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library instruction

Joao Cardoso, Kristian Jensen, Christian Lieven, Anne Sofie Lærke Hansen, Svetlana Galkina, Moritz Emanuel Beber, Emre Özdemir, Markus Herrgard, Henning Redestig, Nikolaus Sonnenschein
Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, for the majority of these methods' implementations are either not published, rely on proprietary software, or do not provide documented interfaces, which has precluded their mainstream adoption in the field. In this work we present cameo, a platform-independent software that enables in silico design of cell factories and targets both experienced modelers as well as users new to the field...
March 20, 2018: ACS Synthetic Biology
Tyler S Klann, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach
Genomic regulatory elements that control gene expression play an important role in many traits and diseases. Identifying the regulatory elements associated with each gene or phenotype and understanding the function of that element remain a significant challenge. To address this technological need, we developed CRISPR/Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. This protocol includes detailed instructions for design and cloning of gRNA libraries, construction of endogenous reporter cell lines via CRISPR/Cas9-mediated knock-in of fluorescent proteins, overall screen design, and recovery of the gRNA library for enrichment analysis...
2018: Methods in Molecular Biology
Hajime Suzuki, Masahiro Kasahara
BACKGROUND: The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long; this situation hampers the use of the full SIMD width of modern processors...
February 19, 2018: BMC Bioinformatics
Seyyed Reza Sadat Ebrahimi, Elgar Enamzadeh, Hossein Babaei
BACKGROUND: Polidocanol is approved for its competence in treatment of varicose veins and spider veins; however, unfortunately, many of its off-label uses are still underappreciated. OBJECTIVE: Lack of an appropriate comprehensive review for off-label uses of this medication troubles physicians about making evidence-based decisions on prescribing it for its various outstanding off-label uses. This article attempts to provide physicians with the latest information concerning successful and unsuccessful use of polidocanol as an alternative treatment for esophageal and gastric varices, tendinopathy and epicondylitis, vascular malformations, varicocele, hydrocele and spermatocele, aneurysmal bone cysts, itching, management of gastrointestinal bleeding, simple renal cysts, reducing the incidence and severity of radio-induced dermatitis, and hemorrhoids...
February 23, 2018: Current Clinical Pharmacology
Swapnil Hiremath, Jeanne Françoise Kayibanda, Benjamin J W Chow, Dean Fergusson, Greg A Knoll, Wael Shabana, Brianna Lahey, Olivia McBride, Alexandra Davis, Ayub Akbari
BACKGROUND: Contrast-induced acute kidney injury (CI-AKI) is defined as worsening of renal function after the administration of iodinated contrast material. In patients with cardiovascular disease, kidney disease, and/or diabetes, renin-angiotensin system blockers, non-steroidal anti-inflammatory drugs, diuretics, and metformin can increase the risk of CI-AKI when undergoing contrast imaging. Despite CI-AKI being the leading iatrogenic cause of acute kidney injury, there is a lack of sufficient scientific evidence supporting which drugs should be stopped, when they should be stopped, and when they should be resumed...
February 21, 2018: Systematic Reviews
Sara Gandini, Domenico Palli, Giuseppe Spadola, Benedetta Bendinelli, Emilia Cocorocchio, Ignazio Stanganelli, Lucia Miligi, Giovanna Masala, Saverio Caini
INTRODUCTION: Several anti-hypertensive drugs have photosensitizing properties, however it remains unclear whether long-term users of these drugs are also at increased risk of skin malignancies. We conducted a literature review and meta-analysis on the association between use of anti-hypertensive drugs and the risk of cutaneous melanoma and non-melanoma skin cancer (NMSC). METHODS: We searched PubMed, EMBASE, Google Scholar and the Cochrane Library, and included observational and experimental epidemiological studies published until February 28th, 2017...
February 2018: Critical Reviews in Oncology/hematology
Jung-Ah Lee, Mona Choi, Sang A Lee, Natalie Jiang
BACKGROUND: Mobile health (mHealth) has continuously been used as a method in behavioral research to improve self-management in patients with chronic diseases. However, the evidence of its effectiveness in chronic disease management in the adult population is still lacking. We conducted a systematic review to examine the effectiveness of mHealth interventions on process measures as well as health outcomes in randomized controlled trials (RCTs) to improve chronic disease management. METHODS: Relevant randomized controlled studies that were published between January 2005 and March 2016 were searched in six databases: PubMed, CINAHL, EMBASE, the Cochrane Library, PsycINFO, and Web of Science...
February 20, 2018: BMC Medical Informatics and Decision Making
Zahra Karimian, Seied Ali Azin, Nasrin Javid, Marzieh Araban, Raziyeh Maasoumi, Shahrokh Aghayan, Effat Merghati Khoie
Background: Professional capacity building (PCB) is the focus point in health-related subjects.The present study was conducted to systematically review the existing sexual health training modules for health care providers. Methods: The following keywords were used to search: training, education, professional capacity, practitioner, sexual health, skill education, module, course, package and curriculum.The term MESH is referred to Medical Subject Headings and the following databases were investigated: MEDLINE, EMBASE, PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), The Cochrane Library and Web of Science, Scopus, Google Scholar, SID,Magiran, and Iranmedex...
2018: Health Promotion Perspectives
Jingcong Zhuang, Xuebin Xing, Di Wang, Zhenxia Du, Jianfeng Wang, Yan Dong, Wenlian Yu, Sajid Hussain Siyal
A non-target analysis was developed for the analysis of extractables from multi-layer coextrusion bags exposed to 4% benzyl alcohol solution and 0.1 M sodium acetate at pH = 5 for defined periods (15 day, 45 day and 90 day) according to manufacturer instructions based on the ultra-performance liquid chromatography (UPLC) quadrupole-time of flight mass spectrometry (Q-TOF MS). In order to confirm the extractables, principal component analysis (PCA) was used to indicate the differences among samples of different periods...
January 19, 2018: Regulatory Toxicology and Pharmacology: RTP
Melissa L Rethlefsen, Mellanye J Lackey, Shirley Zhao
Background: Research into study replication and reporting has led to wide concern about a reproducibility crisis. Reproducibility is coming to the attention of major grant funders, including the National Institutes of Health, which launched new grant application instructions regarding rigor and reproducibility in 2015. Study Purpose: In this case study, the authors present one library's work to help increase awareness of reproducibility and to build capacity for our institution to improve reproducibility of ongoing and future research...
January 2018: Journal of the Medical Library Association: JMLA
Amanda M Nevius, A'Llyn Ettien, Alissa P Link, Laura Y Sobel
Objective: The most recent survey on instruction practices in libraries affiliated with accredited medical institutions in the United States was conducted in 1996. The present study sought to update these data, while expanding to include Canadian libraries. Additional analysis was undertaken to test for statistically significant differences between library instruction in the United States and Canada and between libraries affiliated with highly ranked and unranked institutions. Methods: A twenty-eight-question survey was distributed to libraries affiliated with accredited US and Canadian medical schools to assess what and how often librarians teach, as well as how librarians are involved in the curriculum committee and if they are satisfied with their contact with students and faculty...
January 2018: Journal of the Medical Library Association: JMLA
Jill T Boruff, Pamela Harrison
Objective: This scoping review investigates how knowledge and skills are assessed in the information literacy (IL) instruction for students in physical therapy, occupational therapy, or speech-language pathology, regardless of whether the instruction was given by a librarian. The objectives were to discover what assessment measures were used, determine whether these assessment methods were tested for reliability and validity, and provide librarians with guidance on assessment methods to use in their instruction in evidence-based practice contexts...
January 2018: Journal of the Medical Library Association: JMLA
April J Schweikhard, Toni Hoberecht, Alyssa Peterson, Ken Randall
This study measures how online library instructional tutorials implemented into an evidence-based practice course have impacted the information literacy skills of occupational and physical therapy graduate students. Through a rubric assessment of final course papers, this study compares differences in students' search strategies and cited sources pre- and post-implementation of the tutorials. The population includes 180 randomly selected graduate students from before and after the library tutorials were introduced into the course curriculum...
January 2018: Medical Reference Services Quarterly
Holly Thompson
The National Institutes of Health (NIH) library instruction program provides training services to staff, clinicians, and researchers across NIH and several Department of Health and Human Services (HHS) operating divisions. The audience, training needs, and training topics are diverse and constantly changing. The NIH library has developed several new services and class topics to meet the needs of its NIH and HHS communities. Context, strategies, and future directions for the NIH library instruction program are described...
January 2018: Medical Reference Services Quarterly
Christina Liossi, Alessandro Failo, Daniel E Schoth, Glyn Williams, Richard F Howard
Online educational interventions are increasingly developed for health professionals and students, although graduate and undergraduate medical curricula often contain limited information about how to assess and manage pain. This study reviews the literature on the effectiveness of pain-related online educational resources. Studies were identified through a search of Medline, PsychINFO, Web of Science, CINAHL, PubMed, Scopus, Cochrane Library, Google Scholar, and OpenGrey databases. Search terms included 3 concept blocks: (1) type of intervention-online education, computer-based, e-learning, web-based, and internet-based; (2) population-pediatrician, physician, nurse, psychologist, and medical; and (3) outcome-pain*...
January 9, 2018: Pain
Yu-You Lin, Ming-Ju Hsieh, Jen-Tang Sun, Yi-Chung Chang, Matthew Huei-Ming Ma, Wen-Chu Chiang
AIM: This study aimed to conduct a systematic review and meta-analysis comparing the effect of video-assistance and audio-assistance on quality of dispatcher-instructed cardiopulmonary resuscitation (DI-CPR) for bystanders. METHODS: Five databases were searched, including PubMed, Cochrane library, Embase, Scopus and NIH clinical trial, to find randomized control trials published before June 2017. Qualitative analysis and meta-analysis were undertaken to examine the difference between the quality of video-instructed and audio-instructed dispatcher-instructed bystander CPR...
December 11, 2017: Resuscitation
Gabriel Renaud
Motivation: Research projects involving population genomics routinely need to store genotyping information, population allele counts, combine files from different samples, query the data and export it to various formats. This is often done using bespoke in-house scripts which cannot be easily adapted to new projects and seldom constitute reproducible workflows. Results: We introduce glactools, a set of command-line utilities which can import data from genotypes or population-wide allele counts into an intermediate representation, compute various operations on it and export the data to several file formats used by population genetics software...
November 27, 2017: Bioinformatics
Joanne Marley, Mark A Tully, Alison Porter-Armstrong, Brendan Bunting, John O'Hanlon, Lou Atkins, Sarah Howes, Suzanne M McDonough
BACKGROUND: Individuals with persistent musculoskeletal pain (PMP) have an increased risk of developing co-morbid health conditions and for early-mortality compared to those without pain. Despite irrefutable evidence supporting the role of physical activity in reducing these risks; there has been limited synthesis of the evidence, potentially impacting the optimisation of these forms of interventions. This review examines the effectiveness of interventions in improving levels of physical activity and the components of these interventions...
November 22, 2017: BMC Musculoskeletal Disorders
Philipp N Spahn, Tyler Bath, Ryan J Weiss, Jihoon Kim, Jeffrey D Esko, Nathan E Lewis, Olivier Harismendy
Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service...
November 20, 2017: Scientific Reports
Emmy De Buck, Philippe Vandekerckhove, Karin Hannes
AIM: One of the activities of the Belgian Red Cross is the 'Bridging the Gap' project, in collaboration with local schools. In this project, volunteers join the teaching staff to improve personal development goals in at-risk children with poor performance. The aim of this study was to develop evidence-based guidance for the volunteers to help them choose the right didactical approach for supporting these children. METHOD: Systematic literature searches were performed in three bibliographic databases (the Campbell Library, MEDLINE and ERIC) to find the effectiveness of 16 different didactical activities...
November 14, 2017: International Journal of Evidence-based Healthcare
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