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https://www.readbyqxmd.com/read/28916392/formulation-construction-and-analysis-of-kinetic-models-of-metabolism-a-review-of-modelling-frameworks
#1
REVIEW
Pedro A Saa, Lars K Nielsen
Kinetic models are critical to predict the dynamic behaviour of metabolic networks. Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting their parameters. Recent modelling frameworks promise new ways to overcome this obstacle while retaining predictive capabilities. In this review, we present an overview of the relevant mathematical frameworks for kinetic formulation, construction and analysis. Starting with kinetic formalisms, we next review statistical methods for parameter inference, as well as recent computational frameworks applied to the construction and analysis of kinetic models...
September 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28915268/large-scale-cross-species-chemogenomic-platform-proposes-a-new-drug-discovery-strategy-of-veterinary-drug-from-herbal-medicines
#2
Chao Huang, Yang Yang, Xuetong Chen, Chao Wang, Yan Li, Chunli Zheng, Yonghua Wang
Veterinary Herbal Medicine (VHM) is a comprehensive, current, and informative discipline on the utilization of herbs in veterinary practice. Driven by chemistry but progressively directed by pharmacology and the clinical sciences, drug research has contributed more to address the needs for innovative veterinary medicine for curing animal diseases. However, research into veterinary medicine of vegetal origin in the pharmaceutical industry has reduced, owing to questions such as the short of compatibility of traditional natural-product extract libraries with high-throughput screening...
2017: PloS One
https://www.readbyqxmd.com/read/28915238/a-high-resolution-atlas-of-gene-expression-in-the-domestic-sheep-ovis-aries
#3
Emily L Clark, Stephen J Bush, Mary E B McCulloch, Iseabail L Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C Bruce Whitelaw, Tom C Freeman, Kim M Summers, Alan L Archibald, David A Hume
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28910762/deep-edge-guided-recurrent-residual-learning-for-image-super-resolution
#4
Wenhan Yang, Jiashi Feng, Jianchao Yang, Fang Zhao, Jiaying Liu, Zongming Guo, Shuicheng Yan
In this work, we consider the image super-resolution (SR) problem. The main challenge of image SR is to recover high-frequency details of a low-resolution (LR) image that are important for human perception. To address this essentially illposed problem, we introduce a Deep Edge Guided REcurrent rEsidual (DEGREE) network to progressively recover the highfrequency details. Different from most of existing methods that aim at predicting high-resolution (HR) images directly, DEGREE investigates an alternative route to recover the difference between a pair of LR and HR images by recurrent residual learning...
September 8, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28910696/tissue-microstructure-estimation-using-a-deep-network-inspired-by-a-dictionary-based-framework
#5
Chuyang Ye
Diffusion magnetic resonance imaging (dMRI) captures the anisotropic pattern of water displacement in the neuronal tissue and allows noninvasive investigation of the complex tissue microstructure. A number of biophysical models have been proposed to relate the tissue organization with the observed diffusion signals, so that the tissue microstructure can be inferred. The Neurite Orientation Dispersion and Density Imaging (NODDI) model has been a popular choice and has been widely used for many neuroscientific studies...
September 6, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28905408/resting-state-functional-connectivity-in-the-rat-cervical-spinal-cord-at-9-4-t
#6
Tung-Lin Wu, Feng Wang, Arabinda Mishra, George H Wilson, Nellie Byun, Li Min Chen, John C Gore
PURPOSE: Numerous studies have adopted resting-state functional MRI methods to infer functional connectivity between cortical regions, but very few have translated them to the spinal cord, despite its critical role in the central nervous system. Resting-state functional connectivity between gray matter horns of the spinal cord has previously been shown to be detectable in humans and nonhuman primates, but it has not been reported previously in rodents. METHODS: Resting-state functional MRI of the cervical spinal cord of live anesthetized rats was performed at 9...
September 14, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28904382/multidimensional-encoding-of-brain-connectomes
#7
Cesar F Caiafa, Franco Pestilli
The ability to map brain networks in living individuals is fundamental in efforts to chart the relation between human behavior, health and disease. Advances in network neuroscience may benefit from developing new frameworks for mapping brain connectomes. We present a framework to encode structural brain connectomes and diffusion-weighted magnetic resonance (dMRI) data using multidimensional arrays. The framework integrates the relation between connectome nodes, edges, white matter fascicles and diffusion data...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904202/discrete-dynamical-modeling-of-influenza-infection-suggests-age-dependent-differences-in-immunity
#8
Ericka Keef, Li Ang Zhang, David Swigon, Alisa Urbano, G Bard Ermentrout, Michael Matuszewski, Franklin R Toapanta, Ted M Ross, Robert S Parker, Gilles Clermont
Immunosenescence, an age-related decline in immune function, is a major contributor to morbidity and mortality in the elderly. Older hosts exhibit delayed onset of immunity and prolonged inflammation after an infection, leading to excess damage and greater likelihood of death. Our study applies a rule-based model to infer which components of immune response are most changed in an aged host. Two groups of BALB/c mice (age 12-16 wks and 72-76 wks) were infected at 2 inocula: a survivable 50 PFU dose and a lethal 500 PFU dose...
September 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28903485/editor-s-highlight-mechanistic-toxicity-tests-based-on-an-adverse-outcome-pathway-network-for-hepatic-steatosis
#9
Michelle M Angrish, Charlene A McQueen, Elaine Cohen-Hubal, Maribel Bruno, Yue Ge, Brian N Chorley
Risk assessors use liver endpoints in rodent toxicology studies to assess the safety of chemical exposures. Yet, rodent endpoints may not accurately reflect human responses. For this reason and others, human-based invitro models are being developed and anchored to adverse outcome pathways to better predict adverse human health outcomes. Here, a networked adverse outcome pathway-guided selection of biology-based assays for lipid uptake, lipid efflux, fatty acid oxidation, and lipid accumulation were developed...
September 1, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28903046/genome-scale-architecture-of-small-molecule-regulatory-networks-and-the-fundamental-trade-off-between-regulation-and-enzymatic-activity
#10
Ed Reznik, Dimitris Christodoulou, Joshua E Goldford, Emma Briars, Uwe Sauer, Daniel Segrè, Elad Noor
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets...
September 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/28898266/translating-natural-genetic-variation-to-gene-expression-in-a-computational-model-of-the-drosophila-gap-gene-regulatory-network
#11
Vitaly V Gursky, Konstantin N Kozlov, Ivan V Kulakovskiy, Asif Zubair, Paul Marjoram, David S Lawrie, Sergey V Nuzhdin, Maria G Samsonova
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression...
2017: PloS One
https://www.readbyqxmd.com/read/28893852/root-architecture-shaping-by-the-environment-is-orchestrated-by-dynamic-gene-expression-in-space-and-time
#12
Liam Walker, Clare Boddington, Dafyd Jenkins, Ying Wang, Jesper T Grønlund, Jo Hulsmans, Sanjeev Kumar, Dhaval Patel, Jonathan D Moore, Anthony Carter, Siva Samavedam, Giovanni Bomono, David S Hersh, Gloria M Coruzzi, Nigel J Burroughs, Miriam L Gifford
Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana, at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response non-redundancy...
September 11, 2017: Plant Cell
https://www.readbyqxmd.com/read/28891109/strengthening-community-mental-health-competence-a-realist-informed-case-study-from-dehradun-north-india
#13
Kaaren Mathias, Jeph Mathias, Isabel Goicolea, Michelle Kermode
Few accounts exist of programmes in low- and middle-income countries seeking to strengthen community knowledge and skills in mental health. This case study uses a realist lens to explore how a mental health project in a context with few mental health services, strengthened community mental health competence by increasing community knowledge, creating safer social spaces and engaging partnerships for action. We used predominantly qualitative methods to explore relationships between context, interventions, mechanisms and outcomes in the "natural setting" of a community-based mental health project in Dehradun district, Uttarakhand, North India...
September 11, 2017: Health & Social Care in the Community
https://www.readbyqxmd.com/read/28890691/predicting-intentions-of-a-familiar-significant-other-beyond-the-mirror-neuron-system
#14
Stephanie Cacioppo, Elsa Juan, George Monteleone
Inferring intentions of others is one of the most intriguing issues in interpersonal interaction. Theories of embodied cognition and simulation suggest that this mechanism takes place through a direct and automatic matching process that occurs between an observed action and past actions. This process occurs via the reactivation of past self-related sensorimotor experiences within the inferior frontoparietal network (including the mirror neuron system, MNS). The working model is that the anticipatory representations of others' behaviors require internal predictive models of actions formed from pre-established, shared representations between the observer and the actor...
2017: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/28888644/genetic-diversity-of-porcine-circovirus-type-2-pcv2-in-thailand-during-2009-2015
#15
Nattarat Thangthamniyom, Pradit Sangthong, Pariwat Poolperm, Narut Thanantong, Alongkot Boonsoongnern, Payuda Hansoongnern, Ploypailin Semkum, Nantawan Petcharat, Porntippa Lekcharoensuk
Porcine circovirus type 2 (PCV2), the essential cause of porcine circovirus associated disease (PCVAD), has evolved rapidly and it has been reported worldwide. However, genetic information of PCV2 in Thailand has not been available since 2011. Herein, we studied occurrence and genetic diversity of PCV2 in Thailand and their relationships to the global PCV2 based on ORF2 sequences. The results showed that 306 samples (44.09%) from 56 farms (80%) were PCV2 positive by PCR. Phylogenetic trees constructed by both neighbor-joining and Bayesian Inference yielded similar topology of the ORF2 sequences...
September 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28887489/hardware-emulation-of-stochastic-p-bits-for-invertible-logic
#16
Ahmed Zeeshan Pervaiz, Lakshmi Anirudh Ghantasala, Kerem Yunus Camsari, Supriyo Datta
The common feature of nearly all logic and memory devices is that they make use of stable units to represent 0's and 1's. A completely different paradigm is based on three-terminal stochastic units which could be called "p-bits", where the output is a random telegraphic signal continuously fluctuating between 0 and 1 with a tunable mean. p-bits can be interconnected to receive weighted contributions from others in a network, and these weighted contributions can be chosen to not only solve problems of optimization and inference but also to implement precise Boolean functions in an inverted mode...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28885295/morphometric-analysis-of-rat-spinal-cord-angioarchitecture-by-phase-contrast-radiography-from-2d-to-3d-visualization
#17
Tianding Wu, Yong Cao, Shuangfei Ni, Zixiang Luo, Liyuan Jiang, Hongbin Lu, Jianzhong Hu
STUDY DESIGN: An advanced imaging of vasculature with synchrotron radiation X-ray in a rat model. OBJECTIVE: To develop the potential for quantitative assessment of vessel network from 2D to 3D visualization by synchrotron radiation X-ray phase contrast tomography (XPCT) in rat spinal cord model. SUMMARY OF BACKGROUND DATA: Investigation of microvasculature contributes to the understanding of pathological development of spinal cord injury...
September 6, 2017: Spine
https://www.readbyqxmd.com/read/28883408/loss-of-brain-inter-frequency-hubs-in-alzheimer-s-disease
#18
J Guillon, Y Attal, O Colliot, V La Corte, B Dubois, D Schwartz, M Chavez, F De Vico Fallani
Alzheimer's disease (AD) causes alterations of brain network structure and function. The latter consists of connectivity changes between oscillatory processes at different frequency channels. We proposed a multi-layer network approach to analyze multiple-frequency brain networks inferred from magnetoencephalographic recordings during resting-states in AD subjects and age-matched controls. Main results showed that brain networks tend to facilitate information propagation across different frequencies, as measured by the multi-participation coefficient (MPC)...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28883405/modeling-a-linkage-between-blood-transcriptional-expression-and-activity-in-brain-regions-to-infer-the-phenotype-of-schizophrenia-patients
#19
El Chérif Ibrahim, Vincent Guillemot, Magali Comte, Arthur Tenenhaus, Xavier Yves Zendjidjian, Aida Cancel, Raoul Belzeaux, Florence Sauvanaud, Olivier Blin, Vincent Frouin, Eric Fakra
Hundreds of genetic loci participate to schizophrenia liability. It is also known that impaired cerebral connectivity is directly related to the cognitive and affective disturbances in schizophrenia. How genetic susceptibility and brain neural networks interact to specify a pathological phenotype in schizophrenia remains elusive. Imaging genetics, highlighting brain variations, has proven effective to establish links between vulnerability loci and associated clinical traits. As previous imaging genetics works in schizophrenia have essentially focused on structural DNA variants, these findings could be blurred by epigenetic mechanisms taking place during gene expression...
September 7, 2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28882000/integrative-deep-models-for-alternative-splicing
#20
Anupama Jha, Matthew R Gazzara, Yoseph Barash
Motivation: Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first involves a myriad of techniques such as RNA-Seq and CLIP-Seq to identify splicing regulators and their putative targets. The second involves probabilistic models, also known as splicing codes, which infer regulatory mechanisms and predict splicing outcome directly from genomic sequence...
July 15, 2017: Bioinformatics
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