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https://www.readbyqxmd.com/read/28913919/technical-note-on-the-use-of-cylindrical-ionization-chambers-for-electron-beam-reference-dosimetry
#1
Bryan R Muir, Malcolm R McEwen
PURPOSE: To investigate the use of cylindrical chambers for electron beam dosimetry independent of energy by studying the variability of relative ion chamber perturbation corrections, one of the main concerns for electron beam dosimetry with cylindrical chambers. METHODS: Measurements are made with sets of cylindrical and plane-parallel reference-class chambers as a function of depth in water in 8 MeV and 18 MeV electron beams. The ratio of chamber readings for similar chambers is normalized in a high-energy electron beam and can be thought of as relative perturbation corrections...
September 14, 2017: Medical Physics
https://www.readbyqxmd.com/read/28884399/bias-and-correction-in-rna-seq-data-for-marine-species
#2
Kai Song, Li Li, Guofan Zhang
RNA-seq is a recently developed approach widely used for transcriptome profiling in biological analyses that use next-generation sequencing technologies. Accurate estimation of gene expression levels is critical for answering biological questions. Here, we show that the commonly used measure of gene expression levels, fragments per kilobase of transcript per million mapped reads (FPKM), is biased in transcript length, GC content, and dinucleotide frequencies in the RNA-seq analysis of marine species. We used a generalized linear model to correct the observed biases of FPKM...
September 7, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28881105/decision-aid-use-during-post-biopsy-consultations-for-localized-prostate-cancer
#3
Margaret Holmes-Rovner, Akshay Srikanth, Stephen G Henry, Aisha Langford, David R Rovner, Angela Fagerlin
BACKGROUND: Decision Aids (DAs) effectively translate medical evidence for patients but are not routinely used in clinical practice. Little is known about how DAs are used during patient-clinician encounters. OBJECTIVE: To characterize the content and communicative function of high-quality DAs during diagnostic clinic visits for prostate cancer. PARTICIPANTS: 252 men newly diagnosed with localized prostate cancer who had received a DA, 45 treating physicians at 4 US Veterans Administration urology clinics...
September 7, 2017: Health Expectations: An International Journal of Public Participation in Health Care and Health Policy
https://www.readbyqxmd.com/read/28872219/characterization-of-sediment-bacterial-communities-in-plain-lakes-with-different-trophic-statuses
#4
Wei Huang, Xing Chen, Xia Jiang, Binghui Zheng
Sediment microbial communities play an important role in lake trophic status. This study determined millions of Illumina reads (16S rRNA gene amplicons) to compare the bacterial communities in moderately eutrophic, lightly eutrophic, and moderately trophic regions using a technically consistent approach. The results indicated that the sediments from moderately eutrophic and trophic lake had the higher bacterial diversity than lightly eutrophic lake. Proteobacteria was the most abundant phylum (22.7%-86.2%) across samples from three regions...
September 4, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28868132/comprehensive-comparison-of-pacific-biosciences-and-oxford-nanopore-technologies-and-their-applications-to-transcriptome-analysis
#5
Jason L Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au
Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacBio and ONT, including error pattern, length, mappability and technical improvements over previous platforms. We also evaluated their application to transcriptome analyses, such as isoform identification and quantification and characterization of transcriptome complexity, by comparing the performance of PacBio, ONT and their corresponding Hybrid-Seq strategies (PacBio+Illumina and ONT+Illumina)...
2017: F1000Research
https://www.readbyqxmd.com/read/28856142/preoperative-surgical-rehearsal-using-cadaveric-fresh-tissue-surgical-simulation-increases-resident-operative-confidence
#6
Erin L Weber, Hyuma A Leland, Beina Azadgoli, Michael Minneti, Joseph N Carey
BACKGROUND: Rehearsal is an essential part of mastering any technical skill. The efficacy of surgical rehearsal is currently limited by low fidelity simulation models. Fresh cadaver models, however, offer maximal surgical simulation. We hypothesize that preoperative surgical rehearsal using fresh tissue surgical simulation will improve resident confidence and serve as an important adjunct to current training methods. METHODS: Preoperative rehearsal of surgical procedures was performed by plastic surgery residents using fresh cadavers in a simulated operative environment...
August 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28853213/advances-and-challenges-in-the-detection-of-transcriptome-wide-protein-rna-interactions
#7
REVIEW
Emily C Wheeler, Eric L Van Nostrand, Gene W Yeo
RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking followed by immunoprecipitation and sequencing (CLIP-seq) are state-of-the-art methods used to identify the RNA targets and specific binding sites of RBPs. Historically, CLIP methods have been confounded with challenges such as the requirement for tens of millions of cells per experiment, low RNA yields resulting in libraries that contain a high number of polymerase chain reaction duplicated reads, and technical inconveniences such as radioactive labeling of RNAs...
August 29, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28827752/haplotype-resolved-sweet-potato-genome-traces-back-its-hexaploidization-history
#8
Jun Yang, M-Hossein Moeinzadeh, Heiner Kuhl, Johannes Helmuth, Peng Xiao, Stefan Haas, Guiling Liu, Jianli Zheng, Zhe Sun, Weijuan Fan, Gaifang Deng, Hongxia Wang, Fenhong Hu, Shanshan Zhao, Alisdair R Fernie, Stefan Boerno, Bernd Timmermann, Peng Zhang, Martin Vingron
Here we present the 15 pseudochromosomes of sweet potato, Ipomoea batatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotyping method based on genome assembly, we have produced a half haplotype-resolved genome from ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two recent whole-genome duplication events as occurring about 0...
August 21, 2017: Nature Plants
https://www.readbyqxmd.com/read/28818101/a-new-method-for-sequencing-the-hypervariable-plasmodium-falciparum-gene-var2csa-from-clinical-samples
#9
Antoine Dara, Mark A Travassos, Matthew Adams, Sarah Schaffer DeRoo, Elliott F Drábek, Sonia Agrawal, Miriam K Laufer, Christopher V Plowe, Joana C Silva
BACKGROUND: VAR2CSA, a member of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family, mediates the binding of P. falciparum-infected erythrocytes to chondroitin sulfate A, a surface-associated molecule expressed in placental cells, and plays a central role in the pathogenesis of placental malaria. VAR2CSA is a target of naturally acquired immunity and, as such, is a leading vaccine candidate against placental malaria. This protein is very polymorphic and technically challenging to sequence...
August 17, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28804852/the-overall-hemostatic-potential-ohp-assay
#10
Jennifer Curnow
The principle of the overall hemostatic potential (OHP) assay is the generation of a fibrin time curve by optical density readings, which represent the balance between fibrin generation, triggered by thrombin or tissue factor, and fibrinolysis, triggered by tissue plasminogen activator (tPA). OHP measures the integrated effect of procoagulant, anticoagulant, and fibrinolytic factors, and OHP assay parameters provide a means of quantifying both the coagulation and fibrinolytic potential of platelet poor plasma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28803017/technical-note-use-of-an-automated-grooming-brush-by-heifers-and-potential-for-radiofrequency-identification-based-measurements-of-this-behavior
#11
Rachel L Toaff-Rosenstein, Martin Velez, Cassandra B Tucker
Healthy cattle readily use grooming brushes but this behavior subsides when animals become ill. Tracking use of a brush may provide an opportunity for health monitoring, especially if the process could be automated. We assessed how healthy heifers groom themselves on a brush and hypothesized that radiofrequency identification (RFID) could be used to accurately and automatically record this behavior. Angus and Hereford heifers (n = 16) were fitted with 2 ultra-high-frequency RFID ear tags and monitored in groups of 8 while housed in a pen with an electronic brush, video cameras, and 4 RFID antennas...
August 9, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28794548/informed-consent-process-foundation-of-the-researcher-participant-bond
#12
Amrita Sil, Nilay Kanti Das
Consenting to participate in a clinical research study after being properly and correctly informed upholds the basic ethical principle of "autonomy" in human research. The informed consent is a process by which the physician sensitizes the patient about the nature, procedures, risks benefits, treatment schedules, etc of the study in a language that is non-technical and understandable by the study participant. Informed consent document (ICD) has got two parts: the 'Subject Information Sheet' and the 'Informed Consent Form' (ICF); and they have to be approved by the Institutional Ethics Committee (IEC) before administration...
July 2017: Indian Journal of Dermatology
https://www.readbyqxmd.com/read/28777925/a-career-on-both-sides-of-the-atlantic-memoirs-of-a-molecular-plant-pathologist
#13
Nickolas J Panopoulos
This article recounts the experiences that shaped my career as a molecular plant pathologist. It focuses primarily on technical and conceptual developments in molecular phytobacteriology, shares some personal highlights and untold stories that impacted my professional development, and describes the early years of agricultural biotechnology. Writing this article required reflection on events occurring over several decades that were punctuated by a mid-career relocation across the Atlantic. I hope it will still be useful, informative, and enjoyable to read...
August 4, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28774726/girardia-dorotocephala-transcriptome-sequence-assembly-and-validation-through-characterization-of-piwi-homologs-and-stem-cell-progeny-markers
#14
Eugene Matthew P Almazan, Sydney L Lesko, Michael P Markey, Labib Rouhana
Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities...
August 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28768609/toward-predicting-social-support-needs-in-online-health-social-networks
#15
Min-Je Choi, Sung-Hee Kim, Sukwon Lee, Bum Chul Kwon, Ji Soo Yi, Jaegul Choo, Jina Huh
BACKGROUND: While online health social networks (OHSNs) serve as an effective platform for patients to fulfill their various social support needs, predicting the needs of users and providing tailored information remains a challenge. OBJECTIVE: The objective of this study was to discriminate important features for identifying users' social support needs based on knowledge gathered from survey data. This study also provides guidelines for a technical framework, which can be used to predict users' social support needs based on raw data collected from OHSNs...
August 2, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28765829/transcriptome-of-melanoma-cells-from-two-mouse-models-tyr-nras-q61k-and-tyr-rack1-ha-tyr-nras-q61k
#16
Cécil Campagne, Stéphanie Pons, Diane Esquerre, Jordi Estellé, Emmanuelle Bourneuf, Uwe Maskos, Giorgia Egidy
The transcriptome sequencing of melanoma cells from two mouse models differing in the expression level of the scaffold protein Receptor for activated C kinase (RACK1) are presented. Primary melanoma cells were harvested from Tyr:NRas(Q61K); Pax3(GFP/+) mice, with or without the Tyr:Rack1-HA transgene. Cells were cultured and infected with scramble shRNA or Rack1-targeting shRNA, on technical triplicates of viral infection. Libraries were prepared by selecting polyadenylated mRNAs and RNA Sequencing (RNASeq) was performed...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28734736/analysis-of-medication-adherence-related-notes-from-a-service-oriented-community-pharmacy
#17
Matthew Witry, Rachel Parry, Randal McDonough, Michael Deninger
BACKGROUND: Medication nonadherence is a significant public health problem. Community pharmacists are positioned to intervene, however, the process is not well understood. OBJECTIVE: To classify and quantify the reasons for nonadherence documented by community pharmacists. METHODS: A retrospective content analysis of pharmacist notes related to nonadherence at a service oriented community pharmacy in the Midwest United States. Notes from the site's dispensing custom documentation software were obtained from September 1, 2014 through February 28, 2015 that were labeled "compliance", either prompted by proportion of days covered calculations or entered as a drug therapy problem...
July 15, 2017: Research in Social & Administrative Pharmacy: RSAP
https://www.readbyqxmd.com/read/28729296/analysis-of-30-spinal-angiograms-falsely-reported-as-normal-in-18-patients-with-subsequently-documented-spinal-vascular-malformations
#18
P Barreras, D Heck, B Greenberg, J-P Wolinsky, C A Pardo, P Gailloud
BACKGROUND AND PURPOSE: The early diagnosis of spinal vascular malformations suffers from the nonspecificity of their clinical and radiologic presentations. Spinal angiography requires a methodical approach to offer a high diagnostic yield. The prospect of false-negative studies is particularly distressing when addressing conditions with a narrow therapeutic window. The purpose of this study was to identify factors leading to missed findings or inadequate studies in patients with spinal vascular malformations...
July 20, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28713519/common-solvents-for-making-extraction-of-allergenic-proteins-from-plants-pollens-for-prick-tests-and-related-factors-a-technical-review
#19
REVIEW
Hassan Mansouritorghabeh, Farahzad Jabbari-Azad, Abdolreza Varasteh, Mojtaba Sankian, Reza Farid-Hosseini
Collecting information on influencing factors in developing consistent and high-quality extracts results in accurate diagnosis and effective treatment of type I allergy (IgE mediated). Furthermore, considering that a large number of allergens are currently in practice, any attempt to develop a more effective procedure for preparing extract may be useful. Nowadays, different saline solvents, temperature, incubation time, and PH are being incorporated for preparing allergen extracts. The objective of the current study was to clear and address the commonest of solvent buffers and allied conditions for making extracts of pollens of grasses, trees, and weeds...
May 2017: Electronic Physician
https://www.readbyqxmd.com/read/28695665/analysis-of-large-16s-rrna-illumina-data-sets-impact-of-singleton-read-filtering-on-microbial-community-description
#20
Lucas Auer, Mahendra Mariadassou, Michael O'Donohue, Christophe Klopp, Guillermina Hernandez-Raquet
Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise...
July 11, 2017: Molecular Ecology Resources
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