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https://www.readbyqxmd.com/read/28098989/discovery-of-40-classes-of-per-and-polyfluoroalkyl-substances-in-historical-aqueous-film-forming-foams-afffs-and-afff-impacted-groundwater
#1
Krista A Barzen-Hanson, Simon C Roberts, Sarah J Choyke, Karl Oetjen, Alan McAlees, Nicole Riddell, Robert McCrindle, Patrick Lee Ferguson, Christopher P Higgins, Jennifer A Field
Aqueous film-forming foams (AFFFs), containing per- and polyfluoroalkyl substances (PFASs), are released into the environment during response to fire-related emergencies. Repeated historical applications of AFFF at military sites were a result of fire-fighter training exercises and equipment testing. Recent data on AFFF-impacted groundwater indicates that ~25% of the PFASs remain unidentified. In an attempt to close the mass balance, a systematic evaluation of 3M and fluorotelomer-based AFFFs, commercial products, and AFFF-impacted groundwaters from 15 U...
January 18, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28097056/rhea-a-transparent-and-modular-r-pipeline-for-microbial-profiling-based-on-16s-rrna-gene-amplicons
#2
Ilias Lagkouvardos, Sandra Fischer, Neeraj Kumar, Thomas Clavel
The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs...
2017: PeerJ
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#3
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28092508/ultrasonic-shear-wave-elasticity-imaging-sequencing-and-data-processing-using-a-verasonics-research-scanner
#4
Yufeng Deng, Ned C Rouze, Mark L Palmeri, Kathryn R Nightingale
Ultrasound elasticity imaging has been developed over the last decade to estimate tissue stiffness. Shear wave elasticity imaging (SWEI) quantifies tissue stiffness by measuring the speed of propagating shear waves following acoustic radiation force excitation. This paper presents the sequencing and data processing protocols of SWEI using a Verasonics system. The selection of the sequence parameters in a Verasonics programming script is discussed in detail. The data processing pipeline to calculate group shear wave speed (SWS), including tissue motion estimation, data filtering, and SWS estimation, is demonstrated...
January 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28090644/evaluation-of-a-telehealth-training-package-to-remotely-train-staff-to-conduct-a-preference-assessment
#5
William J Higgins, Kevin C Luczynski, Regina A Carroll, Wayne W Fisher, Oliver C Mudford
Recent advancements in telecommunication technologies make it possible to conduct a variety of healthcare services remotely (e.g., behavioral-analytic intervention services), thereby bridging the gap between qualified providers and consumers in isolated locations. In this study, web-based telehealth technologies were used to remotely train direct-care staff to conduct a multiple-stimulus-without-replacement preference assessment. The training package included three components: (a) a multimedia presentation; (b) descriptive feedback from previously recorded baseline sessions; and (c) scripted role-play with immediate feedback...
January 16, 2017: Journal of Applied Behavior Analysis
https://www.readbyqxmd.com/read/28075205/a-genomic-and-protein-protein-interaction-analyses-of-nonsyndromic-hearing-impairment-in-cameroon-using-targeted-genomic-enrichment-and-massively-parallel-sequencing
#6
Kamogelo Lebeko, Noluthando Manyisa, Emile R Chimusa, Nicola Mulder, Collet Dandara, Ambroise Wonkam
Hearing impairment (HI) is one of the leading causes of disability in the world, impacting the social, economic, and psychological well-being of the affected individual. This is particularly true in sub-Saharan Africa, which carries one of the highest burdens of this condition. Despite this, there are limited data on the most prevalent genes or mutations that cause HI among sub-Saharan Africans. Next-generation technologies, such as targeted genomic enrichment and massively parallel sequencing, offer new promise in this context...
January 11, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28073760/better-diagnostic-signatures-from-rnaseq-data-through-use-of-auxiliary-co-data
#7
Putri W Novianti, Barbara C Snoek, Saskia M Wilting, Mark A van de Wiel
: Our aim is to improve omics based prediction and feature selection using multiple sources of auxiliary information: co-data. Adaptive group regularized ridge regression (GRridge) was proposed to achieve this by estimating additional group-based penalty parameters through an empirical Bayes method at a low computational cost. We illustrate the GRridge method and software on RNA sequencing data sets. The method boosts the performance of an ordinary ridge regression and outperforms other classifiers...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073047/examining-cognitive-examining-cognitive-processes-and-drinking-urge-in-ptsd
#8
Jennifer P Read, Rachel L Bachrach, Jeffrey D Wardell, Scott F Coffey
Despite their centrality to learning theories, strikingly little attention has been paid to the role of cognitions in efforts to understand associations between posttraumatic stress disorder (PTSD) and alcohol drinking. In the present study, we sought to examine information processing pathways for trauma and alcohol information, and the effects of posttraumatic stress and trauma cue exposure on these pathways. Participants were college students (N = 232; 49% female; Mage = 19.56,SD = 1.44) categorized into three diagnostic groups based on current PTSD status determined by structured clinical interview...
December 24, 2016: Behaviour Research and Therapy
https://www.readbyqxmd.com/read/28069635/evaluating-approaches-to-find-exon-chains-based-on-long-reads
#9
Anna Kuosmanen, Tuukka Norri, Veli Mäkinen
: Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task...
January 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069179/rewriting-the-script-time-to-rethink-the-indications-for-myoma-surgery
#10
EDITORIAL
Jacques Donnez, Olivier Donnez, Marie-Madeleine Dolmans
No abstract text is available yet for this article.
January 6, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28067468/sticking-to-the-script-a-curious-case-of-confusion-in-an-esrd-patient
#11
Barry R Gorlitsky, John T Herion
A 60-year-old male Dialysis patient presented with altered mental status and Hypertensive Urgency. He had a significant lesion noted on his glans penis. He was treated for infection and hypertension with expectant management, without significant improvement in his mental acuity. Laboratory and radiologic workup were unrevealing for the etiology. Upon detailed review it was noted he had recently been given Acyclovir for a presumed Herpes Simplex Virus infection. He had been prescribed what is considered correct dosing for an ESRD patient...
January 9, 2017: Hemodialysis International
https://www.readbyqxmd.com/read/28066818/microbiome-helper-a-custom-and-streamlined-workflow-for-microbiome-research
#12
André M Comeau, Gavin M Douglas, Morgan G I Langille
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field...
January 2017: MSystems
https://www.readbyqxmd.com/read/28065520/the-socioecology-of-sexual-and-reproductive-health-care-use-among-young-urban-minority-males
#13
Arik V Marcell, Anthony R Morgan, Renata Sanders, Nicole Lunardi, Nanlesta A Pilgrim, Jacky M Jennings, Kathleen R Page, Penny S Loosier, Patricia J Dittus
PURPOSE: To explore perceptions of facilitators/barriers to sexual and reproductive health (SRH) care use among an urban sample of African-American and Hispanic young men aged 15-24 years, including sexual minorities. METHODS: Focus groups were conducted between April 2013 and May 2014 in one mid-Atlantic U.S. city. Young men aged 15-24 years were recruited from eight community settings to participate in 12 groups. Moderator guide explored facilitators/barriers to SRH care use...
January 5, 2017: Journal of Adolescent Health: Official Publication of the Society for Adolescent Medicine
https://www.readbyqxmd.com/read/28063090/don-t-give-up-a-cyber-ethnography-and-discourse-analysis-of-an-online-infertility-patient-forum
#14
Mihan Lee
Infertility affects women across the socioeconomic spectrum; however, it is by no means egalitarian in its distribution, nor uniform in its lived experience. Evidence shows striking disparities by income, race, and education in infertility prevalence, access to infertility services, and success rates after receiving infertility treatments. However, few studies so far have investigated disparities in patients' access to psychological support during the infertility journey. This paper undertakes a cyber-ethnography of the online patient forum, "Finding a Resolution for Infertility," hosted by RESOLVE: The National Infertility Association...
January 6, 2017: Culture, Medicine and Psychiatry
https://www.readbyqxmd.com/read/28059960/-contemplating-the-next-maneuver-functional-neuroimaging-reveals-intraoperative-decision-making-strategies
#15
Daniel Richard Leff, Gabriella Yongue, Ivo Vlaev, Felipe Orihuela-Espina, David James, Michael J Taylor, Thanos Athanasiou, Ray Dolan, Guang-Zhong Yang, Ara Darzi
OBJECTIVE: To investigate differences in the quality, confidence, and consistency of intraoperative surgical decision making (DM) and using functional neuroimaging expose decision systems that operators use. SUMMARY BACKGROUND DATA: Novices are hypothesized to use conscious analysis (effortful DM) leading to activation across the dorsolateral prefrontal cortex, whereas experts are expected to use unconscious automation (habitual DM) in which decisions are recognition-primed and prefrontal cortex independent...
February 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28059268/optimization-of-lightweight-structure-and-supporting-bipod-flexure-for-a-space-mirror
#16
Yi-Cheng Chen, Bo-Kai Huang, Zhen-Ting You, Chia-Yen Chan, Ting-Ming Huang
This article presents an optimization process for integrated optomechanical design. The proposed optimization process for integrated optomechanical design comprises computer-aided drafting, finite element analysis (FEA), optomechanical transfer codes, and an optimization solver. The FEA was conducted to determine mirror surface deformation; then, deformed surface nodal data were transferred into Zernike polynomials through MATLAB optomechanical transfer codes to calculate the resulting optical path difference (OPD) and optical aberrations...
December 20, 2016: Applied Optics
https://www.readbyqxmd.com/read/28057955/summaries-of-safety-labeling-changes-approved-by-the-fda-boxed-warnings-highlights-july-september-2016
#17
Teresa Rubio
The FDA's MedWatch program safety labeling changes for boxed warnings are compiled quarterly for drugs and therapeutic biologics where important changes have been made to the safety information. Search of Drug Safety Labeling Changes (SLC) database was conducted on October 10, 2016 for date range "7/1/2016-9/30/2016", labeling section "Boxed Warning". These and other label changes are searchable in the Drug Safety Labeling Changes (SLC) database, where data are available to the public in downloadable and searchable formats...
December 2016: Hospital Pharmacy
https://www.readbyqxmd.com/read/28056468/efficacy-of-a-supplemental-phonemic-awareness-curriculum-to-instruct-preschoolers-with-delays-in-early-literacy-development
#18
Howard Goldstein, Arnold Olszewski, Christa Haring, Charles R Greenwood, Luke McCune, Judith Carta, Jane Atwater, Gabriela Guerrero, Naomi Schneider, Tanya McCarthy, Elizabeth S Kelley
Purpose: Children who do not develop early literacy skills, especially phonological awareness (PA) and alphabet knowledge, prior to kindergarten are at risk for reading difficulties. We investigated a supplemental curriculum with children demonstrating delays in these skills. Method: A cluster randomized design with 104 preschool-age children in 39 classrooms was used to determine the efficacy of a supplemental PA curriculum, PAth to Literacy. The curriculum consists of 36 daily scripted 10-min lessons with interactive games designed to teach PA and alphabet skills...
January 1, 2017: Journal of Speech, Language, and Hearing Research: JSLHR
https://www.readbyqxmd.com/read/28049435/detecting-very-low-allele-fraction-variants-using-targeted-dna-sequencing-and-a-novel-molecular-barcode-aware-variant-caller
#19
Chang Xu, Mohammad R Nezami Ranjbar, Zhong Wu, John DiCarlo, Yexun Wang
BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28048909/su-f-p-36-automation-of-linear-accelerator-star-shot-measurement-with-advanced-xml-scripting-and-electronic-portal-imaging-device
#20
N Nguyen, N Knutson, M Schmidt, M Price
PURPOSE: To verify a method used to automatically acquire jaw, MLC, collimator and couch star shots for a Varian TrueBeam linear accelerator utilizing Developer Mode and an Electronic Portal Imaging Device (EPID). METHODS: An XML script was written to automate motion of the jaws, MLC, collimator and couch in TrueBeam Developer Mode (TBDM) to acquire star shot measurements. The XML script also dictates MV imaging parameters to facilitate automatic acquisition and recording of integrated EPID images...
June 2016: Medical Physics
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