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https://www.readbyqxmd.com/read/29031187/modelling-transitions-in-urban-water-systems
#1
W Rauch, C Urich, P M Bach, B C Rogers, F J de Haan, R R Brown, M Mair, D T McCarthy, M Kleidorfer, R Sitzenfrei, A Deletic
Long term planning of urban water infrastructure requires acknowledgement that transitions in the water system are driven by changes in the urban environment, as well as societal dynamics. Inherent to the complexity of these underlying processes is that the dynamics of a system's evolution cannot be explained by linear cause-effect relationships and cannot be predicted under narrow sets of assumptions. Planning therefore needs to consider the functional behaviour and performance of integrated flexible infrastructure systems under a wide range of future conditions...
September 22, 2017: Water Research
https://www.readbyqxmd.com/read/29031136/increased-sensory-noise-and-not-muscle-weakness-explains-changes-in-non-stepping-postural-responses-following-stance-perturbations-in-healthy-elderly
#2
Maarten Afschrift, Friedl De Groote, Sabine Verschueren, Ilse Jonkers
The response to stance perturbations changes with age. The shift from an ankle to a hip strategy with increasing perturbation magnitude occurs at lower accelerations in older than in young adults. This strategy shift has been related to age-related changes in muscle and sensory function. However, the effect of isolated changes in muscle or sensory function on the responses following stance perturbations cannot be determined experimentally since changes in muscle and sensory function occur simultaneously. Therefore, we used predictive simulations to estimate the effect of isolated changes in (rates of change in) maximal joint torques, functional base of support, and sensory noise on the response to backward platform translations...
October 4, 2017: Gait & Posture
https://www.readbyqxmd.com/read/29031082/quantum-associative-memory-with-linear-and-non-linear-algorithms-for-the-diagnosis-of-some-tropical-diseases
#3
J-P Tchapet Njafa, S G Nana Engo
This paper presents the QAMDiagnos, a model of Quantum Associative Memory (QAM) that can be a helpful tool for medical staff without experience or laboratory facilities, for the diagnosis of four tropical diseases (malaria, typhoid fever, yellow fever and dengue) which have several similar signs and symptoms. The memory can distinguish a single infection from a polyinfection. Our model is a combination of the improved versions of the original linear quantum retrieving algorithm proposed by Ventura and the non-linear quantum search algorithm of Abrams and Lloyd...
September 21, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/29029359/a-probabilistic-network-for-the-diagnosis-of-acute-cardiopulmonary-diseases
#4
Alessandro Magrini, Davide Luciani, Federico M Stefanini
In this paper, the development of a probabilistic network for the diagnosis of acute cardiopulmonary diseases is presented in detail. A panel of expert physicians collaborated to specify the qualitative part, which is a directed acyclic graph defining a factorization of the joint probability distribution of domain variables into univariate conditional distributions. The quantitative part, which is a set of parametric models defining these univariate conditional distributions, was estimated following the Bayesian paradigm...
October 13, 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/29029343/an-evaluation-of-different-partitioning-strategies-for-bayesian-estimation-of-species-divergence-times
#5
Konstantinos Angelis, Sandra Álvarez-Carretero, Mario Dos Reis, Ziheng Yang
The explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites that have similar evolutionary characteristics into the same partition and those with different characteristics into different partitions, and then use different models or different values of model parameters for different partitions to account for the among-partition heterogeneity...
July 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029338/to-include-or-not-to-include-the-impact-of-gene-filtering-on-species-tree-estimation-methods
#6
Erin K Molloy, Tandy Warnow
With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that co-estimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci...
September 15, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029267/evaluation-of-universal-versus-genotype-guided-efavirenz-dose-reduction-in-pregnant-women-using-population-pharmacokinetic-modelling
#7
Adeniyi Olagunju, Alessandro Schipani, Oluseye Bolaji, Saye Khoo, Andrew Owen
Objectives: Lack of data on the pharmacokinetics of efavirenz in pregnant women at the 400 mg reduced dose currently prevents universal roll-out. Population pharmacokinetic modelling was used to explore pharmacokinetic endpoints at 200, 400 and 600 mg daily doses in pregnant women stratified by CYP2B6 metabolic status. Methods: The analysis was based on 252 plasma efavirenz concentrations from 77 pregnant women (77 sparse, 175 intensive) who received antiretroviral regimens containing 600 mg of efavirenz...
September 26, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29029264/a-general-model-for-estimating-macroevolutionary-landscapes
#8
Florian C Boucher, Vincent Démery, Elena Conti, Luke J Harmon, Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029231/analysis-of-phylogenomic-tree-space-resolves-relationships-among-marsupial-families
#9
David A Duchêne, Jason G Bragg, Sebastián Duchêne, Linda E Neaves, Sally Potter, Craig Moritz, Rebecca N Johnson, Simon Y W Ho, Mark D B Eldridge
A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029228/development-of-a-whole-task-simulator-for-carotid-endarterectomy
#10
Gabrielle Santangelo, Doran Mix, Ahmed Ghazi, Michael Stoner, G Edward Vates, Jonathan J Stone
BACKGROUND: Surgical education relies on operative exposure with live patients. Carotid endarterectomy (CEA) demands an experienced surgeon with a very low complication rate. The high-risk nature of this procedure and the decline in number of CEAs performed annually has created a gap in residency training. OBJECTIVE: To develop a high-fidelity whole-task simulation for CEA that demonstrates content, construct, and face validity. METHODS: Anatomically accurate models of the human neck were created using multilayered poly-vinyl alcohol hydrogels...
September 27, 2017: Operative Neurosurgery (Hagerstown, Md.)
https://www.readbyqxmd.com/read/29029158/genetic-interaction-network-as-an-important-determinant-of-gene-order-in-genome-evolution
#11
Yu-Fei Yang, Wenqing Cao, Shaohuan Wu, Wenfeng Qian
Although it is generally accepted that eukaryotic gene order is not random, the basic principles of gene arrangement on a chromosome remain poorly understood. Here, we extended existing population genetics theories that were based on two-locus models and proposed a hypothesis that genetic interaction networks drive the evolution of eukaryotic gene order. We predicted that genes with positive epistasis would move toward each other in evolution, during which a negative correlation between epistasis and gene distance formed...
October 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029075/improving-health-systems-performance-in-low-and-middle-income-countries-a-system-dynamics-model-of-the-pay-for-performance-initiative-in-afghanistan
#12
O Alonge, S Lin, T Igusa, D H Peters
System dynamics methods were used to explore effective implementation pathways for improving health systems performance through pay-for-performance (P4P) schemes. A causal loop diagram was developed to delineate primary causal relationships for service delivery within primary health facilities. A quantitative stock-and-flow model was developed next. The stock-and-flow model was then used to simulate the impact of various P4P implementation scenarios on quality and volume of services. Data from the Afghanistan national facility survey in 2012 was used to calibrate the model...
September 23, 2017: Health Policy and Planning
https://www.readbyqxmd.com/read/29028987/in-silico-structural-modelling-of-multiple-epigenetic-marks-on-dna
#13
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary
Summary: There are four known epigenetic cytosine modifications in mammals: 5mC, 5hmC, 5fC and 5caC. The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, F-DNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028985/impact-of-coronary-lumen-reconstruction-on-the-estimation-of-endothelial-shear-stress-in-vivo-comparison-of-three-dimensional-quantitative-coronary-angiography-and-three-dimensional-fusion-combining-optical-coherent-tomography
#14
Jihoon Kweon, Soo-Jin Kang, Young-Hak Kim, June-Goo Lee, Seungbong Han, Hojin Ha, Dong Hyun Yang, Joon-Won Kang, Tae-Hwan Lim, Osung Kwon, Jung-Min Ahn, Pil Hyung Lee, Duk-Woo Park, Seung-Whan Lee, Cheol Whan Lee, Seong-Wook Park, Seung-Jung Park
Aims: It is not clearly elucidated how the fusion technique improves the accuracy of endothelial shear stress (ESS) prediction, in comparison with that of three-dimensional (3D) quantitative coronary angiography (QCA) alone. We aimed to evaluate the difference in geometric measurements and haemodynamic estimation between 3D QCA and a 3D fusion model combining 3D QCA and optical coherence tomography (OCT). Methods and results: Computational fluid dynamics was assessed in the coronary models of 20 patients...
September 25, 2017: European Heart Journal Cardiovascular Imaging
https://www.readbyqxmd.com/read/29028943/a-joint-model-for-mixed-and-truncated-longitudinal-data-and-survival-data-with-application-to-hiv-vaccine-studies
#15
Tingting Yu, Lang Wu, Peter B Gilbert
In HIV vaccine studies, a major research objective is to identify immune response biomarkers measured longitudinally that may be associated with risk of HIV infection. This objective can be assessed via joint modeling of longitudinal and survival data. Joint models for HIV vaccine data are complicated by the following issues: (i) left truncations of some longitudinal data due to lower limits of quantification; (ii) mixed types of longitudinal variables; (iii) measurement errors and missing values in longitudinal measurements; (iv) computational challenges associated with likelihood inference...
September 23, 2017: Biostatistics
https://www.readbyqxmd.com/read/29028924/survivor-bias-in-mendelian-randomization-analysis
#16
Stijn Vansteelandt, Oliver Dukes, Torben Martinussen
Mendelian randomization studies employ genotypes as experimental handles to infer the effect of genetically modified exposures (e.g. vitamin D exposure) on disease outcomes (e.g. mortality). The statistical analysis of these studies makes use of the standard instrumental variables framework. Many of these studies focus on elderly populations, thereby ignoring the problem of left truncation, which arises due to the selection of study participants being conditional upon surviving up to the time of study onset...
September 27, 2017: Biostatistics
https://www.readbyqxmd.com/read/29028922/methods-for-handling-longitudinal-outcome-processes-truncated-by-dropout-and-death
#17
Lan Wen, Graciela Muniz Terrera, Shaun R Seaman
Cohort data are often incomplete because some subjects drop out of the study, and inverse probability weighting (IPW), multiple imputation (MI), and linear increments (LI) are methods that deal with such missing data. In cohort studies of ageing, missing data can arise from dropout or death. Methods that do not distinguish between these reasons for missingness typically provide inference about a hypothetical cohort where no one can die (immortal cohort). It has been suggested that inference about the cohort composed of those who are still alive at any time point (partly conditional inference) may be more meaningful...
September 26, 2017: Biostatistics
https://www.readbyqxmd.com/read/29028905/quality-of-biological-images-reconstructed-using-localization-microscopy-data
#18
Blazej Ruszczycki, Tytus Bernas
Motivation: Fluorescence localization microscopy is extensively used to study the details of spatial architecture of subcellular compartments. This modality relies on determination of spatial positions of fluorophores, labeling an extended biological structure, with precision exceeding the diffraction limit. Several established models describe influence of pixel size, signal-to-noise ratio and optical resolution on the localization precision. The labeling density has been also recognized as important factor affecting reconstruction fidelity of the imaged biological structure...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028881/snp-genotyping-and-parameter-estimation-in-polyploids-using-low-coverage-sequencing-data
#19
Paul D Blischak, Laura S Kubatko, Andrea D Wolfe
Motivation: Genotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single lineage (autopolyploids), inbreeding can result from mixed mating and/or double reduction. For WGDs that involve hybridization (allopolyploids), alleles are typically inherited through independently segregating subgenomes...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028657/combinations-of-interventions-to-achieve-a-national-hiv-incidence-reduction-goal-insights-from-the-agent-based-path-2-0-model
#20
Chaitra Gopalappa, Stephanie L Sansom, Paul G Farnham, Yao-Hsuan Chen
OBJECTIVE: Analyzing HIV care service targets for achieving a national goal of a 25% reduction in annual HIV incidence and evaluating the use of annual HIV diagnoses to measure progress in incidence reduction. DESIGN: Because there are considerable interactions among HIV care services, we model the dynamics of combinations of increases in HIV care continuum targets to identify those that would achieve 25% reductions in annual incidence and diagnoses. METHODS: We used Progression and Transmission of HIV/AIDS (PATH 2...
October 12, 2017: AIDS
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