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Igor Mandric, Sergey Knyazev, Alex Zelikovsky
Summary: Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome, and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location...
March 14, 2018: Bioinformatics
Bin Hua, John Yang, Fengjing Liu, Guocheng Zhu, Baolin Deng, Jingdong Mao
Characterization of dissolved organic matter/nitrogen (DOM/DON) is critical in water quality assessment and nutrient management in watershed or ecosystem. This study was to investigate the link between DOM/DON and its source using fluorescence excitation-emission matrix (EEM) spectroscopy coupled with parallel factor analysis (PARAFAC). Water samples were collected from various aquatic systems in a watershed located in central Missouri, including rural watershed with various land use and land cover (LULC), landfill, and constructed wetland...
March 6, 2018: Chemosphere
Rebekah Carter, Yenna Salamonson, Lucie M Ramjan, Elizabeth Halcomb
BACKGROUND: Timely and meaningful feedback is essential to promote active learning and student engagement with learning. However, achieving this remains elusive, particularly in undergraduate nursing programs that admit large student cohorts. One strategy to provide meaningful en masse feedback is to provide feed-forward support by using exemplars. To date, there has been limited evaluation of the effectiveness of this feedback strategy. OBJECTIVE: To review the impact of using exemplars as a feedback strategy to support student academic writing in higher education...
March 3, 2018: Nurse Education Today
Annet Wijnen, Sjoukje E Bouma, Gesine H Seeber, Lucas H V van der Woude, Sjoerd K Bulstra, Djordje Lazovic, Martin Stevens, Inge van den Akker-Scheek
OBJECTIVE: To assess the therapeutic validity and effectiveness of physiotherapeutic exercise interventions following total hip arthroplasty (THA) for osteoarthritis. DATA SOURCES: The databases Embase, MEDLINE, Cochrane Library, CINAHL and AMED were searched from inception up to February 2017. ELIGIBILITY CRITERIA: Articles reporting results of randomized controlled trials in which physiotherapeutic exercise was compared with usual care or with a different type of physiotherapeutic exercise were included, with the applied interventions starting within six months after THA...
2018: PloS One
Jian Zhang
Transfer entropy from non-uniform embedding is a popular tool for the inference of causal relationships among dynamical subsystems. In this study we present an approach that makes use of low-dimensional conditional mutual information quantities to decompose the original high-dimensional conditional mutual information in the searching procedure of non-uniform embedding for significant variables at different lags. We perform a series of simulation experiments to assess the sensitivity and specificity of our proposed method to demonstrate its advantage compared to previous algorithms...
2018: PloS One
Andrew McDowell, Neeraj Raizada, Sunil D Khaparde, Raghuram Rao, Sanjay Sarin, Aakshi Kalra, Virender Singh Salhotra, Sreenivas Achuthan Nair, Catharina Boehme, Claudia M Denkinger
BACKGROUND: Diagnosing tuberculosis (TB) in children presents considerable challenges. Upfront testing on Xpert® MTB/RIF ('Xpert')-a rapid molecular assay with high sensitivity and specificity-for pediatric presumptive TB patients, as recommended by India's Revised National Tuberculosis Control Program (RNTCP), can pave the way for early TB diagnosis. As part of an ongoing project implemented by Foundation for Innovative New Diagnostics (FIND) dedicated to providing upfront free-of-cost (FOC) Xpert testing to children seeking care in the public and private sectors, a qualitative assessment was designed to understand how national guidelines on TB diagnosis and Xpert technology have been integrated into the pediatric TB care practices of different health providers...
2018: PloS One
Davina Gale, Andrew R J Lawson, Karen Howarth, Mikidache Madi, Bradley Durham, Sarah Smalley, John Calaway, Shannon Blais, Greg Jones, James Clark, Peter Dimitrov, Michelle Pugh, Samuel Woodhouse, Michael Epstein, Ana Fernandez-Gonzalez, Alexandra S Whale, Jim F Huggett, Carole A Foy, Gerwyn M Jones, Hadas Raveh-Amit, Karin Schmitt, Alison Devonshire, Emma Green, Tim Forshew, Vincent Plagnol, Nitzan Rosenfeld
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes...
2018: PloS One
Emily K Compton, Karen Gildemeyer, Tina M Mason, Susan R Hartranft, Steven K Sutton
BACKGROUND: Duffy's Quality-Caring Model guides nursing practice at the H. Lee Moffitt Cancer Center and Research Institute in Tampa, FL. No published studies using this model in oncology were found. OBJECTIVES: The purpose of this article is to determine patients' perceptions of nurse caring behaviors at the time of discharge after surgery. METHODS: A descriptive correlational design was used. Data were collected using Duffy's Caring Assessment Tool (CAT)...
April 1, 2018: Clinical Journal of Oncology Nursing
George Kunnackal John, Lin Wang, Julie Nanavati, Claire Twose, Rajdeep Singh, Gerard Mullin
Dietary alteration of the gut microbiome is an important target in the treatment of obesity. Animal and human studies have shown bidirectional weight modulation based on the probiotic formulation used. In this study, we systematically reviewed the literature and performed a meta-analysis to assess the impact of prebiotics, probiotics and synbiotics on body weight, body mass index (BMI) and fat mass in adult human subjects. We searched Medline (PubMed), Embase, the Cochrane Library and the Web of Science to identify 4721 articles, of which 41 were subjected to full-text screening, yielding 21 included studies with 33 study arms...
March 16, 2018: Genes
William Martinez, James W Pichert, Gerald B Hickson, Casey H Braddy, Amy J Brown, Thomas F Catron, Ilene N Moore, Morgan R Stampfle, Lynn E Webb, William O Cooper
OBJECTIVES: The aims of the study were to develop a valid and reliable taxonomy of coworker reports of alleged unprofessional behavior by physicians and advanced practice professionals and determine the prevalence of reports describing particular types of unprofessional conduct. METHODS: We conducted qualitative content analysis of coworker reports of alleged unprofessional behavior by physicians and advanced practice professionals to create a standardized taxonomy...
March 15, 2018: Journal of Patient Safety
Lucia Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trenor, Ferran Sanz, Manuel Pastor, Javier Saiz
Drug-induced proarrhythmicity is a major concern for regulators and pharmaceutical companies. For novel drug candidates, the standard assessment involves the evaluation of the potassium hERG channels block and the in vivo prolongation of the QT interval. However, this method is known to be too restrictive and to stop the development of potentially valuable therapeutic drugs. The aim of this work is to create an in silico tool for early detection of drug-induced proarrhythmic risk. The system is based on simulations of how different compounds affect the action potential duration (APD) of isolated endocardial, midmyocardial, and epicardial cells as well as the QT prolongation in a virtual tissue...
March 16, 2018: Journal of Chemical Information and Modeling
Joseph P Herbert, Sidish S Venkataraman, Ali H Turkmani, Liang Zhu, Marcia L Kerr, Rajan P Patel, Irma T Ugalde, Stephen A Fletcher, David I Sandberg, Charles S Cox, Ryan S Kitagawa, Arthur L Day, Manish N Shah
OBJECTIVE The objective of this study was to assess the incidence, diagnosis, and treatment of pediatric blunt cerebrovascular injury (BCVI) at a busy Level 1 trauma center and to develop a tool for accurately predicting pediatric BCVI and the need for diagnostic testing. METHODS This is a retrospective cohort study of a prospectively collected database of pediatric patients who had sustained blunt trauma (patient age range 0-15 years) and were treated at a Level 1 trauma center between 2005 and 2015. Digital subtraction angiography, MR angiography, or CT angiography was used to confirm BCVI...
March 16, 2018: Journal of Neurosurgery. Pediatrics
Jocelyne C Whitehead, Lingqian Li, Douglas A McQuiggan, Sara A Gambino, Malcolm A Binns, Jennifer D Ryan
INTRODUCTION: Preferential viewing of novel stimuli in the Visual Paired Comparison task has provided a useful marker of memory and medial temporal lobe function. We created a portable version of the VPC (P-VPC) and contrasted P-VPC metrics against the Montreal Cognitive Assessment (MoCA) in healthy adults, to assess the validity and reliability of the P-VPC as an indicator of memory function across age. A supplementary case series was conducted with individuals diagnosed with Alzheimer's disease (AD) and other dementias, to provide a preliminary illustration of the P-VPC's use as a measure in clinical populations...
March 16, 2018: Journal of Clinical and Experimental Neuropsychology
Michael Schriver, Vincent Kalumire Cubaka, Peter Vedsted, Innocent Besigye, Per Kallestrup
BACKGROUND: External supervision of primary health care facilities to monitor and improve services is common in low-income countries. Currently there are no tools to measure the quality of support in external supervision in these countries. AIM: To develop a provider-reported instrument to assess the support delivered through external supervision in Rwanda and other countries. METHODS: "External supervision: Provider Evaluation of Supervisor Support" (ExPRESS) was developed in 18 steps, primarily in Rwanda...
2018: Global Health Action
Alberto Pilotto, Simone Dini, Nicola Veronese, Julia Daragjati, Manuela Miolo, Monica M Mion, Andrea Fontana, Mario Lo Storto, Martina Zaninotto, Giada Bragato, Alberto Cella, Paolo Carraro, Filomena Addante, Massimiliano Copetti, Mario Plebani
BACKGROUND: To evaluate the prognostic accuracy of pro-ADM (adrenomedullin) in comparison with and in addition to the Multidimensional Prognostic Index (MPI), a validated predictive tool for mortality derived from a Comprehensive Geriatric Assessment (CGA), to predict one-month mortality risk in older patients hospitalized with community-acquired pneumonia (CAP). METHODS: All patients aged 65 years and older, consecutively admitted to an acute geriatric ward with a diagnosis of CAP from February to July 2012...
March 15, 2018: Panminerva Medica
Toru Imai, Junhui Shi, Terence T W Wong, Lei Li, Liren Zhu, Lihong V Wang
Ultraviolet photoacoustic microscopy (UV-PAM) is a promising intraoperative tool for surgical margin assessment (SMA), one that can provide label-free histology-like images with high resolution. In this study, using a microlens array and a one-dimensional (1-D) array ultrasonic transducer, we developed a high-throughput multifocal UV-PAM (MF-UV-PAM). Our new system achieved a 1.6  ±  0.2  μm lateral resolution and produced images 40 times faster than the previously developed point-by-point scanning UV-PAM...
March 2018: Journal of Biomedical Optics
Laura Fangmann, Steffen Teller, Pavel Stupakov, Helmut Friess, Güralp O Ceyhan, Ihsan Ekin Demir
In pancreatic cancer, neural invasion is one of the most common paths of cancer dissemination. Classically, cancer cells actively invade nerves and cause local recurrence and pain. Three-dimensional (3D) neural migration assay has become a standard tool for scientists to study neural invasion by confronting the involved cell types. This protocol introduces Schwann cells, i.e., the most prevalent cell type in peripheral nerves, in a novel heterotypic, glia-cancer-neuron, 3D migration assay for assessing their relevance in the early pathogenesis of neural invasion...
2018: Methods in Molecular Biology
Tim Michael Feenstra, Chris Dickhoff, Jaap Deunk
PURPOSE: Tube thoracostomy is frequently used in thoracic trauma patients. However, there is no consensus on whether low pressure suction or water seal is the optimal method of tube management. Against this background, we performed a systematic review of studies comparing suction and water seal management of chest tubes placed for traumatic chest injuries in adults. Evaluated outcomes are duration of chest tube treatment, length of stay in hospital, incidence of persistent air leak, clotted hemothorax, and the need for (re-)interventions...
March 15, 2018: European Journal of Trauma and Emergency Surgery: Official Publication of the European Trauma Society
Patrick Ip, Winnie Tso, Nirmala Rao, Frederick Ka Wing Ho, Ko Ling Chan, King Wa Fu, Sophia Ling Li, Winnie Goh, Wilfred Hing-Sang Wong, Chun Bong Chow
BACKGROUND: Proper parent-child interaction is crucial for child development, but an assessment tool in Chinese is currently lacking. This study aimed to develop and validate a parent-reported parent-child interaction scale for Chinese preschool children. METHODS: The Chinese parent-child interaction scale (CPCIS) was designed by an expert panel based on the literature and clinical observations in the Chinese context. The initial CPCIS had 14 parent-child interactive activity items...
March 15, 2018: World Journal of Pediatrics: WJP
Shadi Saleh, Mohamad Alameddine, Angie Farah, Nour El Arnaout, Hani Dimassi, Carles Muntaner, Christo El Morr
OBJECTIVES: Assess the effect of selected low-cost eHealth tools on diabetes/hypertension detection and referrals rates in rural settings and refugee camps in Lebanon and explore the barriers to showing-up to scheduled appointments at Primary Healthcare Centers (PHC). METHODS: Community-based screening for diabetes and hypertension was conducted in five rural and three refugee camp PHCs using an eHealth netbook application. Remote referrals were generated based on pre-set criteria...
March 15, 2018: International Journal of Public Health
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