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Stochastic modeling

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https://www.readbyqxmd.com/read/28110115/application-of-an-ecosystem-model-to-evaluate-the-importance-of-different-processes-and-food-web-structure-for-transfer-of-13-elements-in-a-shallow-lake
#1
L Konovalenko, C Bradshaw, E Andersson, U Kautsky
In environmental risk assessments of nuclear waste, there is need to estimate the potential risks of a large number of radionuclides over a long time period during which the environment is likely to change. Usually concentration ratios (CRs) are used to calculate the activity concentrations in organisms. However, CRs are not available for all radionuclides and they are not easily scalable to the varying environment. Here, an ecosystem transport model of elements, which estimates concentrations in organisms using carbon flows and food transfer instead of CR is presented...
January 18, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28110065/stochasticity-heterogeneity-and-variance-in-longevity-in-human-populations
#2
Nienke Hartemink, Trifon I Missov, Hal Caswell
Inter-individual variance in longevity (or any other demographic outcome) may arise from heterogeneity or from individual stochasticity. Heterogeneity refers to differences among individuals in the demographic rates experienced at a given age or stage. Stochasticity refers to variation due to the random outcome of demographic rates applied to individuals with the same properties. The variance due to individual stochasticity can be calculated from a Markov chain description of the life cycle. The variance due to heterogeneity can be calculated from a multistate model that incorporates the heterogeneity...
January 18, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28109128/population-pharmacokinetics-and-pharmacodynamics-of-benralizumab-in-healthy-volunteers-and-patients-with-asthma
#3
B Wang, L Yan, Z Yao, L K Roskos
Benralizumab is a humanized, afucosylated, anti-interleukin-5 receptor α, immunoglobulin G (IgG) 1 κ monoclonal antibody. We developed a population pharmacokinetic (PK)/pharmacodynamic (PD) model for benralizumab by analyzing PK and blood eosinophil count data from two healthy volunteer studies (N = 48) and four studies in patients with asthma (N = 152). Benralizumab PK was dose-proportional and adequately described by a two-compartment model with first-order elimination from the central compartment and first-order absorption from the subcutaneous dosing site...
January 21, 2017: CPT: Pharmacometrics & Systems Pharmacology
https://www.readbyqxmd.com/read/28107585/treatment-and-primary-prevention-in-people-who-inject-drugs-for-chronic-hepatitis-c-infection-is-elimination-possible-in-a-high-prevalence-setting
#4
I Gountas, V Sypsa, O Anagnostou, N K Martin, P Vickerman, E Kafetzopoulos, A Hatzakis
AIMS: To project the impact of scaling up oral antiviral therapy and harm reduction on chronic hepatitis C (CHC) prevalence and incidence among people who inject drugs (PWID) in Greece, to estimate the relationship between required treatment levels and expansion of harm reduction programs to achieve specific targets and to examine whether hepatitis C viruse (HCV) elimination among PWID is possible in this high prevalence setting. DESIGN: A dynamic discrete time, stochastic individual-based model was developed to simulate HCV transmission among PWID incorporating the effect of HCV treatment and harm reduction strategies, and allowing for reinfection following treatment...
January 20, 2017: Addiction
https://www.readbyqxmd.com/read/28107341/complex-dynamics-of-virus-spread-from-low-infection-multiplicities-implications-for-the-spread-of-oncolytic-viruses
#5
Ignacio A Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz
While virus growth dynamics have been well-characterized in several infections, data are typically collected once the virus population becomes easily detectable. Earlier dynamics, however, remain less understood. We recently reported unusual early dynamics in an experimental system using adenovirus infection of human embryonic kidney (293) cells. Under identical experimental conditions, inoculation at low infection multiplicities resulted in either robust spread, or in limited spread that eventually stalled, with both outcomes occurring with approximately equal frequencies...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28106416/stochastic-thermodynamics-of-learning
#6
Sebastian Goldt, Udo Seifert
Virtually every organism gathers information about its noisy environment and builds models from those data, mostly using neural networks. Here, we use stochastic thermodynamics to analyze the learning of a classification rule by a neural network. We show that the information acquired by the network is bounded by the thermodynamic cost of learning and introduce a learning efficiency η≤1. We discuss the conditions for optimal learning and analyze Hebbian learning in the thermodynamic limit.
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28103246/joint-optimization-of-distribution-network-design-and-two-echelon-inventory-control-with-stochastic-demand-and-co2-emission-tax-charges
#7
Shuangyan Li, Xialian Li, Dezhi Zhang, Lingyun Zhou
This study develops an optimization model to integrate facility location and inventory control for a three-level distribution network consisting of a supplier, multiple distribution centers (DCs), and multiple retailers. The integrated model addressed in this study simultaneously determines three types of decisions: (1) facility location (optimal number, location, and size of DCs); (2) allocation (assignment of suppliers to located DCs and retailers to located DCs, and corresponding optimal transport mode choices); and (3) inventory control decisions on order quantities, reorder points, and amount of safety stock at each retailer and opened DC...
2017: PloS One
https://www.readbyqxmd.com/read/28103190/learning-supervised-topic-models-for-classification-and-regression-from-crowds
#8
Filipe Rodrigues, Mariana Lourenco, Bernardete Ribeiro, Francisco Pereira
The growing need to analyze large collections of documents has led to great developments in topic modeling. Since documents are frequently associated with other related variables, such as labels or ratings, much interest has been placed on supervised topic models. However, the nature of most annotation tasks, prone to ambiguity and noise, often with high volumes of documents, deem learning under a single-annotator assumption unrealistic or unpractical for most real-world applications. In this article, we propose two supervised topic models, one for classification and another for regression problems, which account for the heterogeneity and biases among different annotators that are encountered in practice when learning from crowds...
January 5, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28102829/absorbed-dose-evaluation-of-auger-electron-emitting-radionuclides-impact-of-input-decay-spectra-on-dose-point-kernels-and-s-values
#9
Nadia Falzone, Boon Lee, José Fernández-Varea, Christiana Kartsonaki, Andrew Stuchbery, Tibor Kibedi, Katherine Vallis
AIM: The aim of this study was to investigate the impact of decay data provided by the newly developed stochastic atomic relaxation model <i>BrIccEmis</i> on dose point kernels (DPKs- radial dose distribution around a unit point source) and <i>S</i>-values (absorbed dose per unit cumulated activity) of 14 Auger electron (AE) emitting radionuclides, namely <sup>67</sup>Ga, <sup>80m</sup>Br, <sup>89</sup>Zr, <sup>90</sup>Nb, <sup>99m</sup>Tc, <sup>111</sup>In, <sup>117m</sup>Sn, <sup>119</sup>Sb, <sup>123</sup>I, <sup>124</sup>I, <sup>125</sup>I, <sup>135</sup>La, <sup>195m</sup>Pt and <sup>201</sup>Tl...
January 19, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28102757/dysbiosis-in-crohn-s-disease-joint-action-of-stochastic-injuries-and-focal-inflammation-in-the-gut
#10
Ludovica F Buttó, Dirk Haller
Gut homeostasis involves interrelated biological networks that include the immune system, specialized cells of the epithelium, such as Paneth and goblet cells, as well as triggers derived from the microbiota. Disruption of these homeostatic interactions may lead to the pathogenesis of inflammatory bowel diseases (IBD). To develop more targeted and individual treatments in Crohn's disease and ulcerative colitis, it becomes more and more important to link key mechanisms of the disease pathogenesis to distinct IBD subsets...
January 19, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28102174/modeling-dynamics-of-mutants-in-heterogeneous-stem-cell-niche
#11
Leili Shahriyari, Ali Mahdipour Shirayeh
Studying the stem cell (SC) niche architecture is a crucial step for investigating the process of oncogenesis and obtaining an effective stem cell therapy for various cancers. Recently, it has been observed that there are two groups of SCs in the SC niche collaborating with each other to maintain tissue homeostasis: border stem cells (BSCs), which are responsible in controlling the number of non-stem cells as well as stem cells, and central stem cells (CeSCs), which regulate the SC niche. Here, we develop a bi-compartmental stochastic model for the SC niche to study the spread of mutants within the niche...
January 19, 2017: Physical Biology
https://www.readbyqxmd.com/read/28101746/music-preferences-friendship-and-externalizing-behavior-in-early-adolescence-a-siena-examination-of-the-music-marker-theory-using-the-snare-study
#12
Aart Franken, Loes Keijsers, Jan Kornelis Dijkstra, Tom Ter Bogt
Music Marker Theory posits that music is relevant for the structuring of peer groups and that rock, urban, or dance music preferences relate to externalizing behavior. The present study tested these hypotheses, by investigating the role of music preference similarity in friendship selection and the development of externalizing behavior, while taking the effects of friends' externalizing behavior into account. Data were used from the first three waves of the SNARE (Social Network Analysis of Risk behavior in Early adolescence) study (N = 1144; 50% boys; M age = 12...
January 18, 2017: Journal of Youth and Adolescence
https://www.readbyqxmd.com/read/28101632/a-discrete-time-model-for-population-persistence-in-habitats-with-time-varying-sizes
#13
Ying Zhou, William F Fagan
In this paper, we use periodic and stochastic integrodifference models to study the persistence of a single-species population in a habitat with temporally varying sizes. We extend a persistence metric for integral operators on bounded domains to that of integral operators on unbounded domains. Using this metric in the periodic model, we present new perspectives of the critical habitat size problem in the case of dynamically changing habitat sizes. Specifically, we extend the concept of critical habitat size to that of lower minimal limit size in a period-2 scenario, and prove the existence of the lower minimal limit size...
January 18, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28100591/dynamics-and-fate-of-beneficial-mutations-under-lineage-contamination-by-linked-deleterious-mutations
#14
Sophie Pénisson, Tanya Singh, Paul Sniegowski, Philip Gerrish
Beneficial mutations drive adaptive evolution, yet their selective advantage does not ensure their fixation. Haldane's application of single-type branching process theory showed that genetic drift alone could cause the extinction of newly-arising beneficial mutations with high probability. With linkage, deleterious mutations will affect the dynamics of beneficial mutations and might further increase their extinction probability. Here, we model the lineage dynamics of a newly-arising beneficial mutation as a multitype branching process...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28099868/pdc-sgb-prediction-of-effective-drug-combinations-using-a-stochastic-gradient-boosting-algorithm
#15
Qian Xu, Yi Xiong, Hao Dai, Kotni Meena Kumari, Qin Xu, Hong-Yu Ou, Dong-Qing Wei
Combinatorial therapy is a promising strategy for combating complex diseases by improving the efficacy and reducing the side effects. To facilitate the identification of drug combinations in pharmacology, we proposed a new computational model, termed PDC-SGB, to predict effective drug combinations by integrating biological, chemical and pharmacological information based on a stochastic gradient boosting algorithm. To begin with, a set of 352 golden positive samples were collected from the public drug combination database...
January 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28098750/cluster-based-maximum-consensus-time-synchronization-for-industrial-wireless-sensor-networks
#16
Zhaowei Wang, Peng Zeng, Mingtuo Zhou, Dong Li, Jintao Wang
Time synchronization is one of the key technologies in Industrial Wireless Sensor Networks (IWSNs), and clustering is widely used in WSNs for data fusion and information collection to reduce redundant data and communication overhead. Considering IWSNs' demand for low energy consumption, fast convergence, and robustness, this paper presents a novel Cluster-based Maximum consensus Time Synchronization (CMTS) method. It consists of two parts: intra-cluster time synchronization and inter-cluster time synchronization...
January 13, 2017: Sensors
https://www.readbyqxmd.com/read/28098244/stochastic-evolution-in-populations-of-ideas
#17
Robin Nicole, Peter Sollich, Tobias Galla
It is known that learning of players who interact in a repeated game can be interpreted as an evolutionary process in a population of ideas. These analogies have so far mostly been established in deterministic models, and memory loss in learning has been seen to act similarly to mutation in evolution. We here propose a representation of reinforcement learning as a stochastic process in finite 'populations of ideas'. The resulting birth-death dynamics has absorbing states and allows for the extinction or fixation of ideas, marking a key difference to mutation-selection processes in finite populations...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097060/why-choose-random-forest-to-predict-rare-species-distribution-with-few-samples-in-large-undersampled-areas-three-asian-crane-species-models-provide-supporting-evidence
#18
Chunrong Mi, Falk Huettmann, Yumin Guo, Xuesong Han, Lijia Wen
Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models)...
2017: PeerJ
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#19
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28095930/quantitative-risk-assessment-of-the-introduction-of-rabies-into-japan-through-the-importation-of-dogs-and-cats-worldwide
#20
N C L Kwan, K Sugiura, Y Hosoi, A Yamada, E L Snary
Japan has been free from rabies since 1958. A strict import regimen has been adopted since 2004 consisting of identification of an animal with microchip, two-time rabies vaccination, neutralizing antibody titration test and a waiting period of 180 days. The present study aims to quantitatively assess the risk of rabies introduction into Japan through the international importation of dogs and cats and hence provide evidence-based recommendations to strengthen the current rabies prevention system. A stochastic scenario tree model was developed and simulations were run using @RISK...
January 18, 2017: Epidemiology and Infection
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