Browsing by Subject "Computer Simulation"
Now showing items 1-20 of 84
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A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.
(Genetics, 2015-11)We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome ... -
A cerebellar learning model of vestibulo-ocular reflex adaptation in wild-type and mutant mice.
(The Journal of neuroscience : the official journal of the Society for Neuroscience, 2014-05)Mechanisms of cerebellar motor learning are still poorly understood. The standard Marr-Albus-Ito theory posits that learning involves plasticity at the parallel fiber to Purkinje cell synapses under control of the climbing ... -
A framework for integrating the songbird brain.
(J Comp Physiol A Neuroethol Sens Neural Behav Physiol, 2002-12)Biological systems by default involve complex components with complex relationships. To decipher how biological systems work, we assume that one needs to integrate information over multiple levels of complexity. The songbird ... -
A low-cost, portable, and quantitative spectral imaging system for application to biological tissues.
(Opt Express, 2010-06-07)The ability of diffuse reflectance spectroscopy to extract quantitative biological composition of tissues has been used to discern tissue types in both pre-clinical and clinical cancer studies. Typically, diffuse reflectance ... -
A noisy linear map underlies oscillations in cell size and gene expression in bacteria.
(Nature, 2015-07-16)During bacterial growth, a cell approximately doubles in size before division, after which it splits into two daughter cells. This process is subjected to the inherent perturbations of cellular noise and thus requires regulation ... -
A positioning QA procedure for 2D/2D (kV/MV) and 3D/3D (CT/CBCT) image matching for radiotherapy patient setup.
(Journal of applied clinical medical physics, 2009-10-06)A positioning QA procedure for Varian's 2D/2D (kV/MV) and 3D/3D (planCT/CBCT) matching was developed. The procedure was to check: (1) the coincidence of on-board imager (OBI), portal imager (PI), and cone beam CT (CBCT)'s ... -
A Refined Neuronal Population Measure of Visual Attention.
(PloS one, 2015-01)Neurophysiological studies of cognitive mechanisms such as visual attention typically ignore trial-by-trial variability and instead report mean differences averaged across many trials. Advances in electrophysiology allow ... -
A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks.
(PLoS Comput Biol, 2015-08)Understanding the theoretical foundations of how memories are encoded and retrieved in neural populations is a central challenge in neuroscience. A popular theoretical scenario for modeling memory function is the attractor ... -
Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function.
(J Chem Phys, 2010-02-07)Based on Pulay's direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented Roothaan-Hall (ARH) energy function, ... -
Advances to Bayesian network inference for generating causal networks from observational biological data.
(Bioinformatics, 2004-12-12)MOTIVATION: Network inference algorithms are powerful computational tools for identifying putative causal interactions among variables from observational data. Bayesian network inference algorithms hold particular promise ... -
An evaluation of remifentanil-sevoflurane response surface models in patients emerging from anesthesia: model improvement using effect-site sevoflurane concentrations.
(Anesth Analg, 2010-08)INTRODUCTION: We previously reported models that characterized the synergistic interaction between remifentanil and sevoflurane in blunting responses to verbal and painful stimuli. This preliminary study evaluated the ability ... -
Assessment of LD matrix measures for the analysis of biological pathway association.
(Stat Appl Genet Mol Biol, 2010)Complex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD ... -
Calcium-based plasticity model explains sensitivity of synaptic changes to spike pattern, rate, and dendritic location.
(Proceedings of the National Academy of Sciences of the United States of America, 2012-03)Multiple stimulation protocols have been found to be effective in changing synaptic efficacy by inducing long-term potentiation or depression. In many of those protocols, increases in postsynaptic calcium concentration have ... -
Cerebellar learning using perturbations.
(eLife, 2018-11-12)The cerebellum aids the learning of fast, coordinated movements. According to current consensus, erroneously active parallel fibre synapses are depressed by complex spikes signalling movement errors. However, this theory ... -
Characteristics of sequential activity in networks with temporally asymmetric Hebbian learning.
(Proceedings of the National Academy of Sciences of the United States of America, 2020-11-11)Sequential activity has been observed in multiple neuronal circuits across species, neural structures, and behaviors. It has been hypothesized that sequences could arise from learning processes. However, it is still unclear ... -
Communication: Weakening the critical dynamical slowing down of models with SALR interactions.
(The Journal of chemical physics, 2022-11)In systems with frustration, the critical slowing down of the dynamics severely impedes the numerical study of phase transitions for even the simplest of lattice models. In order to help sidestep the gelation-like sluggishness, ... -
Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.
(Nucleic Acids Res, 2010-05)Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, ... -
Comparing habitat suitability and connectivity modeling methods for conserving pronghorn migrations.
(PloS one, 2012-01)Terrestrial long-distance migrations are declining globally: in North America, nearly 75% have been lost. Yet there has been limited research comparing habitat suitability and connectivity models to identify migration corridors ... -
Complex k band diagrams of 3D metamaterial/photonic crystals.
(Opt Express, 2011-09-26)A finite element method (FEM) for solving a complex valued k(ω) vs. ω dispersion curve of a 3D metamaterial/photonic crystal system is presented. This 3D method is a generalization of a previously reported 2D eigenvalue ...
