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https://www.readbyqxmd.com/read/28432882/analysis-of-factors-affecting-the-severity-of-crashes-in-urban-road-intersections
#1
L Mussone, M Bassani, P Masci
Road crashes are events which depend on a variety of factors and which exhibit different magnitudes of outputs when evaluated with respect to the effects on road users. Despite a lot of research into the evaluation of crash likelihood and frequency, only a few works have focused exclusively on crash severity with these limited to sections of freeways and multilane highways. Hence, at present there is a large gap in knowledge on factors affecting the severity of crashes for other road categories, facilities, and scenarios...
April 19, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#2
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28432361/disease-biomarker-identification-from-gene-network-modules-for-metastasized-breast-cancer
#3
Pooja Sharma, Dhruba K Bhattacharyya, Jugal Kalita
Advancement in science has tended to improve treatment of fatal diseases such as cancer. A major concern in the area is the spread of cancerous cells, technically refered to as metastasis into other organs beyond the primary organ. Treatment in such a stage of cancer is extremely difficult and usually palliative only. In this study, we focus on finding gene-gene network modules which are functionally similar in nature in the case of breast cancer. These modules extracted during the disease progression stages are analyzed using p-value and their associated pathways...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431175/minepath-org-a-free-interactive-pathway-analysis-web-server
#4
Lefteris Koumakis, Panos Roussos, George Potamias
Minepath (www.minepath.org) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431030/using-multivariate-base-rates-to-interpret-low-scores-on-an-abbreviated-battery-of-the-delis-kaplan-executive-function-system
#5
Justin E Karr, Mauricio A Garcia-Barrera, James A Holdnack, Grant L Iverson
Objective: Executive function consists of multiple cognitive processes that operate as an interactive system to produce volitional goal-oriented behavior, governed in large part by frontal microstructural and physiological networks. Identification of deficits in executive function in those with neurological or psychiatric conditions can be difficult because the normal variation in executive function test scores, in healthy adults when multiple tests are used, is largely unknown. This study addresses that gap in the literature by examining the prevalence of low scores on a brief battery of executive function tests...
May 1, 2017: Archives of Clinical Neuropsychology: the Official Journal of the National Academy of Neuropsychologists
https://www.readbyqxmd.com/read/28430868/most-visualization-software-for-producing-automated-textbook-style-maps-of-genome-scale-metabolic-networks
#6
James J Kelley, Shay Maor, Min Kyung Kim, Anatoliy Lane, Desmond S Lun
Summary: Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: 1. automation, since GEMs can be quite large; 2. production of understandable maps that provide ease in identification of pathways, reactions, and metabolites; and 3. visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (1), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (2) and comes close to satisfying (3)...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#7
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28430263/energetic-materials-identification-by-laser-induced-breakdown-spectroscopy-combined-with-artificial-neural-network
#8
Amir Hossein Farhadian, Masoud Kavosh Tehrani, Mohammad Hossein Keshavarz, Seyyed Mohammad Reza Darbani
In this study, for the first time to the best of our knowledge, a combination of the laser-induced breakdown spectroscopy (LIBS) technique and artificial neural network (ANN) analysis has been implemented for the identification of energetic materials, including TNT, RDX, black powder, and propellant. Also, aluminum, copper, inconel, and graphite have been used for more accurate investigation and comparison. After the LIBS test and spectrum acquisition on all samples in both air and argon ambient, optimized neural networks were designed by LIBS data...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28429784/sight-and-sound-persistently-out-of-synch-stable-individual-differences-in-audiovisual-synchronisation-revealed-by-implicit-measures-of-lip-voice-integration
#9
Alberta Ipser, Vlera Agolli, Anisa Bajraktari, Fatimah Al-Alawi, Nurfitriani Djaafara, Elliot D Freeman
Are sight and sound out of synch? Signs that they are have been dismissed for over two centuries as an artefact of attentional and response bias, to which traditional subjective methods are prone. To avoid such biases, we measured performance on objective tasks that depend implicitly on achieving good lip-synch. We measured the McGurk effect (in which incongruent lip-voice pairs evoke illusory phonemes), and also identification of degraded speech, while manipulating audiovisual asynchrony. Peak performance was found at an average auditory lag of ~100 ms, but this varied widely between individuals...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429739/a-large-scale-benchmark-of-gene-prioritization-methods
#10
Dimitri Guala, Erik L L Sonnhammer
In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428271/master-transcriptional-regulators-in-cancer-discovery-via-reverse-engineering-approaches-and-subsequent-validation
#11
REVIEW
Bruce Moran, Arman Rahman, Katja Palonen, Fiona T Lanigan, William M Gallagher
Reverse engineering of transcriptional networks using gene expression data enables identification of genes that underpin the development and progression of different cancers. Methods to this end have been available for over a decade and, with a critical mass of transcriptomic data in the oncology arena having been reached, they are ever more applicable. Extensive and complex networks can be distilled into a small set of key master transcriptional regulators (MTR), genes that are very highly connected and have been shown to be involved in processes of known importance in disease...
April 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28428241/heralds-of-parallel-ms-data-independent-acquisition-surpassing-sequential-identification-of-data-dependent-acquisition-in-proteomics
#12
Roland Bruderer, Oliver Martin Bernhardt, Tejas Gandhi, Yue Xuan, Julia Sondermann, Manuela Schmidt, David Gomez-Varela, Lukas Reiter
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the serial limitation of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we quantified over 7,500 proteins of human cell lines and 9,000 proteins of mouse tissues, with fewer than 2...
April 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28427910/stochasticity-of-gene-expression-as-a-motor-of-epigenetics-in-bacteria-from-individual-to-collective-behavior
#13
REVIEW
Stéphanie Bury-Moné, Bianca Sclavi
Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Stochastic gene expression can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by specific genetic network architecture...
April 18, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28427468/learning-from-biomedical-linked-data-to-suggest-valid-pharmacogenes
#14
Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye, Adrien Coulet
BACKGROUND: A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, computational approaches based on the use of background knowledge have been proposed. Until now, only molecular networks or the biomedical literature were used, whereas many other resources are available. METHOD: We propose here to consume a diverse and larger set of resources using linked data related either to genes, drugs or diseases...
April 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28427349/genome-wide-survey-of-mirnas-and-their-evolutionary-history-in-the-ascidian-halocynthia-roretzi
#15
Kai Wang, Christelle Dantec, Patrick Lemaire, Takeshi A Onuma, Hiroki Nishida
BACKGROUND: miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied. RESULTS: We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28427347/comparative-transcriptomics-of-mountain-pine-beetle-pheromone-biosynthetic-tissues-and-functional-analysis-of-cyp6de3
#16
J A Nadeau, J Petereit, R L Tillett, K Jung, M Fotoohi, M MacLean, S Young, K Schlauch, G J Blomquist, C Tittiger
BACKGROUND: The mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) is a highly destructive pest of pine forests in western North America. During flight to a new host tree and initiation of feeding, mountain pine beetles release aggregation pheromones. The biosynthetic pathways of these pheromones are sex-specific and localized in the midgut and fat body, but the enzymes involved have not all been identified or characterized. RESULTS: We used a comparative RNA-Seq analysis between fed and unfed male and female MPB midguts and fat bodies to identify candidate genes involved in pheromone biosynthesis...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28427208/identification-of-differentially-expressed-lncrnas-involved-in-transient-regeneration-of-the-neonatal-c57bl-6j-mouse-heart-by-next-generation-high-throughput-rna-sequencing
#17
Yu-Mei Chen, Hua Li, Yi Fan, Qi-Jun Zhang, Xing Li, Li-Jie Wu, Zi-Jie Chen, Chun Zhu, Ling-Mei Qian
Previous studies have shown that mammalian cardiac tissue has a regenerative capacity. Remarkably, neonatal mice can regenerate their cardiac tissue for up to 6 days after birth, but this capacity is lost by day 7. In this study, we aimed to explore the expression pattern of long noncoding RNA (lncRNA) during this period and examine the mechanisms underlying this process. We found that 685 lncRNAs and 1833 mRNAs were differentially expressed at P1 and P7 by the next-generation high-throughput RNA sequencing...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426795/properties-of-healthcare-teaming-networks-as-a-function-of-network-construction-algorithms
#18
Martin S Zand, Melissa Trayhan, Samir A Farooq, Christopher Fucile, Gourab Ghoshal, Robert J White, Caroline M Quill, Alexander Rosenberg, Hugo Serrano Barbosa, Kristen Bush, Hassan Chafi, Timothy Boudreau
Network models of healthcare systems can be used to examine how providers collaborate, communicate, refer patients to each other, and to map how patients traverse the network of providers. Most healthcare service network models have been constructed from patient claims data, using billing claims to link a patient with a specific provider in time. The data sets can be quite large (106-108 individual claims per year), making standard methods for network construction computationally challenging and thus requiring the use of alternate construction algorithms...
2017: PloS One
https://www.readbyqxmd.com/read/28424653/disentangling-stigma-from-functional-neurological-disorders-conference-report-and-roadmap-for-the-future
#19
Karen S Rommelfanger, Stewart A Factor, Suzette LaRoche, Phyllis Rosen, Raymond Young, Mark H Rapaport
A multidisciplinary expert review of key issues and future directions from the conference "Controversial labels and clinical uncertainties: psychogenic disorders, conversion disorder, and functional symptoms." On October 9 and 10, 2015, a conference entitled "Controversial labels and clinical uncertainties: psychogenic disorders, conversion disorder, and functional symptoms" was held at the Center for Ethics, Emory University, Atlanta, GA, USA. This conference brought together a select group of 30 distinguished thought leaders and practitioners, including ethicists, researchers, clinicians, humanities scholars, and advocates to discuss the unique challenges and controversies related to the diagnosis, treatment, and stigma for patients with what is currently recognized as functional ("psychogenic") neurological disorders...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28424303/distribution-of-genotype-network-sizes-in-sequence-to-structure-genotype-phenotype-maps
#20
Susanna Manrubia, José A Cuesta
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences...
April 2017: Journal of the Royal Society, Interface
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