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https://www.readbyqxmd.com/read/28346089/a-chemogenomic-screening-platform-used-to-identify-chemotypes-perturbing-hsp90-pathways
#1
Fiona M Thomas, Kourtney M Goode, Bartek Rajwa, Andrew B Bieberich, Larisa V Avramova, Tony R Hazbun, V Jo Davisson
Compounds that modulate the heat shock protein (HSP) network have potential in a broad range of research applications and diseases. A yeast-based liquid culture assay that measured time-dependent turbidity enabled the high-throughput screening of different Saccharomyces cerevisae strains to identify HSP modulators with unique molecular mechanisms. A focused set of four strains, with differing sensitivities to Hsp90 inhibitors, was used to screen a compound library of 3680 compounds. Computed turbidity curve functions were used to classify strain responses and sensitivity to chemical effects across the compound library...
January 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28344865/identification-of-genetic-determinants-of-breast-cancer-immune-phenotypes-by-integrative-genome-scale-analysis
#2
Wouter Hendrickx, Ines Simeone, Samreen Anjum, Younes Mokrab, François Bertucci, Pascal Finetti, Giuseppe Curigliano, Barbara Seliger, Luigi Cerulo, Sara Tomei, Lucia Gemma Delogu, Cristina Maccalli, Ena Wang, Lance D Miller, Francesco M Marincola, Michele Ceccarelli, Davide Bedognetti
Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expression data from The Cancer Genome Atlas (TCGA). By using RNA-sequencing data from 1,004 breast cancers, we defined distinct immune phenotypes characterized by progressive expression of transcripts previously associated with immune-mediated rejection...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28344853/snap-a-general-purpose-network-analysis-and-graph-mining-library
#3
Jure Leskovec, Rok Sosič
Large networks are becoming a widely used abstraction for studying complex systems in a broad set of disciplines, ranging from social network analysis to molecular biology and neuroscience. Despite an increasing need to analyze and manipulate large networks, only a limited number of tools are available for this task. Here, we describe Stanford Network Analysis Platform (SNAP), a general-purpose, high-performance system that provides easy to use, high-level operations for analysis and manipulation of large networks...
October 2016: ACM Transactions on Intelligent Systems and Technology
https://www.readbyqxmd.com/read/28344190/an-artificial-intelligence-approach-fit-for-trna-gene-studies-in-the-era-of-big-sequence-data
#4
Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura
Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions...
March 24, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28343420/portable-devices-and-mobile-instruments-for-infectious-diseases-point-of-care-testing
#5
Luc Bissonnette, Michel G Bergeron
Rapidity, simplicity, and portability are highly desirable characteristics of tests and devices designed for performing diagnostics at the point of care (POC), either near patients managed in healthcare facilities or to offer bioanalytical alternatives in external settings. By reducing the turnaround time of the diagnostic cycle, POC diagnostics can reduce the dissemination, morbidity, and mortality of infectious diseases and provide tools to control the global threat of antimicrobial resistance. Areas covered: A literature search of PubMed and Google Scholar, and extensive mining of specialized publications, Internet resources, and manufacturers' websites have been used to organize and write this overview of the challenges and requirements associated with the development of portable sample-to-answer diagnostics, and showcase relevant examples of handheld devices, portable instruments, and less mobile systems which may or could be operated at POC...
March 27, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28343024/sex-estimation-with-the-total-area-of-the-proximal-femur-a-densitometric-approach
#6
Francisco Curate, Anabela Albuquerque, Izilda Ferreira, Eugénia Cunha
The estimation of sex is a central step to establish the biological profile of an anonymous skeletal individual. Imaging techniques, including bone densitometry, have been used to evaluate sex in remains incompletely skeletonized. In this paper, we present a technique for sex estimation using the total area (TA) of the proximal femur, a two-dimensional areal measurement determined through densitometry. TA was acquired from a training sample (112 females; 112 males) from the Coimbra Identified Skeletal Collection (University of Coimbra, Portugal)...
March 8, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28342344/water-hardness-determines-226-ra-uptake-in-the-tropical-freshwater-mussel
#7
Che Doering, Andreas Bollhöfer
Chemical data for freshwater mussels (Velesunio spp.) and water from 15 sampling sites in the Alligator Rivers Region and Rum Jungle uranium provinces in tropical Northern Australia were analysed to develop a predictive model of radium-226 ((226)Ra) bioaccumulation for variable water calcium (Ca) and magnesium (Mg) concentrations. Application of the model as a (226)Ra screening approach for freshwater mussels in tropical waterbodies potentially impacted by operational or remediated uranium mine sites is discussed in relation to Mudginberri Billabong, located approximately 12 km downstream of Ranger uranium mine in the Alligator Rivers Region...
March 22, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28341768/public-reactions-to-e-cigarette-regulations-on-twitter-a-text-mining-analysis
#8
Allison J Lazard, Gary B Wilcox, Hannah M Tuttle, Elizabeth M Glowacki, Jessica Pikowski
BACKGROUND: In May 2016, the Food and Drug Administration (FDA) issued a final rule that deemed e-cigarettes to be within their regulatory authority as a tobacco product. News and opinions about the regulation were shared on social media platforms, such as Twitter, which can play an important role in shaping the public's attitudes. We analysed information shared on Twitter for insights into initial public reactions. METHODS: A text mining approach was used to uncover important topics among reactions to the e-cigarette regulations on Twitter...
March 24, 2017: Tobacco Control
https://www.readbyqxmd.com/read/28341660/the-noncoding-rna-linc-adamts5-cooperates-with-rreb1-to-protect-from-intervertebral-disc-degeneration-through-inhibiting-adamts5-expression
#9
Kun Wang, Yu Song, Wei Liu, Xinghuo Wu, Yukun Zhang, Shuai Li, Liang Kang, Ji Tu, Kangcheng Zhao, Wenbin Hua, Cao Yang
Previous studies have indicated the important roles of ADAMTS5 in intervertebral disc degeneration. However, the mechanisms that regulate ADAMTS5 expression in nuclear pulposus (NP) cells remain largely unknown. Evidence suggests that intergenic transcription may be associated with genes that encode transcriptional regulators. Here, we identified a long intergenic noncoding RNA, linc-ADAMTS5, that was transcribed in the opposite direction of ADAMTS5. In this study, through mining computational algorithm programs, and public available data sets, we identified Ras responsive element binding protein 1 (RREB1) as a crucial transcription factor regulating the expression of ADAMTS5 in NP cells...
March 24, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28340480/using-uhplc-q-trap-ms-as-a-complementary-technique-to-in-depth-mine-uplc-q-tof-ms-data-for-identifying-modified-nucleosides-in-urine
#10
Zhiwei Lu, Qing Wang, Meiling Wang, Shuang Fu, Qingqing Zhang, Zhixin Zhang, Huizhen Zhao, Yuehong Liu, Zhenhai Huang, Ziye Xie, Honghong Yu, Xiaoyan Gao
Modified nucleosides, metabolites of RNA, are potential biomarkers of cancer before the appearance of morphological abnormalities. It is of great significance to comprehensively detect and identify nucleosides in human urine for discovery of cancer biomarkers. However, the lower abundance, the greater polarity and the matrix effects make it difficult to detect urinary nucleosides. In this paper, an integrated method consisted of sample preparation followed by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS) detection and primary identification, then ultra-high performance liquid chromatography coupled with hybrid triple quadrupole linear ion trap mass spectrometer (UHPLC Q-Trap/MS) further identification and validation were introduced...
March 12, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28340317/opportunities-for-crash-and-injury-reduction-a-multi-harm-approach-for-crash-data-analysis
#11
Ann Mallory, Allison Kender, Kevin Moorhouse
OBJECTIVE: A multi-harm approach for analyzing crash and injury data was developed for the ultimate purpose of getting a richer picture of motor vehicle crash outcomes identifying research opportunities in crash safety. METHODS: Methods were illustrated using a retrospective analysis of 69,597 occupant cases from NASS CDS (National Automotive Sampling System Crashworthiness Data System) from 2005 to 2015. Occupant cases were analyzed by frequency and severity of outcome: fatality, injury by AIS (Abbreviated Injury Scale), number of cases, attributable fatality, disability, and injury costs...
March 24, 2017: Traffic Injury Prevention
https://www.readbyqxmd.com/read/28338988/phylogenetics-of-lophotrochozoan-bhlh-genes-and-the-evolution-of-lineage-specific-gene-duplicates
#12
Yongbo Bao, Fei Xu, Sebastian M Shimeld
The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix-loop-helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly-studied Phyla. 56 to 88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define...
March 11, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338930/expath-tool-a-system-for-comprehensively-analyzing-regulatory-pathways-and-coexpression-networks-from-high-throughput-transcriptome-data
#13
Han-Qin Zheng, Nai-Yun Wu, Chi-Nga Chow, Kuan-Chieh Tseng, Chia-Hung Chien, Yu-Cheng Hung, Guan-Zhen Li, Wen-Chi Chang
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data...
March 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338202/hoxa10-promotes-nasopharyngeal-carcinoma-cell-proliferation-and-invasion-via-inducing-the-expression-of-zic2
#14
Z-H Shen, K-M Zhao, T Du
OBJECTIVE: In this study, we aimed to explore the dysregulated genes in nasopharyngeal carcinoma (NPC) and to investigate the regulative effect of HOXA10 on ZIC2 expression and their involvement in NPC cell proliferation and invasion. MATERIALS AND METHODS: Microarray data that compared the transcription profile of NPC tissues and normal tissues was searched in GEO datasets and was re-analyzed. The expression of HOXA10 and ZIC2 mRNA were retrieved in TCGA database...
March 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28337565/blood-trace-metals-in-a-sporadic-amyotrophic-lateral-sclerosis-geographical-cluster
#15
Stefano De Benedetti, Giorgio Lucchini, Cristian Del Bò, Valeria Deon, Alessandro Marocchi, Silvana Penco, Christian Lunetta, Elisabetta Gianazza, Francesco Bonomi, Stefania Iametti
Amyotrophic lateral sclerosis (ALS) is a fatal disorder with unknown etiology, in which genetic and environmental factors interplay to determine the onset and the course of the disease. Exposure to toxic metals has been proposed to be involved in the etiology of the disease either through a direct damage or by promoting oxidative stress. In this study we evaluated the concentration of a panel of metals in serum and whole blood of a small group of sporadic patients, all living in a defined geographical area, for which acid mine drainage has been reported...
March 23, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28337450/scalable-data-mining-algorithms-in-computational-biology-and-biomedicine
#16
EDITORIAL
Quan Zou, Dariusz Mrozek, Qin Ma, Yungang Xu
No abstract text is available yet for this article.
2017: BioMed Research International
https://www.readbyqxmd.com/read/28336799/locating-ethics-in-data-science-responsibility-and-accountability-in-global-and-distributed-knowledge-production-systems
#17
Sabina Leonelli
The distributed and global nature of data science creates challenges for evaluating the quality, import and potential impact of the data and knowledge claims being produced. This has significant consequences for the management and oversight of responsibilities and accountabilities in data science. In particular, it makes it difficult to determine who is responsible for what output, and how such responsibilities relate to each other; what 'participation' means and which accountabilities it involves, with regard to data ownership, donation and sharing as well as data analysis, re-use and authorship; and whether the trust placed on automated tools for data mining and interpretation is warranted (especially as data processing strategies and tools are often developed separately from the situations of data use where ethical concerns typically emerge)...
December 28, 2016: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28334950/downstream-targets-of-gwas-detected-genes-for-breast-lung-and-prostate-and-colon-cancer-converge-to-g1-s-transition-pathway
#18
Olga Y Gorlova, Eugene I Demidenko, Christopher I Amos, Ivan P Gorlov
Genome-wide association studies (GWASs) identified over 500 single nucleotide polymorphisms (SNPs) influencing cancer risk. It is logical to expect the cancer-associated genes to cluster in pathways directly involved in carcinogenesis, e.g. cell cycle. Nevertheless, analyses of the GWAS-detected cancer risk genes usually show no or weak enrichment by known cancer genes.We hypothesized that GWAS-detected cancer risk-associated genes function as upstream regulators of the genes directly involved in carcinogenesis...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334453/not-in-my-backyard-ccs-sites-and-public-perception-of-ccs
#19
Carola Braun
Carbon capture and storage (CCS) is a technology that counteracts climate change by capturing atmospheric emissions of CO2 from human activities, storing them in geological formations underground. However, CCS also involves major risks and side effects, and faces strong public opposition. The whereabouts of 408 potential CCS sites in Germany were released in 2011. Using detailed survey data on the public perception of CCS, this study quantifies how living close to a potential storage site affects the acceptance of CCS...
March 23, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/28334283/the-microbiology-of-oil-sands-tailings-past-present-future
#20
Julia M Foght, Lisa M Gieg, Tariq Siddique
Surface mining of enormous oil sands deposits in northeastern Alberta, Canada since 1967 has contributed greatly to Canada's economy but has also received negative international attention due largely to environmental concerns and challenges. Not only have microbes profoundly affected the composition and behaviour of this petroleum resource over geological time, they currently influence the management of semi-solid tailings in oil sands tailing ponds (OSTP) and tailings reclamation. Historically, microbial impacts on OSTP were generally discounted but next-generation sequencing and biogeochemical studies have revealed unexpectedly diverse indigenous communities and expanded our fundamental understanding of anaerobic microbial functions...
March 9, 2017: FEMS Microbiology Ecology
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