama, Chikara Furusawa
To uncover the processes and mechanisms of cellular physiology, it first necessary to gain an understanding of the underlying metabolic dynamics. Recent studies using a constraint-based approach succeeded in predicting the steady states of cellular metabolic systems by utilizing conserved quantities in the metabolic networks such as carriers such as ATP/ADP as an energy carrier or NADH/NAD+ as a hydrogen carrier. Although such conservation quantities restrict not only the steady state but also the dynamics themselves, the latter aspect has not yet been completely understood...
November 7, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29145393/estimating-the-probabilities-of-rare-arrhythmic-events-in-multiscale-computational-models-of-cardiac-cells-and-tissue
#16
Mark A Walker, Viatcheslav Gurev, John J Rice, Joseph L Greenstein, Raimond L Winslow
Ectopic heartbeats can trigger reentrant arrhythmias, leading to ventricular fibrillation and sudden cardiac death. Such events have been attributed to perturbed Ca2+ handling in cardiac myocytes leading to spontaneous Ca2+ release and delayed afterdepolarizations (DADs). However, the ways in which perturbation of specific molecular mechanisms alters the probability of ectopic beats is not understood. We present a multiscale model of cardiac tissue incorporating a biophysically detailed three-dimensional model of the ventricular myocyte...
November 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29145388/correction-a-unifying-probabilistic-view-of-associative-learning
#17
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1004567.].
November 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29131819/correction-unmet-needs-for-analyzing-biological-big-data-a-survey-of-704-nsf-principal-investigators
#18
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005755.].
November 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29125841/correction-error-robust-modes-of-the-retinal-population-code
#19
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005148.].
November 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29121064/correction-ten-simple-rules-for-structuring-papers
#20
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005619.].
November 2017: PLoS Computational Biology
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