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https://www.readbyqxmd.com/read/28346445/potential-energy-landscapes-identify-the-information-theoretic-nature-of-the-epigenome
#1
Garrett Jenkinson, Elisabet Pujadas, John Goutsias, Andrew P Feinberg
Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345262/purebreeding-of-red-maasai-and-crossbreeding-with-dorper-sheep-in-different-environments-in-kenya
#2
E Zonabend König, E Strandberg, J M K Ojango, T Mirkena, A M Okeyo, J Philipsson
The aim of this article was to study opportunities for improvement of the indigenous and threatened Red Maasai sheep (RM) in Kenya, by comparing purebreeding with crossbreeding with Dorper sheep (D) as a terminal breed, in two different environments (Env. A and a harsher Env. B), assuming different levels of genotype-by-environment interaction (G × E). Breeding goals differed between environments and breeds. Four scenarios of nucleus breeding schemes were stochastically simulated, with the nucleus in Env...
March 27, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28344779/accuracy-of-the-detection-of-binding-events-using-3d-single-particle-tracking
#3
Sara Carozza, Jamie Culkin, John van Noort
BACKGROUND: Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D. However, the precision of D sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion...
2017: BMC Biophysics
https://www.readbyqxmd.com/read/28343023/classification-of-footwear-outsole-patterns-using-fourier-transform-and-local-interest-points
#4
Nicole Richetelli, Mackenzie C Lee, Carleen A Lasky, Madison E Gump, Jacqueline A Speir
Successful classification of questioned footwear has tremendous evidentiary value; the result can minimize the potential suspect pool and link a suspect to a victim, a crime scene, or even multiple crime scenes to each other. With this in mind, several different automated and semi-automated classification models have been applied to the forensic footwear recognition problem, with superior performance commonly associated with two different approaches: correlation of image power (magnitude) or phase, and the use of local interest points transformed using the Scale Invariant Feature Transform (SIFT) and compared using Random Sample Consensus (RANSAC)...
March 4, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28342787/forecasting-ebola-with-a-regression-transmission-model
#5
Jason Asher
We describe a relatively simple stochastic model of Ebola transmission that was used to produce forecasts with the lowest mean absolute error among Ebola Forecasting Challenge participants. The model enabled prediction of peak incidence, the timing of this peak, and final size of the outbreak. The underlying discrete-time compartmental model used a time-varying reproductive rate modeled as a multiplicative random walk driven by the number of infectious individuals. This structure generalizes traditional Susceptible-Infected-Recovered (SIR) disease modeling approaches and allows for the flexible consideration of outbreaks with complex trajectories of disease dynamics...
February 27, 2017: Epidemics
https://www.readbyqxmd.com/read/28342604/economic-considerations-of-breeding-for-polled-dairy-cows-versus-dehorning-in-the-united-states
#6
Nathanael M Thompson, Nicole Olynk Widmar, Michael M Schutz, John B Cole, Christopher A Wolf
This paper examines the costs and benefits of selecting for polled dairy heifers versus traditional dehorning practices. Stochastic budgets were developed to analyze the expected costs (EC) associated with polled dairy genetics. The economic assessment was expanded beyond on-farm cash costs by incorporating cost and benefit estimates to generate industry-wide discussion, and preliminary economic evaluations, surrounding the public acceptance and attitude toward polled genetics versus dehorning calves. Triangular distributions, commonly used to represent distributions with limited data, were used to represent labor costs for dehorning, the likelihood of treatment of calf, and the cost of veterinary treatment...
March 22, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28342549/stream-aquifer-and-in-stream-processes-affecting-nitrogen-along-a-major-river-and-contributing-tributary
#7
Alexander Huizenga, Ryan T Bailey, Timothy K Gates
This study assesses the spatio-temporal patterns of water and nutrient mass exchange in a stream-riparian system of a major river and a contributing tributary in an irrigated semi-arid region. Field monitoring is performed along reaches of the Arkansas River (4.7km) and Timpas Creek (2.0km) in southeastern Colorado during the 2014 growing season, with water quantity and water quality data collected using a network of in-stream sampling sites and groundwater monitoring wells. Mass balance approaches were used to identify temporal and spatial trends in flow, nitrogen (N), and salinity in stream-aquifer exchange...
March 8, 2017: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/28342115/ssh-versus-tse-sequence-protocol-in-rapid-mr-examination-of-pediatric-patients-with-programmable-drainage-system
#8
Eva Brichtová, J Šenkyřík
PURPOSE: A low radiation burden is essential during diagnostic procedures in pediatric patients due to their high tissue sensitivity. Using MR examination instead of the routinely used CT reduces the radiation exposure and the risk of adverse stochastic effects. Our retrospective study evaluated the possibility of using ultrafast single-shot (SSh) sequences and turbo spin echo (TSE) sequences in rapid MR brain imaging in pediatric patients with hydrocephalus and a programmable ventriculoperitoneal drainage system...
March 24, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28341856/autoassociative-memory-and-pattern-recognition-in-micromechanical-oscillator-network
#9
Ankit Kumar, Pritiraj Mohanty
Towards practical realization of brain-inspired computing in a scalable physical system, we investigate a network of coupled micromechanical oscillators. We numerically simulate this array of all-to-all coupled nonlinear oscillators in the presence of stochasticity and demonstrate its ability to synchronize and store information in the relative phase differences at synchronization. Sensitivity of behavior to coupling strength, frequency distribution, nonlinearity strength, and noise amplitude is investigated...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341596/application-of-an-nlme-stochastic-deconvolution-approach-to-level-a-ivivc-modeling
#10
Maziar Kakhi, Sandra Suarez-Sharp, Terry Shepard, Jason Chittenden
Stochastic deconvolution is a parameter estimation method that calculates drug absorption using a non-linear mixed effects model in which the random effects associated with absorption represent a Wiener process. The present work compares, 1) stochastic deconvolution, and 2) numerical deconvolution, using clinical pharmacokinetic data generated for an IVIVC study of extended release (ER) formulations of a BCS class III drug substance. The preliminary analysis found that numerical and stochastic deconvolution yielded superimposable fraction absorbed (Fabs) versus time profiles when supplied with exactly the same externally-determined unit impulse response parameters...
March 21, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28341584/development-of-videogrammetry-as-a-tool-for-gas-particle-fluidization-research
#11
S Anweiler
Many industries use fluidization of solid particles for energy efficiency or environmental friendly process development, and this paper introduces research techniques developed for investigating gas-particle systems At present there is plenty of room for refining gas-particle fluidization process. With the rapidly rising application of mathematical modelling, real time visualization of processes will be widely used for validation of those models in the near future. In presented research, photogrammetry, as a part of close range vision metrology, has been expanded to allow dynamic space and time analysis of the phase concentration distribution inside fluidization devices...
March 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28341132/stochastic-modeling-and-numerical-simulation-of-gene-regulatory-networks-with-protein-bursting
#12
Manuel Pájaro, Antonio A Alonso, Irene Otero-Muras, C Vázquez
Gene expression is inherently stochastic. Advanced single-cell microscopy techniques together with mathematical models for single gene expression led to important insights in elucidating the sources of intrinsic noise in prokaryotic and eukaryotic cells. In addition to the finite size effects due to low copy numbers, translational bursting is a dominant source of stochasticity in cell scenarios involving few short lived mRNA transcripts with high translational efficiency (as is typically the case for prokaryotes), causing protein synthesis to occur in random bursts...
March 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28340415/uncertainty-analysis-for-effluent-trading-planning-using-a-bayesian-estimation-based-simulation-optimization-modeling-approach
#13
J L Zhang, Y P Li, G H Huang, B W Baetz, J Liu
In this study, a Bayesian estimation-based simulation-optimization modeling approach (BESMA) is developed for identifying effluent trading strategies. BESMA incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian estimation, and probabilistic-possibilistic interval programming with fuzzy random coefficients (PPI-FRC) within a general framework. Based on the water quality protocols provided by SWAT, posterior distributions of parameters can be analyzed through Bayesian estimation; stochastic characteristic of nutrient loading can be investigated which provides the inputs for the decision making...
March 6, 2017: Water Research
https://www.readbyqxmd.com/read/28339783/a-stochastic-model-for-tumour-control-probability-that-accounts-for-repair-from-sublethal-damage
#14
Ana Victoria Ponce Bobadilla, Philip K Maini, Helen Byrne
The tumour control probability (TCP) is the probability that a treatment regimen of radiation therapy (RT) eradicates all tumour cells in a given tissue. To decrease the toxic effects on healthy cells, RT is usually delivered over a period of weeks in a series of fractions. This allows tumour cells to repair sublethal damage (RSD) caused by radiation. In this article, we introduce a stochastic model for tumour response to radiotherapy which accounts for the effects of RSD. The tumour is subdivided into two cell types: 'affected' cells which have been damaged by RT and 'unaffected' cells which have not...
February 26, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28338147/symmetry-breaking-during-nanocrystal-growth
#15
Kyle D Gilroy, Hsin-Chieh Peng, Xuan Yang, Aleksey Ruditskiy, Younan Xia
Symmetry breaking is a ubiquitous phenomenon that occurs spontaneously when a system is subjected to changes in size and/or variations in terms of thermodynamic parameters. As a stochastic process, even small fluctuations acting on a system can arbitrarily push it down one of the branches of a bifurcation. In this feature article, we use nanocrystal growth to illustrate the concept of symmetry breaking. Our aim is to convey its importance from a mechanistic perspective, by which one can rationally alter the experimental conditions to manipulate the growth pattern (symmetric vs...
March 24, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28336094/distinct-succession-patterns-of-abundant-and-rare-bacteria-in-temporal-microcosms-with-pollutants
#16
Shuo Jiao, Yantao Luo, Mingmei Lu, Xiao Xiao, Yanbing Lin, Weimin Chen, Gehong Wei
Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl2) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples...
March 21, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28335538/precise-orbit-solution-for-swarm-using-space-borne-gps-data-and-optimized-pseudo-stochastic-pulses
#17
Bingbing Zhang, Zhengtao Wang, Lv Zhou, Jiandi Feng, Yaodong Qiu, Fupeng Li
Swarm is a European Space Agency (ESA) project that was launched on 22 November 2013, which consists of three Swarm satellites. Swarm precise orbits are essential to the success of the above project. This study investigates how well Swarm zero-differenced (ZD) reduced-dynamic orbit solutions can be determined using space-borne GPS data and optimized pseudo-stochastic pulses under high ionospheric activity. We choose Swarm space-borne GPS data from 1-25 October 2014, and Swarm reduced-dynamic orbits are obtained...
March 20, 2017: Sensors
https://www.readbyqxmd.com/read/28335497/ginsenoside-ppd-s-antitumor-effect-via-down-regulation-of-mtor-revealed-by-super-resolution-imaging
#18
Bo Teng, Junguang Jiang, Lijing Zhao, Jing Gao, Junyu Chen, Zhe Liu, Hongda Wang, Binfeng Lu
Derived from Panax ginseng, the natural product 20(S)-Protopanaxadiol (PPD) has been reported for its cytotoxicity against several cancer cell lines. The molecular mechanism is, however, not well understood. Here we show that PPD significantly inhibits proliferation, induces apoptosis and causes G2/M cell cycle arrest in human laryngeal carcinoma cells (Hep-2 cells). PPD also decreases the levels of proteins related to cell proliferation. Moreover, PPD-induced apoptosis is characterized by a dose-dependent down-regulation of Bcl-2 expression and up-regulation of Bax, and is accompanied by the activation of Caspase-3 as well...
March 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28334976/a-sensitivity-analysis-of-rna-folding-nearest-neighbor-parameters-identifies-a-subset-of-free-energy-parameters-with-the-greatest-impact-on-rna-secondary-structure-prediction
#19
Jeffrey Zuber, Hongying Sun, Xiaoju Zhang, Iain McFadyen, David H Mathews
Nearest neighbor parameters for estimating the folding energy changes of RNA secondary structures are used in structure prediction and analysis. Despite their widespread application, a comprehensive analysis of the impact of each parameter on the precision of calculations had not been conducted. To identify the parameters with greatest impact, a sensitivity analysis was performed on the 291 parameters that compose the 2004 version of the free energy nearest neighbor rules. Perturbed parameter sets were generated by perturbing each parameter independently...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334452/quantitative-assessment-of-the-risk-of-release-of-foot-and-mouth-disease-virus-via-export-of-bull-semen-from-israel
#20
A Meyer, L Zamir, A Ben Yair Gilboa, B Gelman, D U Pfeiffer, T Vergne
Various foot-and-mouth disease (FMD) virus strains circulate in the Middle East, causing frequent episodes of FMD outbreaks among Israeli livestock. Since the virus is highly resistant in semen, artificial insemination with contaminated bull semen may lead to the infection of the receiver cow. As a non-FMD-free country with vaccination, Israel is currently engaged in trading bull semen only with countries of the same status. The purpose of this study was to assess the risk of release of FMD virus through export of bull semen in order to estimate the risk for FMD-free countries considering purchasing Israeli bull semen...
March 23, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
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