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https://www.readbyqxmd.com/read/29346387/inferring-the-risk-factors-behind-the-geographical-spread-and-transmission-of-zika-in-the-americas
#1
Lauren M Gardner, András Bóta, Karthik Gangavarapu, Moritz U G Kraemer, Nathan D Grubaugh
BACKGROUND: An unprecedented Zika virus epidemic occurred in the Americas during 2015-2016. The size of the epidemic in conjunction with newly recognized health risks associated with the virus attracted significant attention across the research community. Our study complements several recent studies which have mapped epidemiological elements of Zika, by introducing a newly proposed methodology to simultaneously estimate the contribution of various risk factors for geographic spread resulting in local transmission and to compute the risk of spread (or re-introductions) between each pair of regions...
January 18, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29344882/detection-of-combinatorial-mutational-patterns-in-human-cancer-genomes-by-exclusivity-analysis
#2
Hua Tan, Xiaobo Zhou
Cancer genes may tend to mutate in a co-mutational or mutually exclusive manner in a tumor sample of a specific cancer, which constitute two known combinatorial mutational patterns for a given gene set. Previous studies have established that genes functioning in different signaling pathways can mutate in the same sample, i.e., a tumor from one patient, while genes operating in the same pathway are rarely mutated in the same cancer genome. Therefore, reliable identification of combinatorial mutational patterns of candidate cancer genes has important ramifications in inferring signaling network modules in a particular cancer type...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344147/systematic-analysis-of-the-molecular-mechanism-of-microrna-124-in-hepatoblastoma-cells
#3
Guiming Wang, Hong Liu, Zhigang Wei, Hongyan Jia, Yu Liu, Jiansheng Liu
The present study aimed to identify the molecular mechanisms of microRNA-124 (miRNA-124/miR-124) in hepatoblastoma. The GSE6207 microarray dataset, obtained from the Gene Expression Omnibus database, included samples extracted from HepG2 cells transfected with miR-124 duplex (the experimental group) or negative control (the control group) at 4, 8, 16, 24, 32, 72 and 120 h after transfection. Differentially expressed genes (DEGs) were screened between the two groups. miR-124 activity was inferred based on the expression of its target genes...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343603/mutual-assessment-during-ritualized-fighting-in-mantis-shrimp-stomatopoda
#4
P A Green, S N Patek
Safe and effective conflict resolution is critical for survival and reproduction. Theoretical models describe how animals resolve conflict by assessing their own and/or their opponent's ability (resource holding potential, RHP), yet experimental tests of these models are often inconclusive. Recent reviews have suggested this uncertainty could be alleviated by using multiple approaches to test assessment models. The mantis shrimp Neogonodactylus bredini presents visual displays and ritualistically exchanges high-force strikes during territorial contests...
January 31, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29342231/mapping-gene-regulatory-networks-from-single-cell-omics-data
#5
Mark W E J Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Single-cell techniques are advancing rapidly and are yielding unprecedented insight into cellular heterogeneity. Mapping the gene regulatory networks (GRNs) underlying cell states provides attractive opportunities to mechanistically understand this heterogeneity. In this review, we discuss recently emerging methods to map GRNs from single-cell transcriptomics data, tackling the challenge of increased noise levels and data sparsity compared with bulk data, alongside increasing data volumes. Next, we discuss how new techniques for single-cell epigenomics, such as single-cell ATAC-seq and single-cell DNA methylation profiling, can be used to decipher gene regulatory programmes...
January 12, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29341386/at-the-core-of-reasoning-dissociating-deductive-and-non-deductive-load
#6
John P Coetzee, Martin M Monti
In recent years, neuroimaging methods have been used to investigate how the human mind carries out deductive reasoning. According to some, the neural substrate of language is integral to deductive reasoning. According to others, deductive reasoning is supported by a language-independent distributed network including left frontopolar and frontomedial cortices. However, it has been suggested that activity in these frontal regions might instead reflect non-deductive factors such as working memory load and general cognitive difficulty...
January 16, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/29340865/design-of-a-tripartite-network-for-the-prediction-of-drug-targets
#7
Ryo Kunimoto, Jürgen Bajorath
Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred...
January 16, 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29339482/global-spectral-clustering-in-dynamic-networks
#8
Fuchen Liu, David Choi, Lu Xie, Kathryn Roeder
Community detection is challenging when the network structure is estimated with uncertainty. Dynamic networks present additional challenges but also add information across time periods. We propose a global community detection method, persistent communities by eigenvector smoothing (PisCES), that combines information across a series of networks, longitudinally, to strengthen the inference for each period. Our method is derived from evolutionary spectral clustering and degree correction methods. Data-driven solutions to the problem of tuning parameter selection are provided...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29337235/frequency-specific-effective-connectivity-in-subjects-with-cerebral-infarction-as-revealed-by-nirs-method
#9
Qianying Liu, Bitian Wang, Ying Liu, Zeping Lv, Wenhao Li, Zengyong Li, Yubo Fan
A connectivity-based approach can highlight the network reorganization in the chronic phases after stroke and contributes to the development of therapeutic interventions. Using dynamic Bayesian inference, this study aimed to assess the effective connectivity(EC)in various frequency bands through the near-infrared spectroscopy(NIRS) method in subjects with cerebral infarction(CI). A phase-coupling model was established based on phase information extracted using the wavelet transform of NIRS signals. Coupling strength and the main coupling direction were estimated using dynamic Bayesian inference...
January 11, 2018: Neuroscience
https://www.readbyqxmd.com/read/29336480/species-co-occurrence-networks-can-they-reveal-trophic-and-non-trophic-interactions-in-ecological-communities
#10
Mara A Freilich, Evie Wieters, Bernardo R Broitman, Pablo A Marquet, Sergio A Navarrete
Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically-based, species interaction network from the same region...
January 16, 2018: Ecology
https://www.readbyqxmd.com/read/29336305/inferring-joint-sequence-structural-determinants-of-protein-functional-specificity
#11
Andrew F Neuwald, L Aravind, Stephen F Altschul
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns...
January 16, 2018: ELife
https://www.readbyqxmd.com/read/29335027/fungi-stabilize-connectivity-in-the-lung-and-skin-microbial-ecosystems
#12
Laura Tipton, Christian L Müller, Zachary D Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, Richard Bonneau, Elodie Ghedin
BACKGROUND: No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes than in cataloging which microbes are present, the variety of microbes in the community should be considered. However, the majority of ecological interaction networks for microbiomes built to date have included only bacteria. Joint association inference across multiple domains of life, e...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29329302/phylogeography-and-conservation-genetics-of-the-rare-and-relict-bretschneidera-sinensis-akaniaceae
#13
Mei-Na Wang, Lei Duan, Qi Qiao, Zheng-Feng Wang, Elizabeth A Zimmer, Zhong-Chao Li, Hong-Feng Chen
Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B...
2018: PloS One
https://www.readbyqxmd.com/read/29328958/stdp-based-spiking-deep-convolutional-neural-networks-for-object-recognition
#14
Saeed Reza Kheradpisheh, Mohammad Ganjtabesh, Simon J Thorpe, Timothée Masquelier
Previous studies have shown that spike-timing-dependent plasticity (STDP) can be used in spiking neural networks (SNN) to extract visual features of low or intermediate complexity in an unsupervised manner. These studies, however, used relatively shallow architectures, and only one layer was trainable. Another line of research has demonstrated - using rate-based neural networks trained with back-propagation - that having many layers increases the recognition robustness, an approach known as deep learning. We thus designed a deep SNN, comprising several convolutional (trainable with STDP) and pooling layers...
December 23, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/29325153/network-perturbation-analysis-of-gene-transcriptional-profiles-reveals-protein-targets-and-mechanism-of-action-of-drugs-and-influenza-a-viral-infection
#15
Heeju Noh, Jason E Shoemaker, Rudiyanto Gunawan
Genome-wide transcriptional profiling provides a global view of cellular state and how this state changes under different treatments (e.g. drugs) or conditions (e.g. healthy and diseased). Here, we present ProTINA (Protein Target Inference by Network Analysis), a network perturbation analysis method for inferring protein targets of compounds from gene transcriptional profiles. ProTINA uses a dynamic model of the cell-type specific protein-gene transcriptional regulation to infer network perturbations from steady state and time-series differential gene expression profiles...
January 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29325077/integrating-restriction-site-associated-dna-sequencing-rad-seq-with-morphological-cladistic-analysis-clarifies-evolutionary-relationships-among-major-species-groups-of-bee-orchids
#16
Richard M Bateman, Gábor Sramkó, Ovidiu Paun
Background and Aims: Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus...
January 9, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29324886/changes-in-network-connectivity-during-motor-imagery-and-execution
#17
Yun Kwan Kim, Eunhee Park, Ahee Lee, Chang-Hwan Im, Yun-Hee Kim
BACKGROUND: Recent studies of functional or effective connectivity in the brain have reported that motor-related brain regions were activated during motor execution and motor imagery, but the relationship between motor and cognitive areas has not yet been completely understood. The objectives of our study were to analyze the effective connectivity between motor and cognitive networks in order to define network dynamics during motor execution and motor imagery in healthy individuals. Second, we analyzed the differences in effective connectivity between correct and incorrect responses during motor execution and imagery using dynamic causal modeling (DCM) of electroencephalography (EEG) data...
2018: PloS One
https://www.readbyqxmd.com/read/29322933/integrating-transcriptional-activity-in-genome-scale-models-of-metabolism
#18
Daniel Trejo Banos, Pauline Trébulle, Mohamed Elati
BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322918/a-linear-programming-computational-framework-integrates-phosphor-proteomics-and-prior-knowledge-to-predict-drug-efficacy
#19
Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi
BACKGROUND: In recent years, the integration of 'omics' technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the way of approaching drug discovery. The LINCS public data warehouse provides detailed information about cell responses with various genetic and environmental stressors. It can be greatly helpful in developing new drugs and therapeutics, as well as improving the situations of lacking effective drugs, drug resistance and relapse in cancer therapies, etc...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29321854/phylogenetic-relationships-and-phylogeography-of-relevant-lineages-within-the-complex-campanulaceae-family-in-macaronesia
#20
Tiago Menezes, Maria M Romeiras, Miguel M de Sequeira, Mónica Moura
Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages...
January 2018: Ecology and Evolution
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