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Slava Ilnytskyy, Andriy Bilichak
Next-generation sequencing became a method of choice for the investigation of small RNA transcriptomes in plants and animals. Although a technical side of sequencing itself is becoming routine, and experimental costs are affordable, data analysis still remains a challenge, especially for researchers with limited computational experience. Here, we present a detailed description of a computational workflow designed to take raw sequencing reads as input, to obtain small RNA predictions, and to detect the differentially expressed microRNAs as a result...
2017: Methods in Molecular Biology
B Verillaud, L Robard, J Michel, V Pruliere Escabasse, E Béquignon, L Crampette, O Malard
OBJECTIVES: The authors present the guidelines of the French Oto-Rhino-Laryngology - Head and Neck Surgery Society (Société Française d'Oto-Rhino-Laryngologie et de Chirurgie de la Face et du Cou: SFORL) on second-line treatment of epistaxis in adults, after failure of anterior and/or anterior-posterior nasal packing. METHODS: A multidisciplinary work group was entrusted with a review of the scientific literature on the above topic. Guidelines were drawn up, based on the articles retrieved and the group members' individual experience...
October 17, 2016: European Annals of Otorhinolaryngology, Head and Neck Diseases
David John Webb
Treatment-resistant hypertension (TRH) is defined as the failure to achieve an office BP target of <140/90 mmHg (<130/80 mmHg in patients with chronic kidney disease (CKD) or diabetes) in patients with hypertension (HT), despite adherence to at least 3 antihypertensive medications at optimal tolerated doses, ideally including a diuretic (Calhoun et al., Circulation 2008). TRH identifies patients with hard-to-treat HT, who might benefit from specialist investigation and treatment. Although some studies put the prevalence of TRH as >10%, these levels may be inflated by white-coat hypertension and poor adherence...
September 2016: Journal of Hypertension
Alice Willison, Vicki Tully, Peter Davey
The urine albumin creatinine ratio (UACR) detects abnormal levels of protein in the urine and should be performed annually to detect kidney disease in patients with diabetes mellitus. UK national audits show that 25% of patients do not have annual tests and our data suggested that some patients had more than one test per year. Data from 20 patients showed that 55% had more than one UACR test per year, with a total of 19 unnecessary tests at an estimated cost of £20,000 per year. However 20% had not had a UACR in the previous year, so unreliable testing was potentially causing harm as well as waste...
2016: BMJ Quality Improvement Reports
Jang-Il Sohn, Jin-Wu Nam
As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity...
October 14, 2016: Briefings in Bioinformatics
L Badet, X Matillon, R Codas, J Branchereau, G Karam, M-O Timsit, R Thuret, F Kleinclauss
OBJECTIVES: To perform a State of The Art about the different aspects of pancreas transplantation such as indications, technical features, immunosuppressive strategies and outcomes of simultaneous pancreas-kidney transplantation. MATERIAL AND METHODS: An exhaustive systematic review of the scientific literature was performed in the Medline database ( and Embase ( using different associations of the following keywords (MESH) : « pancreas transplantation; kidney transplantation; simultaneous pancreas-kidney transplantation; immunosuppression »...
October 6, 2016: Progrès en Urologie
Sierra Iwanicki, Catherine Peterson
The extant literature reveals a considerable amount of research examining course work or technical training in psychological assessment, but a dearth of empirical research on assessment supervision. This study examined perspectives on current assessment supervisory practices in professional psychology through an online survey. Descriptive and qualitative data were collected from 125 survey respondents who were members of assessment-focused professional organizations and who had at least 1 year of supervision experience...
October 7, 2016: Journal of Personality Assessment
Christian Rinke, Serene Low, Ben J Woodcroft, Jean-Baptiste Raina, Adam Skarshewski, Xuyen H Le, Margaret K Butler, Roman Stocker, Justin Seymour, Gene W Tyson, Philip Hugenholtz
High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA...
2016: PeerJ
Georgia Kapatai, Carmen L Sheppard, Ali Al-Shahib, David J Litt, Anthony P Underwood, Timothy G Harrison, Norman K Fry
Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective...
2016: PeerJ
Marta Penna, Mark Whiteford, Roel Hompes, Patricia Sylla
AIM: Transanal Total Mesorectal Excision (taTME) has become one of the most promising technical advancement in the surgical treatment of rectal cancer, with rising numbers of surgeons seeking training. We describe our experience with human cadaveric courses for taTME delivered in two countries. METHOD: Four fresh human cadaveric workshops conducted in Oxford, UK in 2015 and two in Chicago, USA in 2013-2014, trained a total of 52 surgeons. Parameters of operative performance for each delegate were recorded...
September 19, 2016: Colorectal Disease: the Official Journal of the Association of Coloproctology of Great Britain and Ireland
David John Webb
Treatment-resistant hypertension (TRH) is defined as the failure to achieve an office BP target of <140/90 mmHg (<130/80 mmHg in patients with chronic kidney disease (CKD) or diabetes) in patients with hypertension (HT), despite adherence to at least 3 antihypertensive medications at optimal tolerated doses, ideally including a diuretic (Calhoun et al., Circulation 2008). TRH identifies patients with hard-to-treat HT, who might benefit from specialist investigation and treatment. Although some studies put the prevalence of TRH as >10%, these levels may be inflated by white-coat hypertension and poor adherence...
September 2016: Journal of Hypertension
J Hubertus, W Piehlmeier, M Heinrich
BACKGROUND: The Critical Incident Reporting System (CIRS) is a tool for employees to report anonymously of near misses. Its efficiency and improvement of safety is proved by many studies. Our department introduced CIRS in 2009 and it is used frequently. As the number of reports decreased over time we asked for factors responsible for the reduced use. METHODS: All employees had access to CIRS and have been trained in several courses of instruction. Accomplished results and consequences were published in biannual newsletters...
September 2016: Klinische Pädiatrie
T H Swartz, M L McGilliard, C S Petersson-Wolfe
Calf behaviors such as step activity, lying bouts, and lying time may be an indicator of calf health and welfare. To reduce time-consuming visual observations, the use of behavioral monitoring systems have been developed to capture these data. Previous studies have validated lying behaviors using an accelerometer (HPG; HOBO Pendant G data logger, Onset Computer Corp., Bourne, MA) in calves. However, the HPG does not measure step activity. The objectives of this study were to (1) validate step activity, lying bouts, and lying time of AfiTag II (AT2; AfiTag II, Afimilk Ltd...
September 7, 2016: Journal of Dairy Science
Turandot Saul, Nicholas C Avitabile, Rachel Berkowitz, Sebastian D Siadecki, Gabriel Rose, Mojdeh Toomarian, Nicole L Kaban, Nicholas Governatori, Maria Suprun
STUDY OBJECTIVES: In a patient with dyspnea and suspected CHF, the evaluation of diastolic function involves: tissue Doppler of the mitral annulus and 2) pulsed wave Doppler of the mitral inflow. We aimed to 1) determine the inter-rater reliability for overall diastolic function and 2) evaluate the reliability of the individual Doppler measurements. METHODS: A convenience sample of adult emergency department patients was prospectively enrolled by 8 EPs who had participated in a 1-hour didactic session...
October 2016: Journal of Emergency Medicine
Ingeborg J De Kok, Lyndon F Cooper, Albert D Guckes, Kathleen McGraw, Robert F Wright, Carlos J Barrero, Sun-Yung Bak, Lisa O Stoner
PURPOSE: A systematic search of the literature was performed to identify and characterize articles reporting the influence of removable partial denture (RPD) therapy on satisfaction and quality of life (QoL). MATERIALS AND METHODS: The literature search for relevant articles published between January 1983 and March 30, 2013 was conducted using keyword searches of electronic databases and complimentary hand searches. The search strategy included the following keyword combinations (MeSH and free-text terms): fail, complication, surviv*, longevity, outcome, patient satisfaction or QoL, and denture or prosthes*, and partial and removable...
September 6, 2016: Journal of Prosthodontics: Official Journal of the American College of Prosthodontists
Philippe Metellus, Salah Boussen, Maxime Guye, Agnes Trebuchon
BACKGROUND: Resection of tumors located within the insula of the dominant hemisphere represents a technical challenge due to complex anatomy including surrounding vasculature and the relationship to functional (motor and language) structures. We report here the case of a successful resection of a left insular glioma in a native deaf signer during an awake craniotomy. CASE DESCRIPTION: Subject A.G., a congenitally deaf right-handed patient who is a native user of Sign Language, presented a seizure one week before he was referred to our department...
September 1, 2016: World Neurosurgery
Otto M Henriksen, Lisbeth Marner, Ian Law
The introduction of hybrid PET/MRI systems allows simultaneous multimodality image acquisition of high technical quality. This technique is well suited for the brain, and particularly in dementia and neuro-oncology. In routine use combinations of well-established MRI sequences and PET tracers provide the most optimal and clinically valuable protocols. For dementia the [18F]-fluorodeoxyglucose (FDG) has merit with a simultaneous four sequence MRI protocol of 20 min supported by supplementary statistical reading tools and quantitative measurements of the hippocampal volume...
October 2016: PET Clinics
Christine E Carter, Jessica A Grahn
Repetition is the most commonly used practice strategy by musicians. Although blocks of repetition continue to be suggested in the pedagogical literature, work in the field of cognitive psychology suggests that repeated events receive less processing, thereby reducing the potential for long-term learning. Motor skill learning and sport psychology research offer an alternative. Instead of using a blocked practice schedule, with practice completed on one task before moving on to the next task, an interleaved schedule can be used, in which practice is frequently alternated between tasks...
2016: Frontiers in Psychology
Andrew S Mason, Janet E Fulton, Paul M Hocking, David W Burt
BACKGROUND: LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact. RESULTS: Using LocaTR 3...
2016: BMC Genomics
Sophia B Georghiou, Marva Seifert, Shou-Yean Lin, Donald Catanzaro, Richard S Garfein, Roberta L Jackson, Valeriu Crudu, Camilla Rodrigues, Thomas C Victor, Antonino Catanzaro, Timothy C Rodwell
BACKGROUND: Rapid molecular diagnostics, with their ability to quickly identify genetic mutations associated with drug resistance in Mycobacterium tuberculosis clinical specimens, have great potential as tools to control multi- and extensively drug-resistant tuberculosis (M/XDR-TB). The Qiagen PyroMark Q96 ID system is a commercially available pyrosequencing (PSQ) platform that has been validated for rapid M/XDR-TB diagnosis. However, the details of the assay's diagnostic and technical performance have yet to be thoroughly investigated in diverse clinical environments...
2016: BMC Infectious Diseases
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