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https://www.readbyqxmd.com/read/28637310/the-metagenomic-data-life-cycle-standards-and-best-practices
#1
Petra Ten Hoopen, Robert D Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, Guy Cochrane
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing.Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637221/digital-direct-detection-of-micrornas-using-single-molecule-arrays
#2
Limor Cohen, Mark R Hartman, Aaron Amardey-Wellington, David R Walt
MicroRNAs (miRNAs) are involved in many biological pathways, and detecting miRNAs accurately is critical for diagnosing a variety of diseases including cancer. However, most current methods for miRNA detection require lengthy sample preparation and amplification steps that can bias the results. In addition, lack of specificity and reproducibility give rise to various challenges in detection of circulating miRNAs in biological samples. In this work, we applied the Single Molecule Array (Simoa) technique to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637180/participatory-design-of-probability-based-decision-support-tools-for-in-hospital-nurses
#3
Alvin D Jeffery, Laurie L Novak, Betsy Kennedy, Mary S Dietrich, Lorraine C Mion
Objective: To describe nurses' preferences for the design of a probability-based clinical decision support (PB-CDS) tool for in-hospital clinical deterioration. Methods: A convenience sample of bedside nurses, charge nurses, and rapid response nurses ( n  = 20) from adult and pediatric hospitals completed participatory design sessions with researchers in a simulation laboratory to elicit preferred design considerations for a PB-CDS tool. Following theme-based content analysis, we shared findings with user interface designers and created a low-fidelity prototype...
June 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#4
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636770/a-technology-training-protocol-for-meeting-qsen-goals-focusing-on-meaningful-learning
#5
Shuhong Luo, Melanie Kalman
The purpose of this paper is to describe and discuss how we designed and developed a 12-step technology training protocol. The protocol is meant to improve meaningful learning in technology education so that nursing students are able to meet the informatics requirements of Quality and Safety Education in Nursing competencies. When designing and developing the training protocol, we used a simplified experiential learning model that addressed the core features of meaningful learning: to connect new knowledge with students' prior knowledge and real-world workflow...
June 21, 2017: Nursing Forum
https://www.readbyqxmd.com/read/28634757/a-uhplc-ms-ms-method-for-profiling-multifunctional-steroids-in-human-hair
#6
Zhen Dong, Caihong Wang, Jinlan Zhang, Zhe Wang
It is important to profile steroids in many physiological and pathological processes. Recently, hair has been used for the long-term measurement of endogenous steroid hormones. Analyzing hair has advantages of being noninvasive and time sequential compared with other bio-specimens. Liquid chromatography-mass spectrometry (LC-MS) techniques have been widely used over the past decades; however, it is challenging to profile estrogens in hair by LC-MS, and more comprehensive steroid profiling is required. In this paper, an ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was developed to simultaneously profile 28 multifunctional steroids, including corticosteroids (n = 6), estrogens (n = 13), androgens (n = 5) and progestogens (n = 4), in human scalp hair in a single run...
June 20, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28634247/clinicians-perceptions-of-screening-for-food-insecurity-in-suburban-pediatric-practice
#7
Deepak Palakshappa, Aditi Vasan, Saba Khan, Leah Seifu, Chris Feudtner, Alexander G Fiks
BACKGROUND: National organizations recommend pediatricians screen for food insecurity (FI). Although there has been growing research in urban practices, little research has addressed FI screening in suburban practices. We evaluated the feasibility, acceptability, and impact of screening in suburban practices. METHODS: We conducted a mixed methods study that implemented FI screening in 6 suburban pediatric primary care practices. We included all children presenting for either a 2-, 15-, or 36-month well-child visit (N = 5645)...
June 20, 2017: Pediatrics
https://www.readbyqxmd.com/read/28634120/highly-reproducible-improved-label-free-quantitative-analysis-of-cellular-phosphoproteome-by-optimization-of-lc-ms-ms-gradient-and-analytical-column-construction
#8
Nagib Ahsan, Judson Belmont, Zhuo Chen, James G Clifton, Arthur R Salomon
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28633961/full-genome-amplification-and-sequencing-of-zika-viruses-using-a-targeted-amplification-approach
#9
Mariana Leguia, Cristhopher D Cruz, Vidal Felices, Armando Torre, Gilda Troncos, Victoria Espejo, Carolina Guevara, Christopher Mores
We have developed methods for full-genome sequencing of Zika viruses (ZIKVs) based on a targeted amplification approach. We used alignments of publicly available complete genome data to design a primer set that selectively amplifies ZIKVs. The approach includes amplification strategies for templates present at both high- and low-copy number, and PCR cycling conditions that have been normalized across genome fragments in order to streamline laboratory handling. Abundant templates can be amplified using a strategy that uses 6 overlapping amplicons to cover the complete viral genome, whereas scarce templates can be amplified using a strategy that uses 11 overlapping amplicons of smaller size...
June 17, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28633390/investigating-microrna-mediated-regulation-of-the-nascent-nuclear-transcripts-in-plants-a-bioinformatics-workflow
#10
Dongliang Yu, Zhonghai Tang, Chaogang Shao, Xiaoxia Ma, Taihe Xiang, Zhihong Fan, Huizhong Wang, Yijun Meng
Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs...
June 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28633385/timiner-ngs-data-mining-pipeline-for-cancer-immunology-and-immunotherapy
#11
Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Summary: Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing (NGS) data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from NGS data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates, and quantification of tumor immunogenicity...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633314/qualitative-identification-of-fentanyl-analogs-and-other-opioids-in-postmortem-cases-by-uhplc-ion-trap-msn
#12
Elisa N Shoff, M Elizabeth Zaney, Joseph H Kahl, George W Hime, Diane M Boland
Since 2013, the Miami-Dade County Medical Examiner Department has experienced an increase in the number of opioid-related deaths. The majority of cases coincided with the introduction of fentanyl into the local heroin supply. From 2014 to 2015, Miami-Dade County experienced a near 600% increase in fentanyl-related deaths, followed by an additional 200% increase in 2016. In 2015, two novel fentanyl analogs were identified in medical examiner cases: beta-hydroxythiofentanyl and acetyl fentanyl. In 2016, four additional fentanyl analogs emerged: para-fluoroisobutyryl fentanyl, butyryl fentanyl, furanyl fentanyl and carfentanil, as well as the synthetic opioid U-47700...
June 13, 2017: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/28631129/optimizing-the-deep-brain-stimulation-care-pathway-in-patients-with-parkinson-s-disease
#13
N J Thomas, P Mertens, T Danaila, G Polo, H Klinger, E Broussolle, S Thobois
Management of Parkinson's disease (PD) using deep brain stimulation (DBS) requires complex care in specialized, multidisciplinary centers. A well-organized, efficient patient flow is crucial to ensure that eligible patients can quickly access DBS. Delays or inefficiencies in patient care may impact a center's ability to meet demand, creating a capacity bottleneck. Analysis of the current practices within a center may help identify areas for improvement. After external audit of the DBS workflow of the Lyon Neurological Hospital and comparison with other European centers, manageable steps were suggested to restructure the care pathway...
June 19, 2017: Journal of Neurology
https://www.readbyqxmd.com/read/28630955/chairside-systems-a-current-review
#14
Markus Zaruba, Albert Mehl
Since Cerec (Chairside Economical Restoration of Esthetic Ceramics) was introduced as the first dental chairside computer-aided design/computer-aided manufacturing (CAD/CAM) system in the mid-1980s, this technology has enjoyed growing popularity, particularly in the recent past. There has been a considerable increase in the number of available chairside systems in only the last few years. One of the main reasons for this is that intraoral scanners have become increasingly better, smaller, and faster, while the design software has become more and more user-friendly...
2017: International Journal of Computerized Dentistry
https://www.readbyqxmd.com/read/28630229/observing-clonal-dynamics-across-spatiotemporal-axes-a-prelude-to-quantitative-fitness-models-for-cancer
#15
Andrew W McPherson, Fong Chun Chan, Sohrab P Shah
The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones...
June 19, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28629348/applying-the-plan-do-study-act-pdsa-approach-to-a-large-pragmatic-study-involving-safety-net-clinics
#16
Jennifer Coury, Jennifer L Schneider, Jennifer S Rivelli, Amanda F Petrik, Evelyn Seibel, Brieshon D'Agostini, Stephen H Taplin, Beverly B Green, Gloria D Coronado
BACKGROUND: The Plan-Do-Study-Act (PDSA) cycle is a commonly used improvement process in health care settings, although its documented use in pragmatic clinical research is rare. A recent pragmatic clinical research study, called the Strategies and Opportunities to STOP Colon Cancer in Priority Populations (STOP CRC), used this process to optimize the research implementation of an automated colon cancer screening outreach program in intervention clinics. We describe the process of using this PDSA approach, the selection of PDSA topics by clinic leaders, and project leaders' reactions to using PDSA in pragmatic research...
June 19, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28628634/protein-signature-in-cerebrospinal-fluid-and-serum-of-alzheimer-s-disease-patients-the-case-of-apolipoprotein-a-1-proteoforms
#17
Chiara Fania, Beatrice Arosio, Daniele Capitanio, Enrica Torretta, Cristina Gussago, Evelyn Ferri, Daniela Mari, Cecilia Gelfi
In the diagnosis of Alzheimer's disease (AD) total tau (T-tau), tau phosphorylated at threonine 181 (P-tau181), and the 42 amino acid isoform of alpha β-amyloid (Aβ) are well established surrogate CSF markers. However, there is a constant need for new diagnostic markers to identify the disease at a very early stage. The identification of new molecules for AD diagnosis and monitoring in CSF is hampered by several "confounding" factors including intra- and inter-individual, pre-analytical and analytical variabilities...
2017: PloS One
https://www.readbyqxmd.com/read/28628409/impact-of-measurement-time-on-clinical-workflow-in-different-manual-methods-of-region-of-interest-positioning-for-adc-quantification
#18
Adriano M Priola, Sandro M Priola
No abstract text is available yet for this article.
July 2017: Radiology
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#19
Alexey V Melnik, Pieter C Dorrestein, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28625663/development-of-complete-dentures-based-on-digital-intraoral-impressions-case-report
#20
Jing-Huan Fang, Xueyin An, Seung-Mi Jeong, Byung-Ho Choi
PATIENT: A 60-year-old man presented for refabrication of his maxillary complete denture. In this case, a digital process was chosen to replace the ill-fitted complete maxillary denture. A specialized scan retractor was used to retract the mobile tissues of the lips, cheeks and vestibule while taking a digital impression. The interocclusal record obtained in the patient's mouth was scanned in order to digitally register the occlusal vertical dimension. The denture base and teeth were designed on virtual models that were mounted at the occlusal vertical dimension, and were made using CAD/CAM technology...
June 15, 2017: Journal of Prosthodontic Research
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