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https://www.readbyqxmd.com/read/28742119/doestrare-a-statistical-test-to-identify-local-enrichments-in-rare-genomic-variants-associated-with-disease
#1
Elodie Persyn, Matilde Karakachoff, Solena Le Scouarnec, Camille Le Clézio, Dominique Campion, French Exome Consortium, Jean-Jacques Schott, Richard Redon, Lise Bellanger, Christian Dina
Next-generation sequencing technologies made it possible to assay the effect of rare variants on complex diseases. As an extension of the "common disease-common variant" paradigm, rare variant studies are necessary to get a more complete insight into the genetic architecture of human traits. Association studies of these rare variations show new challenges in terms of statistical analysis. Due to their low frequency, rare variants must be tested by groups. This approach is then hindered by the fact that an unknown proportion of the variants could be neutral...
2017: PloS One
https://www.readbyqxmd.com/read/28741904/prevention-of-childhood-obesity-and-food-policies-in-latin-america-from-research-to-practice
#2
R Pérez-Escamilla, C K Lutter, C Rabadan-Diehl, A Rubinstein, A Calvillo, C Corvalán, C Batis, E Jacoby, S Vorkoper, L Kline, E Ewart-Pierce, J A Rivera
BACKGROUND: Addressing childhood obesity in Latin America requires a package of multisectoral, evidence-based policies that enable environments conducive to healthy lifestyles. OBJECTIVE: Identify and examine key elements to translating research into effective obesity policies in Latin America. METHODS: We examined obesity prevention policies through case studies developed with an expert in the specific policy. Policies were selected based on their level of implementation, visibility and potential impact to reduce childhood obesity...
July 2017: Obesity Reviews: An Official Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28738880/level-of-mitoses-in-non-muscle-invasive-papillary-urothelial-carcinomas-pta-and-pt1-at-initial-bladder-biopsy-is-a-simple-and-powerful-predictor-of-clinical-outcome-a-multi-center-study-in-south-korea
#3
Ji Eun Kwon, Nam Hoon Cho, Yeong-Jin Choi, So Dug Lim, Yong Mee Cho, Sun Young Jun, Sanghui Park, Young A Kim, Sung-Sun Kim, Mi Sun Choe, Jung-Dong Lee, Dae Yong Kang, Jae Y Ro, Hyun-Jung Kim
BACKGROUND: Histologic grade is the most important predictor of the clinical outcome of non-muscle invasive (Ta, T1) papillary urothelial carcinoma (NMIPUCa), but its ambiguous criteria diminish its power to predict recurrence/progression for individual patients. We attempted to find an objective and reproducible histologic predictor of NMIPUCa that correlates well with the clinical outcome. METHODS: A total of 296 PUCas were collected from the Departments of Surgical Pathology of 11 institutions in South Korea...
July 24, 2017: Diagnostic Pathology
https://www.readbyqxmd.com/read/28738841/identifying-and-mitigating-batch-effects-in-whole-genome-sequencing-data
#4
Jennifer A Tom, Jens Reeder, William F Forrest, Robert R Graham, Julie Hunkapiller, Timothy W Behrens, Tushar R Bhangale
BACKGROUND: Large sample sets of whole genome sequencing with deep coverage are being generated, however assembling datasets from different sources inevitably introduces batch effects. These batch effects are not well understood and can be due to changes in the sequencing protocol or bioinformatics tools used to process the data. No systematic algorithms or heuristics exist to detect and filter batch effects or remove associations impacted by batch effects in whole genome sequencing data...
July 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28738582/metaboqc-a-tool-for-correcting-untargeted-metabolomics-data-with-mass-spectrometry-detection-using-quality-controls
#5
Mónica Calderón-Santiago, María A López-Bascón, Ángela Peralbo-Molina, Feliciano Priego-Capote
Nowadays most metabolomic studies involve the analysis of large sets of samples to find a representative metabolite pattern associated to the factor under study. During a sequence of analyses the instrument signals can be subjected to the influence of experimental variability sources. Implementation of quality control (QC) samples to check the contribution of experimental variability is the most common approach in metabolomics. This practice is based on the filtration of molecular entities experiencing a variation coefficient higher than that measured in the QC data set...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28736700/profiling-and-characterization-of-a-longissimus-dorsi-muscle-microrna-dataset-from-an-f2-duroc%C3%A2-%C3%A3-%C3%A2-pietrain-pig-resource-population
#6
Kaitlyn R Daza, Juan P Steibel, Deborah Velez-Irizarry, Nancy E Raney, Ronald O Bates, Catherine W Ernst
To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~ 5.5 months of age) from a Duroc × Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1 × 50 bp format. After processing, 232,826,977 total reads were aligned to the Sus scrofa reference genome (v10.2.79), with 74...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28736692/evaluating-the-impact-of-a-hiv-low-risk-express-care-task-shifting-program-a-case-study-of-the-targeted-learning-roadmap
#7
Linh Tran, Constantin T Yiannoutsos, Beverly S Musick, Kara K Wools-Kaloustian, Abraham Siika, Sylvester Kimaiyo, Mark J van der Laan, Maya Petersen
In conducting studies on an exposure of interest, a systematic roadmap should be applied for translating causal questions into statistical analyses and interpreting the results. In this paper we describe an application of one such roadmap applied to estimating the joint effect of both time to availability of a nurse-based triage system (low risk express care (LREC)) and individual enrollment in the program among HIV patients in East Africa. Our study population is comprised of 16,513 subjects found eligible for this task-shifting program within 15 clinics in Kenya between 2006 and 2009, with each clinic starting the LREC program between 2007 and 2008...
December 2016: Epidemiologic Methods
https://www.readbyqxmd.com/read/28736600/equivalence-tests-a-practical-primer-for-t-tests-correlations-and-meta-analyses
#8
Daniël Lakens
Scientists should be able to provide support for the absence of a meaningful effect. Currently, researchers often incorrectly conclude an effect is absent based a nonsignificant result. A widely recommended approach within a frequentist framework is to test for equivalence. In equivalence tests, such as the two one-sided tests (TOST) procedure discussed in this article, an upper and lower equivalence bound is specified based on the smallest effect size of interest. The TOST procedure can be used to statistically reject the presence of effects large enough to be considered worthwhile...
May 2017: Social Psychological and Personality Science
https://www.readbyqxmd.com/read/28736320/comparison-of-urinary-tract-infection-rates-associated-with-transurethral-catheterization-suprapubic-tube-and-clean-intermittent-catheterization-in-the-postoperative-setting-a-network-meta-analysis
#9
Christopher S Han, Sinae Kim, Kushan D Radadia, Philip T Zhao, Sammy E Elsamra, Ephrem O Olweny, Robert E Weiss
PURPOSE: A network meta-analysis was performed of available randomized controlled trials (RCT) to elucidate the risks of urinary tract infection (UTI) associated with transurethral catheterization (TUC), suprapubic tube (SPT) and intermittent catheterization (IC) in the postoperative setting. MATERIALS AND METHODS: PubMed, EMBASE and Google Scholar searches were performed for eligible RCTs from January 1980 to July 2015 that included patients who had TUC, SPT, or IC at the time of surgery and catheterization lasting up to postoperative day 30...
July 20, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28736121/potential-of-circulatory-procalcitonin-as-a-biomarker-reflecting-inflammation-among-south-indian-diabetic-foot-ulcers
#10
Dhamodharan Umapathy, Sireesh Dornadula, Arvind Rajagopalan, Narayana Murthy, Vairamani Mariappanadar, Rajesh Kesavan, Ramkumar Kunka Mohanram
OBJECTIVE: Diabetic foot ulcer (DFU), the major complication associated with diabetes mellitus, has been shown to precede amputation in up to 90% of cases. Recent data reveal that procalcitonin (PCT) is a valid marker for the diagnosis of bacterial infections compared with traditional markers like white blood cell count, C-reactive protein levels, and erythrocyte sedimentation rate in DFU patients. Furthermore, cytokines are proposed to act as modulators and mediators for the expression and release of PCT into the circulation...
July 20, 2017: Journal of Vascular Surgery
https://www.readbyqxmd.com/read/28735767/measuring-participation-in-chronic-back-pain-patients-the-5-item-pain-disability-index
#11
Ashley B McKillop, Linda J Carroll, Bruce D Dick, Michele C Battié
BACKGROUND CONTEXT: Of the three broad outcome domains of body functions and structures, activities, and participation (e.g., engaging in valued social roles) outlined in the World Health Organization's (WHO) International Classification of Functioning, Disability and Health (ICF), it has been argued that participation is the most important to individuals, particularly those with chronic health problems. Yet, participation is not commonly measured in back pain research. PURPOSE: The aim of this study was to investigate the construct validity of a modified 5-Item Pain Disability Index (PDI) score as a measure of participation in people with chronic back pain...
July 20, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28735766/risk-factor-analysis-for-predicting-vertebral-body-re-collapse-after-posterior-instrumented-fusion-in-thoracolumbar-burst-fracture
#12
Hae-Dong Jang, Jae Chul Lee, Jae-Wan Soh, Sung-Woo Choi, Hyeung-Kyu Cho, Byung-Joon Shin
BACKGROUND CONTEXT: In the posterior instrumented fusion surgery for thoracolumbar (T-L) burst fracture, early postoperative re-collapse of well-reduced vertebral body fracture could induces critical complications such as correction loss, post-traumatic kyphosis, metal failure, often lead to revision surgery. Furthermore, re-collapse is quite difficult to predict because of the variety of risk factors and no widely accepted accurate prediction systems existed. Although load sharing classification (LSC) has been known to help to decide the need for additional anterior column support, this radiographic scoring system has several critical limitations...
July 20, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28735696/the-network-structure-of-posttraumatic-stress-symptoms-in-children-and-adolescents-exposed-to-disasters
#13
Justin D Russell, Erin L Neill, Victor G Carrión, Carl F Weems
OBJECTIVE: To evaluate current theoretical assumptions about the nature of pediatric posttraumatic stress disorder (PTSD) by examining the network structure of PTSD in a sample of youth exposed to disasters and testing for age differences. Network analysis provides the opportunity to identify "central" symptoms that might hold an outsized influence over others and are important targets for research and treatment. The authors hypothesized that particular symptoms would exhibit greater influence over others...
August 2017: Journal of the American Academy of Child and Adolescent Psychiatry
https://www.readbyqxmd.com/read/28734193/improved-225-ac-daughter-retention-in-inpo4-containing-polymersomes
#14
R M de Kruijff, K Drost, L Thijssen, A Morgenstern, F Bruchertseifer, D Lathouwers, H T Wolterbeek, A G Denkova
Alpha-emitting radionuclides like actinium-225 ((225)Ac) are ideal candidates for the treatment of small metastasised tumours, where the long half-life of (225)Ac enables it to also reach less accessible tumours. The main challenge lies in retaining the recoiled alpha-emitting daughter nuclides, which are decoupled from targeting agents upon emission of an alpha particle and can subsequently cause unwanted toxicity to healthy tissue. Polymersomes, vesicles composed of amphiphilic block copolymers, are capable of transporting (radio)pharmaceuticals to tumours, and are ideal candidates for the retention of these daughter nuclides...
July 16, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28733216/sldassay-a-software-package-and-web-tool-for-analyzing-limiting-dilution-assays
#15
Ilana M Trumble, Andrew G Allmon, Nancy M Archin, Joseph Rigdon, Owen Francis, Pedro L Baldoni, Michael G Hudgens
Serial limiting dilution (SLD) assays are used in many areas of infectious disease related research. This paper presents SLDAssay, a free and publicly available R software package and web tool for analyzing data from SLD assays. SLDAssay computes the maximum likelihood estimate (MLE) for the concentration of target cells, with corresponding exact and asymptotic confidence intervals. Exact and asymptotic goodness of fit p-values, and a bias-corrected (BC) MLE are also provided. No other publicly available software currently implements the BC MLE or the exact methods...
July 18, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28731140/integrated-analysis-of-genome%C3%A2-wide-gene-expression-and-dna-methylation-microarray-of-diffuse-large-b%C3%A2-cell-lymphoma-with-tet-mutations
#16
Pengfei Liu, Wenhua Jiang, Jinkun Zhao, Huilai Zhang
Diffuse large B-cell lymphoma (DLBCL), the most frequently occurring type of lymphoid malignancy, has been demonstrated to be associated with mutations of Ten‑Eleven Translocation (TET). In order to explore the association between DLBCL and TET mutations, the present study analyzed the gene expression and methylation profiles in human DLBCL biopsy tissues with wildtype and mutated TET2. The microarray dataset GSE37365, containing two subseries: the genome‑wide gene expression dataset GSE37362 and the DNA methylation microarray dataset GSE37363, was downloaded from the Gene Expression Omnibus database...
July 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28729233/dynamo-a-modular-platform-for-monitoring-process-outcome-and-algorithm-based-treatment-planning-in-psychotherapy
#17
Tim Kaiser, Anton Rupert Laireiter
BACKGROUND: In recent years, the assessment of mental disorders has become more and more personalized. Modern advancements such as Internet-enabled mobile phones and increased computing capacity make it possible to tap sources of information that have long been unavailable to mental health practitioners. OBJECTIVE: Software packages that combine algorithm-based treatment planning, process monitoring, and outcome monitoring are scarce. The objective of this study was to assess whether the DynAMo Web application can fill this gap by providing a software solution that can be used by both researchers to conduct state-of-the-art psychotherapy process research and clinicians to plan treatments and monitor psychotherapeutic processes...
July 20, 2017: JMIR Medical Informatics
https://www.readbyqxmd.com/read/28728362/estimation-of-genetic-parameters-of-the-productive-and-reproductive-traits-in-ethiopian-holstein-using-multi-trait-models
#18
Wondossen Ayalew, Mohammed Aliy, Enyew Negussie
Objective: The objective of this study was to estimate genetic parameters for productive and reproductive traits. Methods: The data included production and reproduction records of animals that have calved between 1979 and 2013. The genetic parameters were estimated using multivariate mixed models (DMU) package, fitting univariate and multivariate mixed models with average information restricted maximum likelihood (AI-REML) algorithm. Results: The estimates of heritability for milk production traits from the first three lactation records were 0...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28727280/two-novel-effectors-of-trafficking-and-maturation-of-the-yeast-plasma-membrane-h-atpase
#19
Yosef Geva, Jonathan Crissman, Eric C Arakel, Natalia Gómez-Navarro, Silvia G Chuartzman, Kyle R Stahmer, Blanche Schwappach, Elizabeth A Miller, Maya Schuldiner
The endoplasmic reticulum (ER) is the entry site of proteins into the endomembrane system. Proteins exit the ER via COPII vesicles in a selective manner, mediated either by direct interaction with the COPII coat or aided by cargo receptors. Despite the fundamental role of such receptors in protein sorting, only a few have been identified. To further define the machinery that packages secretory cargo and targets proteins from the ER to Golgi membranes, we used multiple systematic approaches, which revealed two uncharacterized proteins that mediate the trafficking and maturation of Pma1, the essential yeast plasma membrane proton ATPase...
July 20, 2017: Traffic
https://www.readbyqxmd.com/read/28726986/board-invited-review-quantifying-water-use-in-ruminant-production
#20
G Legesse, K H Ominski, K A Beauchemin, S Pfister, M Martel, E J McGeough, A Y Hoekstra, R Kroebel, M R C Cordeiro, T A McAllister
The depletion of water resources, in terms of both quantity and quality, has become a major concern both locally and globally. Ruminants, in particular, are under increased public scrutiny due to their relatively high water use per unit of meat or milk produced. Estimating the water footprint of livestock production is a relatively new field of research for which methods are still evolving. This review describes the approaches used to quantify water use in ruminant production systems as well as the methodological and conceptual issues associated with each approach...
May 2017: Journal of Animal Science
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