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https://www.readbyqxmd.com/read/28926390/misconceptions-misuses-and-misinterpretations-of-p-values-and-significance-testing
#1
Joel J Gagnier, Hal Morgenstern
The interpretation and reporting of p values and significance testing in biomedical research are fraught with misconceptions and inaccuracies. Publications of peer-reviewed research in orthopaedics are not immune to such problems. The American Statistical Association (ASA) recently published an official statement on the use, misuse, and misinterpretation of statistical testing and p values in applied research. The ASA statement discussed 6 principles: (1) "P-values can indicate how incompatible the data are with a specified statistical model...
September 20, 2017: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/28905878/detecting-splicing-patterns-in-genes-involved-in-hereditary-breast-and-ovarian-cancer
#2
Grégoire Davy, Antoine Rousselin, Nicolas Goardon, Laurent Castéra, Valentin Harter, Angelina Legros, Etienne Muller, Robin Fouillet, Baptiste Brault, Anna S Smirnova, Fréderic Lemoine, Pierre de la Grange, Marine Guillaud-Bataille, Virginie Caux-Moncoutier, Claude Houdayer, Françoise Bonnet, Cécile Blanc-Fournier, Pascaline Gaildrat, Thierry Frebourg, Alexandra Martins, Dominique Vaur, Sophie Krieger
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28892903/immunohistochemical-study-of-muc1-and-muc5ac-expression-in-gall-bladder-lesions
#3
Amit Bhoge, Siddhi Gaurish Sinai Khandeparkar, Avinash R Joshi, Bageshri Gogate, Maithili Mandar Kulkarni, Pallavi Bhayekar
INTRODUCTION: Immunohistochemical (IHC) markers of mucin family are associated with various Gallbladder Lesions (GBLs). AIM: To study the distribution of GBL with respect to age and sex as well as to analyse the IHC profile of MUC1 and MUC5AC in GBLs and attempt correlation with clinical and histopathological findings. MATERIALS AND METHODS: The present study was conducted over a period of six years. A technique of manual tissue array was employed for cases subjected to IHC using MUC1 and MUC5AC...
July 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28892494/infections-by-human-gastrointestinal-helminths-are-associated-with-changes-in-faecal-microbiota-diversity-and-composition
#4
Timothy P Jenkins, Yasara Rathnayaka, Piyumali K Perera, Laura E Peachey, Matthew J Nolan, Lutz Krause, Rupika S Rajakaruna, Cinzia Cantacessi
Investigations of the impact that patent infections by soil-transmitted gastrointestinal nematode parasites exert on the composition of the host gut commensal flora are attracting growing interest by the scientific community. However, information collected to date varies across experiments, and further studies are needed to identify consistent relationships between parasites and commensal microbial species. Here, we explore the qualitative and quantitative differences between the microbial community profiles of cohorts of human volunteers from Sri Lanka with patent infection by one or more parasitic nematode species (H+), as well as that of uninfected subjects (H-) and of volunteers who had been subjected to regular prophylactic anthelmintic treatment (Ht)...
2017: PloS One
https://www.readbyqxmd.com/read/28842085/what-is-the-current-role-and-factors-for-success-of-the-journal-club-in-podiatric-foot-and-ankle-surgery-residency-training-programs
#5
Eric So, Christopher F Hyer, Marcus P Richardson, Randall C Thomas
The journal club (JC) is a traditional part of postgraduate medical education, although little has been written on its current role in podiatric surgical training programs. The goal of the present study was to determine how JCs are conducted and the factors associated with their success. Anonymous electronic surveys were distributed to all podiatric foot and ankle surgical training program directors in the United States with a valid e-mail address. A total of 202 surveys were initially e-mailed to training program directors, with a second and third round sent to those who did not respond...
September 2017: Journal of Foot and Ankle Surgery: Official Publication of the American College of Foot and Ankle Surgeons
https://www.readbyqxmd.com/read/28832626/the-effect-of-bacopa-monnieri-on-gene-expression-levels-in-sh-sy5y-human-neuroblastoma-cells
#6
How-Wing Leung, Gabriel Foo, Gokulakrishna Banumurthy, Xiaoran Chai, Sujoy Ghosh, Tora Mitra-Ganguli, Antonius M J VanDongen
Bacopa monnieri is a plant used as a nootropic in Ayurveda, a 5000-year-old system of traditional Indian medicine. Although both animal and clinical studies supported its role as a memory enhancer, the molecular and cellular mechanism underlying Bacopa's nootropic action are not understood. In this study, we used deep sequencing (RNA-Seq) to identify the transcriptome changes upon Bacopa treatment on SH-SY5Y human neuroblastoma cells. We identified several genes whose expression levels were regulated by Bacopa...
2017: PloS One
https://www.readbyqxmd.com/read/28817155/genetic-variation-of-15-autosomal-strs-in-a-population-sample-of-bedouins-residing-in-the-area-of-the-fourth-nile-cataract-sudan
#7
Andrzej Ossowski, Jaroslaw Piatek, Miroslaw Parafiniuk, Aleksandra Pudlo, Witold Pepinski, Malgorzata Skawronska, Michal Szeremeta, Anna Niemcunowicz-Janica, Ireneusz Soltyszewski
The purpose of the paper was to report allelic frequencies of 15 autosomal STR markers (AmpFlSTR NGM PCR Amplification Kit) for Bedouin inhabitants in the area of the Fourth Nile Cataract in Sudan, and compute commonly used population and forensic biostatistical parameters. Buccal swabs were collected from 117 unrelated individuals. DNA was extracted using DNA QIAamp(®) DNA Mini Kit, and quantitated with Quantifiler Human Quantification Kit in a 7500 Real-Time PCR System. Amplification of 15 AmpFlSTR NGM PCR Kit loci was performed in PCR System 9700...
August 17, 2017: Anthropologischer Anzeiger; Bericht über die Biologisch-anthropologische Literatur
https://www.readbyqxmd.com/read/28797473/biomarker-research-to-improve-clinical-outcomes-of-peritoneal-dialysis-consensus-of-the-european-training-and-research-in-peritoneal-dialysis-eutripd-network
#8
REVIEW
Christoph Aufricht, Robert Beelen, Matthias Eberl, Michel Fischbach, Donald Fraser, Achim Jörres, Klaus Kratochwill, Manuel LópezCabrera, Peter Rutherford, Claus-Peter Schmitt, Nicholas Topley, Janusz Witowski
Peritoneal dialysis (PD) therapy substantially requires biomarkers as tools to identify patients who are at the highest risk for PD-related complications and to guide personalized interventions that may improve clinical outcome in the individual patient. In this consensus article, members of the European Training and Research in Peritoneal Dialysis Network (EuTRiPD) review the current status of biomarker research in PD and suggest a selection of biomarkers that can be relevant to the care of PD patients and that are directly accessible in PD effluents...
August 8, 2017: Kidney International
https://www.readbyqxmd.com/read/28797205/jialiang-li-and-shuangge-ma-survival-analysis-in-medicine-and-genetics-li-jialiang-and-ma-shuangge-survival-analysis-in-medicine-and-genetics-chapman-hall-crc-biostatistics-series-new-york-2013-xvii-363-pp-hb-isbn-978-1-4398-9311-1-%C3%A2-51
#9
https://www.readbyqxmd.com/read/28795844/sample-size-adjustment-designs-with-time-to-event-outcomes-a-caution
#10
Boris Freidlin, Edward L Korn
BACKGROUND: Sample size adjustment designs, which allow increasing the study sample size based on interim analysis of outcome data from a randomized clinical trial, have been increasingly promoted in the biostatistical literature. Although it is recognized that group sequential designs can be at least as efficient as sample size adjustment designs, many authors argue that a key advantage of these designs is their flexibility; interim sample size adjustment decisions can incorporate information and business interests external to the trial...
August 1, 2017: Clinical Trials: Journal of the Society for Clinical Trials
https://www.readbyqxmd.com/read/28794544/biostatistics-series-module-10-brief-overview-of-multivariate-methods
#11
Avijit Hazra, Nithya Gogtay
Multivariate analysis refers to statistical techniques that simultaneously look at three or more variables in relation to the subjects under investigation with the aim of identifying or clarifying the relationships between them. These techniques have been broadly classified as dependence techniques, which explore the relationship between one or more dependent variables and their independent predictors, and interdependence techniques, that make no such distinction but treat all variables equally in a search for underlying relationships...
July 2017: Indian Journal of Dermatology
https://www.readbyqxmd.com/read/28780001/endocrinology-meets-metabolomics-achievements-pitfalls-and-challenges
#12
REVIEW
Janina Tokarz, Mark Haid, Alexander Cecil, Cornelia Prehn, Anna Artati, Gabriele Möller, Jerzy Adamski
The metabolome, although very dynamic, is sufficiently stable to provide specific quantitative traits related to health and disease. Metabolomics requires balanced use of state-of-the-art study design, chemical analytics, biostatistics, and bioinformatics to deliver meaningful answers to contemporary questions in human disease research. The technology is now frequently employed for biomarker discovery and for elucidating the mechanisms underlying endocrine-related diseases. Metabolomics has also enriched genome-wide association studies (GWAS) in this area by providing functional data...
August 2, 2017: Trends in Endocrinology and Metabolism: TEM
https://www.readbyqxmd.com/read/28751520/validation-of-the-singapore-nomogram-for-outcome-prediction-in-breast-phyllodes-tumours-in-a-large-patient-cohort
#13
Tze Wei Chng, Mihir Gudi, Swee Ho Lim, HuiHua Li, Puay Hoon Tan
AIMS: To validate the Singapore nomogram for outcome prediction in breast phyllodes tumours in a large cohort of Singaporean patients, as previous validation studies were conducted on small numbers of patients. We also investigate the association of fibroadenomas and phyllodes tumours within a subset of our cohort. METHODS: Histological parameters, surgical margin status and clinical follow-up data of 259 women diagnosed with phyllodes tumours were analysed. Patients with concurrent malignant or premalignant disease were excluded from the validation to minimise confounding influences...
July 27, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28732082/osteosarcoma-enters-a-post-genomic-era-with-in-silico-opportunities-generation-of-the-high-dimensional-database-for-facilitating-sarcoma-biology-research-a-report-from-the-children-s-oncology-group-and-the-quadw-foundation
#14
Jason Glover, Tsz-Kwong Man, Donald A Barkauskas, David Hall, Tanya Tello, Mary Beth Sullivan, Richard Gorlick, Katherine Janeway, Holcombe Grier, Ching Lau, Jeffrey A Toretsky, Scott C Borinstein, Chand Khanna, Timothy M Fan
The prospective banking of osteosarcoma tissue samples to promote research endeavors has been realized through the establishment of a nationally centralized biospecimen repository, the Children's Oncology Group (COG) biospecimen bank located at the Biopathology Center (BPC)/Nationwide Children's Hospital in Columbus, Ohio. Although the physical inventory of osteosarcoma biospecimens is substantive (>15,000 sample specimens), the nature of these resources remains exhaustible. Despite judicious allocation of these high-value biospecimens for conducting sarcoma-related research, a deeper understanding of osteosarcoma biology, in particular metastases, remains unrealized...
2017: PloS One
https://www.readbyqxmd.com/read/28729085/-lies-damned-lies-and-statistics-biostatistics-and-prognostication-for-patients
#15
EDITORIAL
Joseph S Alpert
No abstract text is available yet for this article.
July 17, 2017: American Journal of Medicine
https://www.readbyqxmd.com/read/28685497/linear-combinations-come-alive-in-crossover-designs
#16
Jonathan J Shuster
Before learning anything about statistical inference in beginning service courses in biostatistics, students learn how to calculate the mean and variance of linear combinations of random variables. Practical precalculus examples of the importance of these exercises can be helpful for instructors, the target audience of this paper. We shall present applications to the "1-sample" and "2-sample" methods for randomized short-term 2-treatment crossover studies, where patients experience both treatments in random order with a "washout" between the active treatment periods...
July 6, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28679647/technical-stability-and-biological-variability-in-micrornas-from-dried-blood-spots-a-lung-cancer-therapy-monitoring-showcase
#17
Mustafa Kahraman, Thomas Laufer, Christina Backes, Hannah Schrörs, Tobias Fehlmann, Nicole Ludwig, Jochen Kohlhaas, Eckart Meese, Thomas Wehler, Robert Bals, Andreas Keller
BACKGROUND: Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results. METHODS: We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions...
September 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28652472/proteomic-biostatistic-integrated-approach-for-finding-the-underlying-molecular-determinants-of-hypertension-in-human-plasma
#18
Prathibha R Gajjala, Vera Jankowski, Georg Heinze, Grzegorz Bilo, Alberto Zanchetti, Heidi Noels, Elisa Liehn, Paul Perco, Anna Schulz, Christian Delles, Felix Kork, Erik Biessen, Krzysztof Narkiewicz, Kalina Kawecka-Jaszcz, Juergen Floege, Davide Soranna, Walter Zidek, Joachim Jankowski
Despite advancements in lowering blood pressure, the best approach to lower it remains controversial because of the lack of information on the molecular basis of hypertension. We, therefore, performed plasma proteomics of plasma from patients with hypertension to identify molecular determinants detectable in these subjects but not in controls and vice versa. Plasma samples from hypertensive subjects (cases; n=118) and controls (n=85) from the InGenious HyperCare cohort were used for this study and performed mass spectrometric analysis...
August 2017: Hypertension
https://www.readbyqxmd.com/read/28624481/mir-34a-overexpression-predicts-poor-prognostic-outcome-in-colorectal-adenocarcinoma-independently-of-clinicopathological-factors-with-established-prognostic-value
#19
Stamatia-Maria Rapti, Christos K Kontos, Spyridon Christodoulou, Iordanis N Papadopoulos, Andreas Scorilas
OBJECTIVES: MicroRNA-34a (miR-34a) is regulated by TP53 and, in response, downregulates the expression of a gamut of protein-coding genes, including apoptosis regulators, transcription factors, cyclins, and cyclin-dependent kinases. Its upregulation initiates a reprogramming of gene expression and promotes apoptosis. The purpose of this study was the investigation of the potential clinical significance of miR-34a as a molecular prognostic biomarker in colorectal adenocarcinoma using an in-house real-time quantitative PCR (qPCR) methodology...
June 15, 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28616413/the-condition-of-interdisciplinary-communication-among-various-educational-and-research-departments-of-isfahan-university-of-medical-sciences
#20
Elaheh Mazaheri, Ehsan Geraei, Firoozeh Zare-Farashbandi, Ahmad Papi
BACKGROUND: The study aimed to assess interdisciplinary communication among various Educational and Research Departments of Isfahan University of Medical Sciences (IUMS) in clinical medical sciences using social network analysis. MATERIALS AND METHODS: The study was carried out using scientometrics method and interdisciplinary communication network analysis. Interdisciplinary network of 1298 articles in medical sciences published in Journal of Isfahan Medical School was evaluated using macro- and micro-level criteria of network analysis...
2017: Journal of Education and Health Promotion
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