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Karin Meinike Jørgensen, Karen M T Astvad, Rasmus Krøger Hare, Maiken Cavling Arendrup
Olorofim is a novel antifungal agent with in vitro activity against Aspergillus and some other moulds. Here we addressed technical aspects for EUCAST olorofim testing and generated contemporary MIC data.EUCAST E.Def 9.3.1 testing was performed comparing two plate preparation methods (serial-dilution in medium (serial-plates) versus pre-dilution in DMSO (ISO-plates)), two lots of olorofim, visual (visual-MIC) versus spectrophotometer (spec-MIC) reading and four polystyrene plates using 34-53 Aspergillus isolates from five genera...
May 21, 2018: Antimicrobial Agents and Chemotherapy
Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis
The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach...
2018: Methods in Molecular Biology
Derek Powell, Martin Keil, Dru Brenner, Liliana Lim, Ellen M Markman
Communication is a cooperative endeavor that goes well beyond decoding sentences' literal meaning. Listeners actively construe the meaning of utterances from both their literal meanings and the pragmatic principles that govern communication. When communicators make pragmatically infelicitous statements, the effects can be similar to paltering-misleading speech that evokes false inferences from true statements. The American Diabetes Association's (ADA's) "Diabetes Myths" website provides a real-world case study in such misleading communications...
May 1, 2018: Psychological Science
Dale B Read, Ben Jones, Sean Williams, Padraic Phibbs, Josh Darrall-Jones, Greg Roe, Jonathon Weakley, Andrew Rock, Kevin Till
PURPOSE: This study quantified the frequencies and timings of rugby union match-play phases (i.e., attacking, defending, ball in play (BIP) and ball out of play (BOP)) and then compared the physical characteristics of attacking, defending and BOP between forwards and backs. METHODS: Data were analysed from 59 male rugby union academy players (259 observations). Each player wore a micro-technology device (Optimeye S5, Catapult) with video footage analysed for phase timings and frequencies...
May 10, 2018: International Journal of Sports Physiology and Performance
Matthias Löbe, Sebastian Stäubert, Colleen Goldberg, Ivonne Haffner, Alfred Winter
BACKGROUND: Medical plaintext documents contain important facts about patients, but they are rarely available for structured queries. The provision of structured information from natural language texts in addition to the existing structured data can significantly speed up the search for fulfilled inclusion criteria and thus improve the recruitment rate. OBJECTIVES: This work is aimed at supporting clinical trial recruitment with text mining techniques to identify suitable subjects in hospitals...
2018: Studies in Health Technology and Informatics
Gabriel A Al-Ghalith, Benjamin Hillmann, Kaiwei Ang, Robin Shields-Cutler, Dan Knights
Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation...
May 2018: MSystems
Travis McLennon, Chun-Yip Hon
Exposure of ice resurfacer operators to indoor air contaminants was measured in six indoor ice arenas. A standardized questionnaire on technical and operational features was employed and indoor airborne concentrations of carbon monoxide (CO), carbon dioxide (CO2 ), nitric oxide (NO), nitrogen dioxide (NO2 ), sulfur dioxide (SO2 ), and total volatile organic compounds (VOCs) were measured. Air samples were collected using a range of direct reading instruments attached to the driver's seat of the resurfacer. The range of mean exposure concentrations via positional sampling (i...
May 2, 2018: International Journal of Occupational and Environmental Health
Stefanie M Croghan, Paul Carroll, Sarah Reade, Amy E Gillis, Paul F Ridgway
 While an explosion in technological sophistication has revolutionized surgery within the operating theatre, delivery of surgical ward-based care has seen little innovation.  Use of telepresence allowing off-site clinicians communicate with patients has been largely restricted to outpatient settings or use of complex, expensive, static devices.  We designed a prospective study to ascertain feasibility and face validity of a remotely controlled mobile audiovisual drone (LUCY) to access inpatients.  This device is, uniquely, lightweight, freely mobile and emulates 'human' interaction by swiveling and adjusting height to patients' eye-level...
May 2, 2018: Journal of Innovation in Health Informatics
Marta Gòdia, Fabiana Quoos Mayer, Julieta Nafissi, Anna Castelló, Joan Enric Rodríguez-Gil, Armand Sánchez, Alex Clop
The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPureTM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing...
April 26, 2018: Systems Biology in Reproductive Medicine
Todd L Demmy, Sai Yendamuri, Thomas A D'Amico, William R Burfeind
BACKGROUND: Despite the slow adoption of Minimally Invasive Lobectomy (MIL), it is now a preferred approach for early lung cancer. Nevertheless, ongoing concerns regarding MIL oncologic effectiveness has led to calls for prospective, randomized trials. METHODS: Retrospective analysis of on-line databases, collected readings and other scholarly experiences of the experienced authors were used to construct this review. All available reports containing long-term survival comparisons for open versus MIL were tabulated...
April 17, 2018: Annals of Thoracic Surgery
Christian Münch, Ivan Dikic
In the version of this News & Views originally published, owing to a technical error some incorrect characters were introduced into the second sentence of the main text, starting "Autophagy can be divided into non-selective...", where "caspringDE@2017n" should have read 'can'. This has now been corrected in all versions of this News & Views.
April 19, 2018: Nature Cell Biology
Zhuoran Han, Jingfeng Sun, Aijun Lv, Anli Wang
This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high-throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols...
April 17, 2018: MicrobiologyOpen
Jose Mario Bello Pineda, Robert K Bradley
Although branchpoint recognition is an essential component of intron excision during the RNA splicing process, the branchpoint itself is frequently assumed to be a basal, rather than regulatory, sequence feature. However, this assumption has not been systematically tested due to the technical difficulty of identifying branchpoints and quantifying their usage. Here, we analyzed ∼1.31 trillion reads from 17,164 RNA sequencing data sets to demonstrate that almost all human introns contain multiple branchpoints...
April 17, 2018: Genes & Development
Elaine L Larson, Alan Teller, Alejandra N Aguirre, Jhia Jackson, Dodi Meyer
Introduction: We aimed to improve the research consenting process by developing and evaluating simplified consent forms. Methods: Four templates written at the eighth-tenth grade reading level were developed and trialed by a group of experts in clinical research, health literacy, national regulatory requirements, and end users. Researchers from protocols which had received expedited review were surveyed at 2 time points regarding their use and assessment of the templates...
August 2017: Journal of Clinical and Translational Science
C Bortoluzzi, K L Paras, T J Applegate, G G Verocai
Monitoring Eimeria shedding has become more important due to the recent restrictions to the use of antibiotics within the poultry industry. Therefore, there is a need for the implementation of more precise and accurate quantitative diagnostic techniques. The objective of this study was to compare the precision and accuracy between the Mini-FLOTAC and the McMaster techniques for quantitative diagnosis of Eimeria maxima oocyst in poultry. Twelve pools of excreta samples of broiler chickens experimentally infected with E...
April 30, 2018: Veterinary Parasitology
Jean Monlong, Simon L Girard, Caroline Meloche, Maxime Cadieux-Dion, Danielle M Andrade, Ron G Lafreniere, Micheline Gravel, Dan Spiegelman, Alexandre Dionne-Laporte, Cyrus Boelman, Fadi F Hamdan, Jacques L Michaud, Guy Rouleau, Berge A Minassian, Guillaume Bourque, Patrick Cossette
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs...
April 12, 2018: PLoS Genetics
Sonia Gaur, Stephanie Harmon, Sherif Mehralivand, Sandra Bednarova, Brian P Calio, Dordaneh Sugano, Abhinav Sidana, Maria J Merino, Peter A Pinto, Bradford J Wood, Joanna H Shih, Peter L Choyke, Baris Turkbey
BACKGROUND: Prostate Imaging-Reporting and Data System v. 2 (PI-RADSv2) provides standardized nomenclature for interpretation of prostate multiparametric MRI (mpMRI). Inclusion of additional features for categorization may provide benefit to stratification of disease. PURPOSE: To prospectively compare PI-RADSv2 to a qualitative in-house system for detecting prostate cancer on mpMRI. STUDY TYPE: Prospective. POPULATION: In all, 338 patients who underwent mpMRI May 2015-May 2016, with subsequent MRI/transrectal ultrasound fusion-guided biopsy...
March 31, 2018: Journal of Magnetic Resonance Imaging: JMRI
Kristie Hadden, Latrina Y Prince, C Lowry Barnes
BACKGROUND: In response to an assessment of organizational health literacy practices at a major academic health center, this case study evaluated the health literacy demands of patient-reported outcome measures commonly used in orthopedic surgery practices to identify areas for improvement. METHODS: A mixed-methods approach was used to analyze the readability and patient feedback of orthopedic patient-reported outcome materials. Qualitative results were derived from focus group notes, observations, recordings, and consensus documents...
April 2018: Quality Management in Health Care
Neda Gholizadeh Sendani, Alireza Karimian, Clara Ferreira, Parham Alaei
PURPOSE: To evaluate dependence of measured dose on size and location of region of interest (ROI) in Gafchromic EBT3 film dosimetry. METHODS: Gafchromic EBT3 films were irradiated perpendicularly using the 6MV beam from a linear accelerator at 10 cm depth (100 cm SSD) of a 30×30×20 cm3 solid water phantom for a range of field sizes of 6×6 to 100×100 mm2 . Image-J software was used for reading pieces of film. The appropriate location of ROIs in scanned films were found by two methods...
March 26, 2018: Medical Physics
Jeremiah J Minich, Qiyun Zhu, Stefan Janssen, Ryan Hendrickson, Amnon Amir, Russ Vetter, John Hyde, Megan M Doty, Kristina Stillwell, James Benardini, Jae H Kim, Eric E Allen, Kasthuri Venkateswaran, Rob Knight
Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90...
May 2018: MSystems
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