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https://www.readbyqxmd.com/read/27905872/knockdown-of-ggct-inhibits-cell-proliferation-and-induces-late-apoptosis-in-human-gastric-cancer
#1
Wenjie Zhang, Lei Chen, Honggang Xiang, Chunhua Hu, Weibin Shi, Ping Dong, Wenjie Lv
BACKGROUND: Gamma glutamylcyclotransferase (GGCT) has been proved to be involved in various cancers, but the biological function of GGCT in gastric cancer is still largely unknown. METHODS: The expression level of GGCT was evaluated by informatics analyses based on the Oncomine database. GGCT gene was then effectively knocked down via lentivirus mediated short hairpin RNA (shRNA) system. Then a series of functional assays, including MTT, colony formation and flow cytometry analysis were conducted on gastric cancer cells following GGCT knockdown...
December 1, 2016: BMC Biochemistry
https://www.readbyqxmd.com/read/27903644/a-reference-data-set-of-5-4-million-phased-human-variants-validated-by-genetic-inheritance-from-sequencing-a-three-generation-17-member-pedigree
#2
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern, Semyon Kruglyak, Elliott H Margulies, Gil McVean, David R Bentley
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27900588/modeling-informatics-at-vertex-pharmaceuticals-incorporated-our-philosophy-for-sustained-impact
#3
Georgia McGaughey, W Patrick Walters
Molecular modelers and informaticians have the unique opportunity to integrate cross-functional data using a myriad of tools, methods and visuals to generate information. Using their drug discovery expertise, information is transformed to knowledge that impacts drug discovery. These insights are often times formulated locally and then applied more broadly, which influence the discovery of new medicines. This is particularly true in an organization where the members are exposed to projects throughout an organization, such as in the case of the global Modeling & Informatics group at Vertex Pharmaceuticals...
November 29, 2016: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/27899677/the-mouse-gene-expression-database-gxd-2017-update
#4
Jacqueline H Finger, Constance M Smith, Terry F Hayamizu, Ingeborg J McCright, Jingxia Xu, Meiyee Law, David R Shaw, Richard M Baldarelli, Jon S Beal, Olin Blodgett, Jeff W Campbell, Lori E Corbani, Jill R Lewis, Kim L Forthofer, Pete J Frost, Sharon C Giannatto, Lucie N Hutchins, Dave B Miers, Howie Motenko, Kevin R Stone, Janan T Eppig, James A Kadin, Joel E Richardson, Martin Ringwald
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#5
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899570/mouse-genome-database-mgd-2017-community-knowledge-resource-for-the-laboratory-mouse
#6
Judith A Blake, Janan T Eppig, James A Kadin, Joel E Richardson, Cynthia L Smith, Carol J Bult
The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and efficient use of MGD in the advancement of scientific knowledge...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899244/editorial-overview-carbohydrate-protein-interactions-and-glycosylation-integrating-structural-biology-informatics-and-systems-modelling-to-understand-glycan-structure-and-glycan-protein-interactions
#7
EDITORIAL
Harry J Gilbert, Nagasuma Chandra
No abstract text is available yet for this article.
November 26, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27898037/analyses-of-evolutionary-characteristics-of-the-hemagglutinin-esterase-gene-of-influenza-c-virus-during-a-period-of-68-years-reveals-evolutionary-patterns-different-from-influenza-a-and-b-viruses
#8
Yuki Furuse, Yoko Matsuzaki, Hidekazu Nishimura, Hitoshi Oshitani
Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses...
November 26, 2016: Viruses
https://www.readbyqxmd.com/read/27896988/precision-medicine-data-and-discovery-for-improved-health-and-therapy
#9
Alexander A Morgan, Dana C Crawford, Josh C Denny, Sean D Mooney, Bruce J Aronow, Steven E Brenner
The major goal of precision medicine is to improve human health. A feature that unites much research in the field is the use of large datasets such as genomic data and electronic health records. Research in this field includes examination of variation in the core bases of DNA and their methylation status, through variations in metabolic and signaling molecules, all the way up to broader systems level changes in physiology and disease presentation. Intermediate goals include understanding the individual drivers of disease that differentiate the cause of disease in each individual...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896745/molecular-similarity-concepts-for-informatics-applications
#10
Jürgen Bajorath
The assessment of small molecule similarity is a central task in chemoinformatics and medicinal chemistry. A variety of molecular representations and metrics are applied to computationally evaluate and quantify molecular similarity. A critically important aspect of molecular similarity analysis in chemoinformatics and pharmaceutical research is that one is typically not interested in quantifying the degree of structural or chemical similarity between compounds per se, but rather in extrapolating from molecular similarity to property similarity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895956/steps-in-moving-evidence-based-health-informatics-from-theory-to-practice
#11
REVIEW
Michael Rigby, Farah Magrabi, Philip Scott, Persephone Doupi, Hannele Hypponen, Elske Ammenwerth
OBJECTIVES: To demonstrate and promote the importance of applying a scientific process to health IT design and implementation, and of basing this on research principles and techniques. METHODS: A review by international experts linked to the IMIA Working Group on Technology Assessment and Quality Development. RESULTS: Four approaches are presented, linking to the creation of national professional expectations, adherence to research-based standards, quality assurance approaches to ensure safety, and scientific measurement of impact...
October 2016: Healthcare Informatics Research
https://www.readbyqxmd.com/read/27893907/patterns-and-perceptions-of-asynchronous-video-discussion-in-a-graduate-health-sciences-course
#12
Mollie Cummins, Naresh Sundar Rajan, Chad Hodge, Ramkiran Gouripeddi
BACKGROUND: Studies of graduate online education indicate a need for increased interaction among students and faculty. However, it can be challenging to foster a high level of scholarly interaction and engagement in fully online courses. The objective of this study was to evaluate student perceptions and participation patterns related to online, asynchronous video discussion in a graduate health sciences course. METHOD: An asynchronous video discussion was piloted in a 2014 interprofessional informatics course and students were subsequently surveyed to determine their perceptions of this approach...
December 1, 2016: Journal of Nursing Education
https://www.readbyqxmd.com/read/27893502/implementing-a-4c-approach-to-quality-improvement
#13
Michelle McGonigal
Designing a quality improvement activity can be labor intensive and intimidating to facilitators who have not been specially trained in process improvement methodologies. To simplify the process, a team was formed with the specific task of developing a basic model that addresses key concepts in change theory. The 2010 Institute of Medicine report stresses the importance of health care professionals working together, collaboratively, to use data to improve patient outcomes and improve care nationally. In addition, as noted in Quality and Safety Education for Nurses (2013), competencies have been developed to promote frontline problem solving including using data for quality improvement, providing safe care, functioning in collaborative teams, respecting and addressing patient and family concerns, applying evidence-based practice, and using informatics to make decisions...
January 2017: Critical Care Nursing Quarterly
https://www.readbyqxmd.com/read/27891528/preparing-nursing-home-data-from-multiple-sites-for-clinical-research-a-case-study-using-observational-health-data-sciences-and-informatics
#14
Richard D Boyce, Steven M Handler, Jordan F Karp, Subashan Perera, Charles F Reynolds
INTRODUCTION: A potential barrier to nursing home research is the limited availability of research quality data in electronic form. We describe a case study of converting electronic health data from five skilled nursing facilities to a research quality longitudinal dataset by means of open-source tools produced by the Observational Health Data Sciences and Informatics (OHDSI) collaborative. METHODS: The Long-Term Care Minimum Data Set (MDS), drug dispensing, and fall incident data from five SNFs were extracted, translated, and loaded into version 4 of the OHDSI common data model...
2016: EGEMS
https://www.readbyqxmd.com/read/27891247/librarians-and-scientists-partner-to-address-data-management-taking-collaboration-to-the-next-level
#15
Andrea Medina-Smith, Kimberly A Tryka, Barbara P Silcox, Robert J Hanisch
PURPOSE: This study looks at the changing way in which the Information Services Office (ISO) at the National Institute of Standards and Technology (NIST) provides services to NIST scientific and technical staff throughout their research and publishing cycles. These services include the more traditional services of a research library as well as publishing NIST technical reports and The Journal of Research of NIST, and preserving and exhibiting scientific instruments and other artifacts...
2016: Digit Libr Perspect
https://www.readbyqxmd.com/read/27888947/an-asynchronous-online-collaboration-between-radiologists-and-patients-harnessing-the-power-of-informatics-to-design-the-ideal-patient-portal
#16
Tessa S Cook, Arun Krishnaraj, Marc H Willis, Christine Abbott, James V Rawson
No abstract text is available yet for this article.
December 2016: Journal of the American College of Radiology: JACR
https://www.readbyqxmd.com/read/27885364/bidirectional-rnn-for-medical-event-detection-in-electronic-health-records
#17
Abhyuday N Jagannatha, Hong Yu
Sequence labeling for extraction of medical events and their attributes from unstructured text in Electronic Health Record (EHR) notes is a key step towards semantic understanding of EHRs. It has important applications in health informatics including pharmacovigilance and drug surveillance. The state of the art supervised machine learning models in this domain are based on Conditional Random Fields (CRFs) with features calculated from fixed context windows. In this application, we explored recurrent neural network frameworks and show that they significantly out-performed the CRF models...
June 2016: Proceedings of the Conference
https://www.readbyqxmd.com/read/27885254/aldehyde-dehydrogenase-is-used-by-cancer-cells-for-energy-metabolism
#18
Joon Hee Kang, Seon-Hyeong Lee, Dongwan Hong, Jae-Seon Lee, Hee-Sung Ahn, Ju-Hyun Ahn, Tae Wha Seong, Chang-Hun Lee, Hyonchol Jang, Kyeong Man Hong, Cheolju Lee, Jae-Ho Lee, Soo-Youl Kim
We found that non-small-cell lung cancer (NSCLC) cells express high levels of multiple aldehyde dehydrogenase (ALDH) isoforms via an informatics analysis of metabolic enzymes in NSCLC and immunohistochemical staining of NSCLC clinical tumor samples. Using a multiple reaction-monitoring mass spectrometry analysis, we found that multiple ALDH isozymes were generally abundant in NSCLC cells compared with their levels in normal IMR-90 human lung cells. As a result of the catalytic reaction mediated by ALDH, NADH is produced as a by-product from the conversion of aldehyde to carboxylic acid...
November 25, 2016: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/27881428/genome-transcriptome-and-proteome-the-rise-of-omics-data-and-their-integration-in-biomedical-sciences
#19
Claudia Manzoni, Demis A Kia, Jana Vandrovcova, John Hardy, Nicholas W Wood, Patrick A Lewis, Raffaele Ferrari
Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine...
November 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27880896/rnf166-determines-recruitment-of-adaptor-proteins-during-antibacterial-autophagy
#20
Robert J Heath, Gautam Goel, Leigh A Baxt, Jason S Rush, Vishnu Mohanan, Geraldine L C Paulus, Vijay Jani, Kara G Lassen, Ramnik J Xavier
Xenophagy is a form of selective autophagy that involves the targeting and elimination of intracellular pathogens through several recognition, recruitment, and ubiquitination events. E3 ubiquitin ligases control substrate selectivity in the ubiquitination cascade; however, systematic approaches to map the role of E3 ligases in antibacterial autophagy have been lacking. We screened more than 600 putative human E3 ligases, identifying E3 ligases that are required for adaptor protein recruitment and LC3-bacteria colocalization, critical steps in antibacterial autophagy...
November 22, 2016: Cell Reports
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