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Network function prediction

T Pamminger, W O H Hughes
The evolution of complex societies with obligate reproductive division of labour represents one of the major transitions in evolution. In such societies, functionally sterile individuals (workers) perform many of fitness-relevant behaviours including allomaternal ones, without getting any direct fitness benefits. The question of how such worker division of labour has evolved remains controversial. The reproductive groundplan hypothesis (RGPH) offers a powerful proximate explanation for this evolutionary leap...
October 26, 2016: Evolution; International Journal of Organic Evolution
Feng Q He, Markus Ollert
Identification of key genes for a given physiological or pathological process is an essential but still very challenging task for the entire biomedical research community. Statistics-based approaches, such as genome-wide association study (GWAS)- or quantitative trait locus (QTL)-related analysis have already made enormous contributions to identifying key genes associated with a given disease or phenotype, the success of which is however very much dependent on a huge number of samples. Recent advances in network biology, especially network inference directly from genome-scale data and the following-up network analysis, opens up new avenues to predict key genes driving a given biological process or cellular function...
October 26, 2016: Advances in Biochemical Engineering/biotechnology
Qing-Ju Jiao, Yan Huang, Hong-Bin Shen
Biological networks are effective tools for studying molecular interactions. Modular structure, in which genes or proteins may tend to be associated with functional modules or protein complexes, is a remarkable feature of biological networks. Mining modular structure from biological networks enables us to focus on a set of potentially important nodes, which provides a reliable guide to future biological experiments. The first fundamental challenge in mining modular structure from biological networks is that the quality of the observed network data is usually low owing to noise and incompleteness in the obtained networks...
October 26, 2016: Molecular BioSystems
Burak Himmetoglu
We present an application of the boosted regression tree algorithm for predicting ground state energies of molecules made up of C, H, N, O, P, and S (CHNOPS). The PubChem chemical compound database has been incorporated to construct a dataset of 16 242 molecules, whose electronic ground state energies have been computed using density functional theory. This dataset is used to train the boosted regression tree algorithm, which allows a computationally efficient and accurate prediction of molecular ground state energies...
October 7, 2016: Journal of Chemical Physics
Chengwei Wang, Celso Grebogi, Murilo S Baptista
The electric power system is one of the cornerstones of modern society. One of its most serious malfunctions is the blackout, a catastrophic event that may disrupt a substantial portion of the system, playing havoc to human life and causing great economic losses. Thus, understanding the mechanisms leading to blackouts and creating a reliable and resilient power grid has been a major issue, attracting the attention of scientists, engineers, and stakeholders. In this paper, we study the blackout problem in power grids by considering a practical phase-oscillator model...
September 2016: Chaos
Amanda Elton, Christopher T Smith, Michael H Parrish, Charlotte A Boettiger
Excessively choosing immediate over larger future rewards, or delay discounting (DD), associates with multiple clinical conditions. Individual differences in DD likely depend on variations in the activation of and functional interactions between networks, representing possible endophenotypes for associated disorders, including alcohol use disorders. Numerous fMRI studies have probed the neural bases of DD, but investigations of large-scale networks remain scant. We addressed this gap by testing whether activation within large-scale networks during Now/Later decision-making predicts individual differences in DD...
October 25, 2016: Journal of Cognitive Neuroscience
Liangliang Quan, Yang Wang, Jiulong Liang, Tao Qiu, Hongyi Wang, Ye Zhang, Yu Zhang, Qiang Hui, Kai Tao
In the present study, we aimed to reveal the molecular mechanisms responsible for the differentiation of human adipose tissue-derived stem cells (hASCs) into myocytes and osteoblasts. Microarray data GSE37329 were obtained from the Gene Expression Omnibus database, including three hASC cell lines from healthy donors, two osteogenic lineages and two myogenic lineages from the in vitro‑induction of hASCs. Differentially expressed genes (DEGs) in the two lineages were firstly screened. Subsequently, the underlying functions of the two sets of DEGs were investigated by Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, followed by protein-protein interaction (PPI) network construction...
October 25, 2016: International Journal of Molecular Medicine
Rintaro Saito, Anaïs Rocanin-Arjo, Young-Hyun You, Manjula Darshi, Benjamin Van Espen, Satoshi Miyamoto, Jessica Pham, Minya Pu, Simone Romoli, Loki Natarajan, Wenjun Ju, Matthias Kretzler, Robert Nelson, Keiichiro Ono, Dana Thomasova, Shrikant R Mulay, Trey Ideker, Vivette D'Agati, Ergin Beyret, Juan Carlos Izpisua Belmonte, Hans Joachim Anders, Kumar Sharma
To derive new insights in diabetic complications, we integrated publicly available human protein-protein interaction (PPI) networks with global metabolic networks using metabolomic data from patients with diabetic nephropathy. We focused on the participating proteins in the network that were computationally predicted to connect the urine metabolites. MDM2 had the highest significant number of PPI connections. As validation, significant downregulation of MDM2 gene expression was found in both glomerular and tubulointerstitial compartments of kidney biopsy tissue from 2 independent cohorts of patients with diabetic nephropathy...
October 20, 2016: JCI Insight
Juan I Fuxman Bass, Carles Pons, Lucie Kozlowski, John S Reece-Hoyes, Shaleen Shrestha, Amy D Holdorf, Akihiro Mori, Chad L Myers, Albertha Jm Walhout
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences...
October 24, 2016: Molecular Systems Biology
Michael Eickenberg, Alexandre Gramfort, Gaël Varoquaux, Bertrand Thirion
Convolutional networks used for computer vision represent candidate models for the computations performed in mammalian visual systems. We use them as a detailed model of human brain activity during the viewing of natural images by constructing predictive models based on their different layers and BOLD fMRI activations. Analyzing the predictive performance across layers yields characteristic fingerprints for each visual brain region: early visual areas are better described by lower level convolutional net layers and later visual areas by higher level net layers, exhibiting a progression across ventral and dorsal streams...
October 21, 2016: NeuroImage
Hongyoon Choi, Kyong Hwan Jin
BACKGROUND: Automated segmentation of brain structures is an important task in structural and functional image analysis. We developed a fast and accurate method for the striatum segmentation using deep convolutional neural networks (CNN). NEW METHOD: T1 magnetic resonance (MR) images were used for our CNN-based segmentation, which require neither image feature extraction nor nonlinear transformation. We employed two serial CNN, Global and Local CNN: The Global CNN determined approximate locations of the striatum...
October 21, 2016: Journal of Neuroscience Methods
Zuzana Novak, Mary Aglipay, Nick Barrowman, Keith O Yeates, Miriam H Beauchamp, Jocelyn Gravel, Stephen B Freedman, Isabelle Gagnon, Gerard Gioia, Kathy Boutis, Emma Burns, Andrée-Anne Ledoux, Martin H Osmond, Roger L Zemek
Importance: Persistent postconcussion symptoms (PPCS) pose long-term challenges and can negatively affect patients' health-related quality of life (HRQoL). To date, no large comprehensive study has addressed the association between PPCS and HRQoL. Objectives: To determine the association between HRQoL and PPCS at 4 weeks after concussion and assess the degree of impairment of HRQoL in the subsequent 12 weeks. Design, Setting, and Participants: In a prospective, multicenter cohort study (Predicting Persistent Postconcussive Problems in Pediatrics [5P]) from August 14, 2013, to September 30, 2014, children aged 5 to 18 years who presented to the emergency department within 48 hours after head injury and were considered to have an acute concussion were enrolled across 9 pediatric emergency departments within the Pediatric Emergency Research Canada Network...
October 24, 2016: JAMA Pediatrics
Balázs Ligeti, Ottilia Menyhárt, Ingrid Petrič, Balázs Győrffy, Sándor Pongor
BACKGROUND: Biomedical sciences use a variety of data sources on drug molecules, genes, proteins, diseases and scientific publications etc. This system can be best pictured as a giant data-network linked together by physical, functional, logical and similarity relationships. A new hypothesis or discovery can be considered as a new link that can be deduced from the existing connections. For instance, interactions of two pharmacons - if not already known - represent a testable novel hypothesis...
October 21, 2016: Current Pharmaceutical Design
Samantha V Abram, Krista M Wisner, Jaclyn M Fox, Deanna M Barch, Lei Wang, John G Csernansky, Angus W MacDonald, Matthew J Smith
Impaired cognitive empathy is a core social cognitive deficit in schizophrenia associated with negative symptoms and social functioning. Cognitive empathy and negative symptoms have also been linked to medial prefrontal and temporal brain networks. While shared behavioral and neural underpinnings are suspected for cognitive empathy and negative symptoms, research is needed to test these hypotheses. In two studies, we evaluated whether resting-state functional connectivity between data-driven networks, or components (referred to as, inter-component connectivity), predicted cognitive empathy and experiential and expressive negative symptoms in schizophrenia subjects...
October 24, 2016: Human Brain Mapping
Ebrahim Alipanahpour Dil, Mehrorang Ghaedi, Arash Asfaram
The present research is focused on the synthesis and characterization of zinc (II) oxide nanorods loaded on activated carbon (ZnO-NRs-AC) to prepare an outstanding adsorbent for the simultaneous adsorption of heavy metals and dyes as hazardous pollutant using ultrasound energy. The adsorbent was identified by Scanning Electron Microscope (SEM), Transmission Electron Microscopy (TEM), Energy-dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD) analysis. The individual effects and possible interactions between the most effective variables including initial metal ions (Cd(2+) and Co(2+)) and azo dyes (methylene blue (MB) and crystal violet (CV)) concentration, adsorbent dosage and ultrasonic time on the responses were investigated by response surface methodology (RSM) and optimum conditions was fixed at Cd(2+), Co(2+), MB and CV concentrations were 25, 24, 18 and 14mgL(-1), respectively, 0...
January 2017: Ultrasonics Sonochemistry
Ebrahim Alipanahpour Dil, Mehrorang Ghaedi, Arash Asfaram
Present study is based on describing an ultrasound-assisted dispersive liquid-liquid microextraction coupled with derivative spectrophotometry (UAS-DLLME-UV-vis) as useful technique for selective determination of crystal violet (CV) and azure b (Az-B). The significant factors like pH, extractor volume, disperser value and extraction time contribution and their numerical coefficient in quadratic model were calculated according to central composite design (CCD). According to desirability function (DF) as good criterion the best experimental conditions was adjusted and selected at pH of 7...
January 2017: Ultrasonics Sonochemistry
Clare Paterson, Yanhong Wang, Thomas M Hyde, Daniel R Weinberger, Joel E Kleinman, Amanda J Law
OBJECTIVE: Genes implicated in schizophrenia are enriched in networks differentially regulated during human CNS development. Neuregulin 3 (NRG3), a brain-enriched neurotrophin, undergoes alternative splicing and is implicated in several neurological disorders with developmental origins. Isoform-specific increases in NRG3 are observed in schizophrenia and associated with rs10748842, a NRG3 risk polymorphism, suggesting NRG3 transcriptional dysregulation as a molecular mechanism of risk...
October 24, 2016: American Journal of Psychiatry
Yousef Sakieh, Abdolrassoul Salmanmahiny, Seyed Hamed Mirkarimi
Continuous surface of urbanization suitability, as an input to many urban growth models (UGM), has a significant role on a proper calibration process. The present study evaluates and compares the simulation success of the Cellular Automata-Markov Chain (CA-MC) model through multiple methods. For this, a series of mapping algorithms are applied ranging from empirical methods such as multi-criteria evaluation (MCE) to statistical algorithms without spatially explicit suitability mapping rules such as logistic regression (LR) and multi-layer perceptron (MLP) neural network and finally statistical and spatially explicit rule-based methods such as SLEUTH-Genetic Algorithm (SLEUTH-GA) model...
November 2016: Environmental Monitoring and Assessment
Ying Yang, Jing Wang, Cyntia Bailer, Vladimir Cherkassky, Marcel Adam Just
The aim of the study was to test the cross-language generative capability of a model that predicts neural activation patterns evoked by sentence reading, based on a semantic characterization of the sentence. In a previous study on English monolingual speakers (Wang, Cherkassky, & Just, submitted), a computational model performed a mapping from a set of 42 concept-level semantic features (Neurally Plausible Semantic Features, NPSFs) as well as 6 thematic role markers to neural activation patterns (assessed with fMRI), to predict activation levels in a network of brain locations...
October 19, 2016: NeuroImage
Joachim Niehren, Cristian Versari, Mathias John, François Coutte, Philippe Jacques
We wish to predict changes of reaction networks with partial kinetic information that lead to target changes of their steady states. The changes may be either increases or decreases of influxes, reaction knockouts, or multiple changes of these two kinds. Our prime applications are knockout prediction tasks for metabolic and regulation networks. In a first step, we propose a formal modeling language for reaction networks with partial kinetic information. The modeling language has a graphical syntax reminiscent to Petri nets...
October 18, 2016: Bio Systems
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