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https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#1
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28534756/opportunities-for-data-science-in-the-pharmaceutical-industry-the-use-of-data-to-find-efficiencies-in-drug-development-can-t-come-too-soon
#2
Nirmal Keshava
By the numbers, 2016 was not a good year for the U.S. pharmaceutical industry. As of early December, only 19 new drugs had been approved by the Food and Drug Administration (FDA), fewer than half of those approved in 2015 and the lowest number since 2007. Further, the FDA approved only 61% of submissions in 2016, compared to 95% in 2015 [1]. And, among the largest companies, the return on investment for research and development (R&D) fell to 3.7% [2].
May 2017: IEEE Pulse
https://www.readbyqxmd.com/read/28534384/global-knowledge-of-medicine-experiences-from-tuzla-and-banjaluka-bosnia-herzegovina
#3
Rajko Igić
When English became lingua franca, a significant change in the language of scientific publication in Central and Eastern European countries occurred; many journals instead of the local language, and German, French or Russian used English. The shift occurred due to the intention of both the journal editors and contributors to achieve international recognition and inclusion of the journal in prestigious international medical databases. As a consequence, publications in English are cited on average six times more frequently than those in German, Japanese or French...
March 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28534381/evaluation-of-complementary-and-alternative-medicine-trials-registered-in-clinicaltrials-gov-database
#4
Omer Dizdar, Emre Bilgin, Serkan Akin, Saadettin Kilickap, Mutlu Hayran
PURPOSE: Complementary and alternative medicine (CAM) products are increasingly used because they are perceived as natural, relatively low-cost and probably effective therapies for various diseases including cancer. We aimed to determine the quantity and major characteristics of recent herbal/alternative medicine trials registered in clinicaltrials. gov in patients with cancer. METHODS: "Cancer AND (herbal OR complementary OR alternative)" key words were used to query clinicaltrials...
March 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28533120/evaluation-of-new-chemical-entities-as-substrates-of-liver-transporters-in-the-pharmaceutical-industry-response-to-regulatory-requirements-and-future-steps
#5
Noriko Okudaira
This article discusses the evaluation of drug candidates as hepatic transporter substrates. Recently, research on the applications of hepatic transporters in the pharmaceutical industry has improved to meet the requirements of the regulatory guidelines for the evaluation of drug interactions. To identify the risk of transporter-mediated drug-drug interactions (DDIs) at an early stage of drug development, we employed a strategy of reviewing the in vivo animal pharmacokinetics and tissue distribution data obtained in the discovery stage together with the in vitro data obtained for regulatory submission...
May 19, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28530426/poetry-corner
#6
Shayna Fox Lee
This section briefly presents poetry with a psychology theme. This submission was made by The Cummings Center for the History of Psychology's reference archivist Lizette Royer. Two transcribed poems by Knight Dunlap are presented. (PsycINFO Database Record
May 2017: History of Psychology
https://www.readbyqxmd.com/read/28529710/introducing-the-brassica-information-portal-towards-integrating-genotypic-and-phenotypic-brassica-crop-data
#7
Annemarie H Eckes, Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A Irwin, Carlos Horro, John M Hancock, Graham King, Sarah C Dyer, Wiktor Jurkowski
The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data...
2017: F1000Research
https://www.readbyqxmd.com/read/28521838/does-the-use-of-the-informed-healthcare-choices-ihc-primary-school-resources-improve-the-ability-of-grade-5-children-in-uganda-to-assess-the-trustworthiness-of-claims-about-the-effects-of-treatments-protocol-for-a-cluster-randomised-trial
#8
Allen Nsangi, Daniel Semakula, Andrew D Oxman, Matthew Oxman, Sarah Rosenbaum, Astrid Austvoll-Dahlgren, Laetitia Nyirazinyoye, Margaret Kaseje, Iain Chalmers, Atle Fretheim, Nelson K Sewankambo
BACKGROUND: The ability to appraise claims about the benefits and harms of treatments is crucial for informed health care decision-making. This research aims to enable children in East African primary schools (the clusters) to acquire and retain skills that can help them make informed health care choices by improving their ability to obtain, process and understand health information. The trial will evaluate (at the individual participant level) whether specially designed learning resources can teach children some of the key concepts relevant to appraising claims about the benefits and harms of health care interventions (treatments)...
May 18, 2017: Trials
https://www.readbyqxmd.com/read/28521506/new-products
#9
Andreas Mandelis
In order to supplement manufacturers' information, this Department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
March 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28520867/activity-of-ceftolozane-tazobactam-against-surveillance-and-problem-enterobacteriaceae-pseudomonas-aeruginosa-and-non-fermenters-from-the-british-isles
#10
David M Livermore, Shazad Mushtaq, Daniele Meunier, Katie L Hopkins, Robert Hill, Rachael Adkin, Aiysha Chaudhry, Rachel Pike, Peter Staves, Neil Woodford
Background: We assessed the activity of ceftolozane/tazobactam against consecutive isolates collected in the BSAC Bacteraemia Surveillance from 2011 to 2015 and against 'problem' isolates sent to the UK national reference laboratory from July 2015, when routine testing began. Methods: Susceptibility testing was by BSAC agar dilution with resistance mechanisms identified by PCR and interpretive reading. Results: Data were reviewed for 6080 BSAC surveillance isolates and 5473 referred organisms...
May 16, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28515955/effects-of-resistant-dextrin-for-weight-loss-in-overweight-adults-a-systematic-review-with-a-meta-analysis-of-randomized-controlled-trials
#11
Junichi Mukai, Yuta Tsuge, Michiko Yamada, Katsuya Otori, Koichiro Atsuda
BACKGROUND: Randomized controlled trials (RCTs) reported that resistant dextrin (RD) exerted pleiotropic effects on humans. However, limited information is available on the effects of RD for weight loss. We conducted a systematic review with a meta-analysis to summarize the available literature and compare the efficacy of RD for weight loss with that of a placebo in overweight adults. METHODS: We searched the electronic databases MEDLINE, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL), CINAHL, Web of Science, ClincalTrials...
2017: Journal of Pharmaceutical Health Care and Sciences
https://www.readbyqxmd.com/read/28515922/primary-primitive-neuroectodermal-tumor-of-the-cervix-a-report-of-two-cases-and-review-of-the-literature
#12
Xiaofeng Wang, Yan Gao, Yanning Xu, Yixin Liu, Pengpeng Qu
Peripheral primitive neuroectodermal tumor (PNET) of the cervix uteri is extremely rare. Two cases of PNET of the cervix are presented herein. Two female patients, aged 48 and 43 years, presented with irregular uterine bleeding over the course of 1 year, and increased urinary frequency for 1 month, respectively. On gynecological examination, a mass in the cervix was palpated and a biopsy performed. The findings of the initial biopsy revealed small-cell carcinoma in both patients. Following neoadjuvant chemotherapy and radiotherapy, radical hysterectomy was performed in both patients...
May 2017: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28515511/approvals-submission-and-important-labeling-changes-for-us-marketed-pharmaceuticals
#13
(no author information available yet)
This monthly feature will help readers keep current on new drug, new indications, dosage forms and safety-related changes in labeling or use. Efforts have been made to assure the accuracy of this information; however, if there are any questions, please let us know at jgeneral@ku.edu.
April 2017: Hospital Pharmacy
https://www.readbyqxmd.com/read/28515314/the-mzidentml-data-standard-version-1-2-supporting-advances-in-proteome-informatics
#14
Juan Antonio Vizcaíno, Gerhard Mayer, Simon R Perkins, Harald Barsnes, Marc Vaudel, Yasset Perez-Riverol, Tobias Ternent, Julian Uszkoreit, Martin Eisenacher, Lutz Fischer, Juri Rappsilber, Eugen Netz, Mathias Walzer, Oliver Kohlbacher, Alexander Leitner, Robert J Chalkley, Fawaz Ghali, Salvador Martínez-Bartolomé, Eric W Deutsch, Andrew R Jones
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012 - capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (i) scores associated with localization of modifications on peptides; (ii) statistics performed at the level of peptides; (iii) identification of cross-linked peptides; and (iv) support for proteogenomics approaches...
May 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28510355/the-national-landscape-of-living-kidney-donor-follow-up-in-the-united-states
#15
Macey L Henderson, Alvin G Thomas, Ashton Shaffer, Allan B Massie, Xun Luo, Courtenay M Holscher, Tanjala S Purnell, Krista Lentine, Dorry L Segev
In 2013, OPTN/UNOS mandated that transplant centers collect data on living kidney donors (LKDs) at 6-months, 1-year, and 2-years post-donation, with policy-defined thresholds for the proportion of complete living donor follow-up (LDF) data submitted in a timely manner (60 days before or after the expected visit date). While mandated, it was unclear how centers across the country would perform in meeting thresholds, given potential donor and center-level challenges of LDF. To better understand the impact of this policy, we studied SRTR data for 31,615 LKDs between 1/2010-6/2015, comparing proportions of complete and timely LDF form submissions pre- and post-policy implementation...
May 16, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28503844/typeloader-a-fast-and-efficient-automated-workflow-for-the-annotation-and-submission-of-novel-full-length-hla-alleles
#16
V Surendranath, V Albrecht, J D Hayhurst, B Schöne, J Robinson, S G E Marsh, A H Schmidt, V Lange
Recent years have seen a rapid increase in the discovery of novel allelic variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons encoding the peptide binding domains of novel HLA alleles are submitted. As a result, the IPD-IMGT/HLA Database lacks sequence information outside those regions for the majority of known alleles. This has implications for the application of the new sequencing technologies, which deliver sequence data often covering the complete gene. As these technologies simplify the characterization of the complete gene regions, it is desirable for novel alleles to be submitted as full-length sequences to the database...
May 14, 2017: HLA
https://www.readbyqxmd.com/read/28502166/grouping-of-petroleum-substances-as-example-uvcbs-by-ion-mobility-mass-spectrometry-to-enable-chemical-composition-based-read-across
#17
Fabian Alexander Grimm, William K Russell, Yu-Syuan Luo, Yasuhiro Iwata, Weihsueh A Chiu, Tim Roy, Peter J Boogaard, Hans B Ketelslegers, Ivan Rusyn
Substances of Unknown or Variable composition, Complex reaction products, and Biological materials (UVCBs), including many refined petroleum products, present a major challenge in regulatory submissions under the EU Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) and US High Production Volume regulatory regimes. The inherent complexity of these substances, as well as variability in composition obfuscates detailed chemical characterization of each individual substance and their grouping for human and environmental health evaluation through read-across...
May 14, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28495065/the-miniaturized-pediatric-continuous-flow-device-preclinical-assessment-in-the-chronic-sheep-model
#18
Iki Adachi, Sarah Burki, David Horne, Gil G Costas, Taylor Spangler, Robert Jarvik, John Teal, J Timothy Baldwin, Kurt Dasse, M Patricia Massicotte, Jeff Conger, William E Cohn, Charles D Fraser
BACKGROUND: The Infant Jarvik 2015 is an implantable axial-flow ventricular assist device (VAD) that has undergone the major evolutionary design modifications to improve hemocompatibility. This study was conducted in anticipation of data submission to the US Food and Drug Administration to obtain Investigational Device Exemption approval. METHODS: The VAD was implanted via a left thoracotomy in Barbado sheep (n = 10, 26 (19-34] kg). Anticoagulation was maintained with coumadin, with a target international normalized ratio of greater than the individual sheep's baseline values...
March 11, 2017: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/28495032/meat-science-from-1976-a-history-of-the-journal
#19
REVIEW
D A Ledward, D L Hopkins
The journal Meat Science was first published in 1976/77 and it initially comprised 4 issues per year. The first issue contained 4 papers and the first volume (4 issues) contained 27 articles, a mixture of papers and research notes. Its growth/popularity increased, and it has continued to thrive and in 2016 of the 1010 papers processed 292 were accepted. Over 90% of the papers published in the first volume were concerned with muscle biochemistry/meat properties. During the last years of the 20th century, meat products and their properties became a far larger proportion of the submissions as did those concerned with nutrition and safety...
May 3, 2017: Meat Science
https://www.readbyqxmd.com/read/28488256/the-rate-of-publication-of-free-papers-at-the-2008-and-2010-european-society-of-sports-traumatology-knee-surgery-and-arthroscopy-congresses
#20
Jeffrey Kay, Muzammil Memon, Joelle Rogozinsky, Darren de Sa, Nicole Simunovic, Romain Seil, Jon Karlsson, Olufemi Rolland Ayeni
BACKGROUND: The purpose of this study was to evaluate the frequency with which free papers presented at the 2008 and 2010 European Society of Sports Traumatology Knee Surgery and Arthroscopy (ESSKA) congress were ultimately published in peer-reviewed journals. Moreover, this study evaluated whether any correlations exist between the level of evidence of the free papers and their frequency of publication or the impact factor of the journals in which they are published. METHODS: Free papers presented at the 2008 and 2010 ESSKA congresses were included for assessment...
December 2017: Journal of Experimental Orthopaedics
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