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https://www.readbyqxmd.com/read/29351717/prediction-of-protein-configurational-entropy-popcoen
#1
Martin Goethe, Jan Gleixner, Ignacio Fita, J Miguel Rubi
A knowledge-based method for configurational entropy prediction of proteins is presented which is extremely fast compared to previous approaches because it does not involve any kind of configurational sampling. Instead, the configurational entropy of a query fold is estimated by evaluating an artificial neural network which was trained on molecular-dynamics simulations of about 1000 proteins. The predicted entropy can be incorporated into a large class of protein software based on cost-function minimization/evaluation in which configurational entropy is currently neglected for performance reasons...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29351231/molecular-network-based-identification-of-competing-endogenous-rnas-in-thyroid-carcinoma
#2
Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaonan Zhou, Min Tang, Yuhua Yao, Jialiang Yang
RNAs may act as competing endogenous RNAs (ceRNAs), a critical mechanism in determining gene expression regulations in many cancers. However, the roles of ceRNAs in thyroid carcinoma remains elusive. In this study, we have developed a novel pipeline called Molecular Network-based Identification of ceRNA (MNIceRNA) to identify ceRNAs in thyroid carcinoma. MNIceRNA first constructs micro RNA (miRNA)-messenger RNA (mRNA)long non-coding RNA (lncRNA) networks from miRcode database and weighted correlation network analysis (WGCNA), based on which to identify key drivers of differentially expressed RNAs between normal and tumor samples...
January 19, 2018: Genes
https://www.readbyqxmd.com/read/29351215/multi-sensor-data-integration-using-deep-learning-for-characterization-of-defects-in-steel-elements
#3
Grzegorz Psuj
Nowadays, there is a strong demand for inspection systems integrating both high sensitivity under various testing conditions and advanced processing allowing automatic identification of the examined object state and detection of threats. This paper presents the possibility of utilization of a magnetic multi-sensor matrix transducer for characterization of defected areas in steel elements and a deep learning based algorithm for integration of data and final identification of the object state. The transducer allows sensing of a magnetic vector in a single location in different directions...
January 19, 2018: Sensors
https://www.readbyqxmd.com/read/29349868/workplace-alcohol-harm-reduction-intervention-in-australia-cluster-non-randomised-controlled-trial
#4
Ken Pidd, Ann Roche, Jacqui Cameron, Nicole Lee, Linda Jenner, Vinita Duraisingam
INTRODUCTION AND AIMS: The workplace holds substantial potential as an alcohol harm reduction and prevention setting. Few studies have rigorously examined strategies to reduce workplace alcohol-related harm. Hence, an in-situ 3 year trial of a comprehensive alcohol harm reduction intervention in Australian manufacturing workplaces was undertaken. DESIGN AND METHODS: Informed by a gap analysis, a multi-site trial was undertaken. Three manufacturing industry companies, located at four separate worksites, with a minimum of 100 employees were recruited through a local industry network...
January 18, 2018: Drug and Alcohol Review
https://www.readbyqxmd.com/read/29348878/identification-of-cancer-prognosis-associated-functional-modules-using-differential-co-expression-networks
#5
Wenshuai Yu, Shengjie Zhao, Yongcui Wang, Brian Nlong Zhao, Weiling Zhao, Xiaobo Zhou
The rapid accumulation of cancer-related data owing to high-throughput technologies has provided unprecedented choices to understand the progression of cancer and discover functional networks in multiple cancers. Establishment of co-expression networks will help us to discover the systemic properties of carcinogenesis features and regulatory mechanisms of multiple cancers. Here, we proposed a computational workflow to identify differentially co-expressed gene modules across 8 cancer types by using combined gene differential expression analysis methods and a higher-order generalized singular value decomposition...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348485/motor-signatures-of-emotional-reactivity-in-frontotemporal-dementia
#6
Charles R Marshall, Chris J D Hardy, Lucy L Russell, Camilla N Clark, Rebecca L Bond, Katrina M Dick, Emilie V Brotherhood, Cath J Mummery, Jonathan M Schott, Jonathan D Rohrer, James M Kilner, Jason D Warren
Automatic motor mimicry is essential to the normal processing of perceived emotion, and disrupted automatic imitation might underpin socio-emotional deficits in neurodegenerative diseases, particularly the frontotemporal dementias. However, the pathophysiology of emotional reactivity in these diseases has not been elucidated. We studied facial electromyographic responses during emotion identification on viewing videos of dynamic facial expressions in 37 patients representing canonical frontotemporal dementia syndromes versus 21 healthy older individuals...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348434/identification-of-genetic-elements-in-metabolism-by-high-throughput-mouse-phenotyping
#7
Jan Rozman, Birgit Rathkolb, Manuela A Oestereicher, Christine Schütt, Aakash Chavan Ravindranath, Stefanie Leuchtenberger, Sapna Sharma, Martin Kistler, Monja Willershäuser, Robert Brommage, Terrence F Meehan, Jeremy Mason, Hamed Haselimashhadi, Tertius Hough, Ann-Marie Mallon, Sara Wells, Luis Santos, Christopher J Lelliott, Jacqueline K White, Tania Sorg, Marie-France Champy, Lynette R Bower, Corey L Reynolds, Ann M Flenniken, Stephen A Murray, Lauryl M J Nutter, Karen L Svenson, David West, Glauco P Tocchini-Valentini, Arthur L Beaudet, Fatima Bosch, Robert B Braun, Michael S Dobbie, Xiang Gao, Yann Herault, Ala Moshiri, Bret A Moore, K C Kent Lloyd, Colin McKerlie, Hiroshi Masuya, Nobuhiko Tanaka, Paul Flicek, Helen E Parkinson, Radislav Sedlacek, Je Kyung Seong, Chi-Kuang Leo Wang, Mark Moore, Steve D Brown, Matthias H Tschöp, Wolfgang Wurst, Martin Klingenspor, Eckhard Wolf, Johannes Beckers, Fausto Machicao, Andreas Peter, Harald Staiger, Hans-Ulrich Häring, Harald Grallert, Monica Campillos, Holger Maier, Helmut Fuchs, Valerie Gailus-Durner, Thomas Werner, Martin Hrabe de Angelis
Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29347271/machine-learning-approach-for-local-classification-of-crystalline-structures-in-multiphase-systems
#8
C Dietz, T Kretz, M H Thoma
Machine learning is one of the most popular fields in computer science and has a vast number of applications. In this work we will propose a method that will use a neural network to locally identify crystal structures in a mixed phase Yukawa system consisting of fcc, hcp, and bcc clusters and disordered particles similar to plasma crystals. We compare our approach to already used methods and show that the quality of identification increases significantly. The technique works very well for highly disturbed lattices and shows a flexible and robust way to classify crystalline structures that can be used by only providing particle positions...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347206/detection-of-time-delays-and-directional-interactions-based-on-time-series-from-complex-dynamical-systems
#9
Huanfei Ma, Siyang Leng, Chenyang Tao, Xiong Ying, Jürgen Kurths, Ying-Cheng Lai, Wei Lin
Data-based and model-free accurate identification of intrinsic time delays and directional interactions is an extremely challenging problem in complex dynamical systems and their networks reconstruction. A model-free method with new scores is proposed to be generally capable of detecting single, multiple, and distributed time delays. The method is applicable not only to mutually interacting dynamical variables but also to self-interacting variables in a time-delayed feedback loop. Validation of the method is carried out using physical, biological, and ecological models and real data sets...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#10
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346327/enhanced-isotopic-ratio-outlier-analysis-iroa-peak-detection-and-identification-with-ultra-high-resolution-gc-orbitrap-ms-potential-application-for-investigation-of-model-organism-metabolomes
#11
Yunping Qiu, Robyn D Moir, Ian M Willis, Suresh Seethapathy, Robert C Biniakewitz, Irwin J Kurland
Identifying non-annotated peaks may have a significant impact on the understanding of biological systems. In silico methodologies have focused on ESI LC/MS/MS for identifying non-annotated MS peaks. In this study, we employed in silico methodology to develop an Isotopic Ratio Outlier Analysis (IROA) workflow using enhanced mass spectrometric data acquired with the ultra-high resolution GC-Orbitrap/MS to determine the identity of non-annotated metabolites. The higher resolution of the GC-Orbitrap/MS, together with its wide dynamic range, resulted in more IROA peak pairs detected, and increased reliability of chemical formulae generation (CFG)...
January 18, 2018: Metabolites
https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#12
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29345616/inhibition-of-oxidative-stress-in-cholinergic-projection-neurons-fully-rescues-aging-associated-olfactory-circuit-degeneration-in-drosophila
#13
Ashiq Hussain, Atefeh Pooryasin, Mo Zhang, Laura F Loschek, Marco La Fortezza, Anja B Friedrich, Catherine-Marie Blais, Habibe K Üçpunar, Vicente A Yépez, Martin Lehmann, Nicolas Gompel, Julien Gagneur, Stephan J Sigrist, Ilona C Grunwald Kadow
Loss of the sense of smell is among the first signs of natural aging and neurodegenerative diseases such as Alzheimer's and Parkinson's. Cellular and molecular mechanisms promoting this smell loss are not understood. Here, we show that Drosophila melanogaster also loses olfaction before vision with age. Within the olfactory circuit, cholinergic projection neurons show a reduced odor response accompanied by a defect in axonal integrity and reduction in synaptic marker proteins. Using behavioral functional screening, we pinpoint that expression of the mitochondrial reactive oxygen scavenger SOD2 in cholinergic projection neurons is necessary and sufficient to prevent smell degeneration in aging flies...
January 18, 2018: ELife
https://www.readbyqxmd.com/read/29344895/bioinformatics-approaches-to-predict-drug-responses-from-genomic-sequencing
#14
Neel S Madhukar, Olivier Elemento
Fulfilling the promises of precision medicine will depend on our ability to create patient-specific treatment regimens. Therefore, being able to translate genomic sequencing into predicting how a patient will respond to a given drug is critical. In this chapter, we review common bioinformatics approaches that aim to use sequencing data to predict sample-specific drug susceptibility. First, we explain the importance of customized drug regimens to the future of medical care. Second, we discuss the different public databases and community efforts that can be leveraged to develop new methods for identifying new predictive biomarkers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344889/quantitative-analysis-of-tyrosine-kinase-signaling-across-differentially-embedded-human-glioblastoma-tumors
#15
Hannah Johnson, Forest M White
Glioblastoma is the most aggressive primary brain tumor with a poor mean survival even with the current standard of care. Kinase signaling analyses of clinical glioblastoma samples provide a physiologically relevant view of oncogenic signaling networks. Here, we describe the methods that enable the quantification of protein expression profiles and phosphotyrosine signaling across flash frozen and optimal cutting temperature (OCT) compound embedded tumor specimens. The data derived from these experiments can be used to identify the intra- and inter-patient heterogeneity present in these tumors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344882/detection-of-combinatorial-mutational-patterns-in-human-cancer-genomes-by-exclusivity-analysis
#16
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/29344651/identification-of-genes-and-pathways-in-the-synovia-of-women-with-osteoarthritis-by-bioinformatics-analysis
#17
Bobin Mi, Guohui Liu, Wu Zhou, Huijuan Lv, Yi Liu, Jing Liu
Osteoarthritis (OA) has a high prevalence in female patients and sex may be a key factor affecting the progression of OA. The aim of the present study was to identify genetic signatures in the synovial membranes of female patients with OA and to elucidate the potential associated molecular mechanisms. The gene expression profiles of the GSE55457 and GSE55584 datasets were obtained from the Gene Expression Omnibus database. Data of two synovial membranes from normal female individuals (GSM1337306 and GSM1337310) and two synovial membranes from female patients affected by OA (GSM1337327 and GSM1337330) were obtained from the dataset GSE55457, and those of three synovial membranes from female patients affected by OA (GSM1339628, GSM1339629 and GSM1339632) were obtained from the dataset GSE55584...
January 15, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29344193/identification-of-differentially-expressed-molecular-functions-associated-with-breast-cancer-using-gibbs-sampling
#18
Gang Zhou, Ming-Qian Lu, Dao-Jun Li, Bao-An Gao, Rong Guo
The aim of the present study was to identify differentially expressed molecular functions (DEMFs) for breast cancer using the Gibbs sampling approach. Molecular functions (MFs) were obtained on the basis of the Bayesian Approach for Geneset Selection package. Subsequently, MFs were converted into Markov chains (MCs) prior to calculating their probabilities, utilizing the MC Monte Carlo algorithm. DEMFs were identified with probabilities ≥0.8 and the gene compositions were studied. Finally, a co-expression network was constructed via the empirical Bayes method and a pathway enrichment analysis of genes in DEMFs was performed...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344166/identification-and-functional-analysis-of-risk-related-micrornas-for-the-prognosis-of-patients-with-bladder-urothelial-carcinoma
#19
Ji Gao, Hongyan Li, Lei Liu, Lide Song, Yanting Lv, Yuping Han
The aim of the present study was to investigate risk-related microRNAs (miRs) for bladder urothelial carcinoma (BUC) prognosis. Clinical and microRNA expression data downloaded from the Cancer Genome Atlas were utilized for survival analysis. Risk factor estimation was performed using Cox's proportional regression analysis. A microRNA-regulated target gene network was constructed and presented using Cytoscape. In addition, the Database for Annotation, Visualization and Integrated Discovery was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, followed by protein-protein interaction (PPI) network analysis...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344148/identification-of-potentially-critical-differentially-methylated-genes-in-nasopharyngeal-carcinoma-a-comprehensive-analysis-of-methylation-profiling-and-gene-expression-profiling
#20
Lian Hui, Jingru Zhang, Xiaoxu Ding, Xing Guo, Xuejun Jang
The present study aimed to identify potentially critical differentially methylated genes associated with the progression of nasopharyngeal carcinoma (NPC). Methylation profiling data of GSE62336 deposited in the Gene Expression Omnibus database were used to identify differentially methylated regions (DMRs) and differentially methylated CpG islands (DMIs). Concurrently, differentially expressed genes (DEGs) were identified using a meta-analysis of three gene expression datasets (GSE53819, GSE13597 and GSE12452)...
December 2017: Oncology Letters
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