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https://www.readbyqxmd.com/read/27882571/a-note-on-statistical-repeatability-and-study-design-for-high-throughput-assays
#1
George Nicholson, Chris Holmes
Characterizing the technical precision of measurements is a necessary stage in the planning of experiments and in the formal sample size calculation for optimal design. Instruments that measure multiple analytes simultaneously, such as in high-throughput assays arising in biomedical research, pose particular challenges from a statistical perspective. The current most popular method for assessing precision of high-throughput assays is by scatterplotting data from technical replicates. Here, we question the statistical rationale of this approach from both an empirical and theoretical perspective, illustrating our discussion using four example data sets from different genomic platforms...
November 24, 2016: Statistics in Medicine
https://www.readbyqxmd.com/read/27870452/sex-hormones-and-genotype-interact-to-influence-psychiatric-disease-treatment-and-behavioral-research
#2
REVIEW
Aarthi R Gobinath, Elena Choleris, Liisa A M Galea
Sex differences exist in the vulnerability, incidence, manifestation, and treatment of numerous neurological and psychiatric diseases. Despite this observation prominent in the literature, little consideration has been given to possible sex differences in outcome in both preclinical and clinical research. This Mini-Review highlights evidence supporting why studying sex differences matter for advances in brain health as well as improving treatment for neurological and psychiatric disease. Additionally, we discuss some statistical and methodological considerations in evaluating sex differences as well as how differences in the physiology of the sexes can contribute to sex difference in disease incidence and manifestation...
January 2, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27869223/insight-into-the-metabolic-mechanism-of-scoparone-on-biomarkers-for-inhibiting-yanghuang-syndrome
#3
Heng Fang, Aihua Zhang, Jingbo Yu, Liang Wang, Chang Liu, Xiaohang Zhou, Hui Sun, Qi Song, Xijun Wang
Scoparone (6,7-dimethoxycoumarin) is the representative ingredient of Yinchenhao (Artemisia capillaris Thunb.) which is a famous Chinese medicinal herb and shows favorable efficacy for all kinds of liver disease, specifically for the treatment of Yanghuang syndrome (YHS). The precise molecular mechanism concerning the action of scoparone on YHS is yet to be fully elucidated. The aim of the present study was to determine the mechanism of scoparone and evaluate its efficacy on metabolite levels. The differential expression of metabolites responsible for the pharmacological effects of scoparone was characterized and the protection effect of scoparone against this disease...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27866835/over-using-chemotherapy-in-the-adjuvant-setting
#4
Giuseppe Curigliano, Carmen Criscitiello, Angela Esposito, Giancarlo Pruneri
Avoidance of unnecessary or ineffective treatment should be one of the main goals in adjuvant breast oncology today. Unfortunately, both patients and doctors hunt for tiny statistical differences in survival curves. This search could not only lead to an oncological approach of unlimited addition that we will not be able to afford, but would also end inevitably in indeterminate overtreatment with substantial risks of unexpected toxic effects eating away whatever progress we might make. "Do not harm" remains the main principle in medicine...
November 17, 2016: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/27853751/quantitative-mri-radiomics-in-the-prediction-of-molecular-classifications-of-breast-cancer-subtypes-in-the-tcga-tcia-data-set
#5
Hui Li, Yitan Zhu, Elizabeth S Burnside, Erich Huang, Karen Drukker, Katherine A Hoadley, Cheng Fan, Suzanne D Conzen, Margarita Zuley, Jose M Net, Elizabeth Sutton, Gary J Whitman, Elizabeth Morris, Charles M Perou, Yuan Ji, Maryellen L Giger
Using quantitative radiomics, we demonstrate that computer-extracted magnetic resonance (MR) image-based tumor phenotypes can be predictive of the molecular classification of invasive breast cancers. Radiomics analysis was performed on 91 MRIs of biopsy-proven invasive breast cancers from National Cancer Institute's multi-institutional TCGA/TCIA. Immunohistochemistry molecular classification was performed including estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and for 84 cases, the molecular subtype (normal-like, luminal A, luminal B, HER2-enriched, and basal-like)...
2016: NPJ Breast Cancer
https://www.readbyqxmd.com/read/27853465/epigenetic-dna-methylation-profiling-with-msre-a-quantitative-ngs-approach-using-a-parkinson-s-disease-test-case
#6
Adam G Marsh, Matthew T Cottrell, Morton F Goldman
Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27830252/findings-from-the-section-on-bioinformatics-and-translational-informatics
#7
H Dauchel, T Lecroq
OBJECTIVES: To summarize excellent current research and propose a selection of best papers published in 2015 in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD: We provide a synopsis of the articles selected for the IMIA Yearbook 2016, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section...
November 10, 2016: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/27826610/identification-of-long-bone-fractures-in-radiology-reports-using-natural-language-processing-to-support-healthcare-quality-improvement
#8
Robert W Grundmeier, Aaron J Masino, T Charles Casper, Jonathan M Dean, Jamie Bell, Rene Enriquez, Sara Deakyne, James M Chamberlain, Elizabeth R Alpern
BACKGROUND: Important information to support healthcare quality improvement is often recorded in free text documents such as radiology reports. Natural language processing (NLP) methods may help extract this information, but these methods have rarely been applied outside the research laboratories where they were developed. OBJECTIVE: To implement and validate NLP tools to identify long bone fractures for pediatric emergency medicine quality improvement. METHODS: Using freely available statistical software packages, we implemented NLP methods to identify long bone fractures from radiology reports...
November 9, 2016: Applied Clinical Informatics
https://www.readbyqxmd.com/read/27825144/genetic-variants-associated-with-gastrointestinal-symptoms-in-fabry-disease
#9
Maria Teresa Di Martino, Francesca Scionti, Simona Sestito, Angela Nicoletti, Mariamena Arbitrio, Pietro Hiram Guzzi, Valentina Talarico, Federica Altomare, Maria Teresa Sanseviero, Giuseppe Agapito, Antonio Pisani, Eleonora Riccio, Osvaldo Borrelli, Daniela Concolino, Licia Pensabene
Gastrointestinal symptoms (GIS) are often among the earliest presenting events in Fabry disease (FD), an X-linked lysosomal disorder caused by the deficiency of α-galactosidase A. Despite recent advances in clinical and molecular characterization of FD, the pathophysiology of the GIS is still poorly understood. To shed light either on differential clinical presentation or on intervariability of GIS in FD, we genotyped 1936 genetic markers across 231 genes that encode for drug-metabolizing enzymes and drug transport proteins in 49 FD patients, using the DMET Plus platform...
November 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27818668/an-approach-based-on-hplc-fingerprint-and-chemometrics-to-quality-consistency-evaluation-of-matricaria-chamomilla-l-commercial-samples
#10
Agnieszka Viapiana, Wiktoria Struck-Lewicka, Pawel Konieczynski, Marek Wesolowski, Roman Kaliszan
Chamomile has been used as an herbal medication since ancient times and is still popular because it contains various bioactive phytochemicals that could provide therapeutic effects. In this study, a simple and reliable HPLC method was developed to evaluate the quality consistency of nineteen chamomile samples through establishing a chromatographic fingerprint, quantification of phenolic compounds and determination of antioxidant activity. For fingerprint analysis, 12 peaks were selected as the common peaks to evaluate the similarities of commercial samples of chamomile obtained from different manufacturers...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27807752/bayesian-computation-methods-for-inferring-regulatory-network-models-using-biomedical-data
#11
Tianhai Tian
The rapid advancement of high-throughput technologies provides huge amounts of information for gene expression and protein activity in the genome-wide scale. The availability of genomics, transcriptomics, proteomics, and metabolomics dataset gives an unprecedented opportunity to study detailed molecular regulations that is very important to precision medicine. However, it is still a significant challenge to design effective and efficient method to infer the network structure and dynamic property of regulatory networks...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27797501/mosaic-a-modular-single-molecule-analysis-interface-for-decoding-multi-state-nanopore-data
#12
Jacob H Forstater, Kyle Briggs, Joseph W F Robertson, Jessica Ettedgui, Olivier Marie-Rose, Canute Vaz, John J Kasianowicz, Vincent Tabard-Cossa, Arvind Balijepalli
Biological and solid-state nanometer-scale pores are the basis for numerous emerging analytical technologies for use in precision medicine. We developed MOSAIC (Modular Single-molecule Analysis Interface), an open source analysis software that improves the accuracy and throughput of nanopore-based measurements. Two key algorithms are implemented: ADEPT, which uses a physical model of the nanopore system to characterize short-lived events that do not reach their steady state current, and CUSUM+, a version of the cumulative sum statistical method optimized for longer events that do...
October 31, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27757023/is-it-appropriate-regarding-patient-preference-to-take-myrtol-standardized-enteric-coated-soft-capsules-after-a-meal-rather-than-at-fasted-state-a-food-drug-pharmacokinetic-interaction-study-in-healthy-chinese-volunteers
#13
Ting-Ting Zhao, Ling-Ling Zhu, Meng Chen, Quan Zhou
BACKGROUND: According to prescribing information for Myrtol standardized enteric-coated soft capsules, the medicine should be taken on an empty stomach. Some patients may experience stomach discomfort after oral administration in fasted state and would prefer to take the medicine after a meal. However, there is no literature addressing the effect of meal on absorption of this drug; therefore, it is desirable to explore the feasibility of taking the capsule after a meal from pharmacokinetic perspective...
2016: Patient Preference and Adherence
https://www.readbyqxmd.com/read/27737817/isolation-characterization-and-quantification-of-an-anxiolytic-constituent-mahanimbine-from-murraya-koenigii-linn-spreng-leaves
#14
Jyoti Dahiya, Jitender Singh, Ashwani Kumar, Anupam Sharma
ETHNOPHARMACOLOGICAL RELEVANCE: Leaves of M. koenigii Linn. Spreng (Rutaceae) have been used as traditional medicine for anxiety disorders. Aim of the study was to isolate antianxiety principle(s) from the leaves of M. koenigii using bioactivity guided approach. MATERIAL AND METHODS: Hydroalcoholic extract of M. koenigii leaves was prepared using soxhlet apparatus, and the same was evaluated for antianxiety activity at 250, 500 and 750mg/kg, po, using Elevated plus-maze (EPM)...
October 10, 2016: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/27719649/precision-medicine-and-a-patient-orientated-approach-is-this-the-future-for-tracking-cardiovascular-disorders
#15
Etheresia Pretorius
The latest statistics from the 2016 heart disease and stroke statistics update shows that cardiovascular disease is the leading global cause of death, currently accounting for more than 17.3 million deaths per year. Type II diabetes is also on the rise with out-of-control numbers. To address these pandemics, we need to treat patients using an individualized patient care approach, but simultaneously gather data to support the precision medicine initiative. Last year the NIH announced the precision medicine initiative to generate novel knowledge regarding diseases, with a near-term focus on cancers, followed by a longer-term aim, applicable to a whole range of health applications and diseases...
October 6, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27688016/probiotics-for-the-prevention-of-pediatric-antibiotic-associated-diarrhea
#16
Shelby R Hayes, Ashley J Vargas
: Goldenberg JZ, Lytvyn L, Steurich J, Parkin P, Mahant S, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea.Cochrane Database Syst Rev2015, Issue 12. Art. No.: CD004827. http://dx.doi.org/10.1002/14651858.CD004827.pub4. BACKGROUND: Antibiotics are frequently prescribed in children. They alter the microbial balance within the gastrointestinal tract, commonly resulting in antibiotic-associated diarrhea (AAD). Probiotics may prevent AAD via restoration of the gut microflora...
November 2016: Explore: the Journal of Science and Healing
https://www.readbyqxmd.com/read/27666372/guidelines-for-large-scale-sequence-based-complex-trait-association-studies-lessons-learned-from-the-nhlbi-exome-sequencing-project
#17
Paul L Auer, Alex P Reiner, Gao Wang, Hyun Min Kang, Goncalo R Abecasis, David Altshuler, Michael J Bamshad, Deborah A Nickerson, Russell P Tracy, Stephen S Rich, Suzanne M Leal
Massively parallel whole-genome sequencing (WGS) data have ushered in a new era in human genetics. These data are now being used to understand the role of rare variants in complex traits and to advance the goals of precision medicine. The technological and computing advances that have enabled us to generate WGS data on thousands of individuals have also outpaced our ability to perform analyses in scientifically and statistically rigorous and thoughtful ways. The past several years have witnessed the application of whole-exome sequencing (WES) to complex traits and diseases...
October 6, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27661007/strategies-for-power-calculations-in-predictive-biomarker-studies-in-survival-data
#18
Dung-Tsa Chen, Po-Yu Huang, Hui-Yi Lin, Eric B Haura, Scott J Antonia, W Douglas Cress, Jhanelle E Gray
PURPOSE: Biomarkers and genomic signatures represent potentially predictive tools for precision medicine. Validation of predictive biomarkers in prospective or retrospective studies requires statistical justification of power and sample size. However, the design of these studies is complex and the statistical methods and associated software are limited, especially in survival data. Herein, we address common statistical design issues relevant to these two types of studies and provide guidance and a general template for analysis...
September 19, 2016: Oncotarget
https://www.readbyqxmd.com/read/27650680/discovery-screening-and-evaluation-of-a-plasma-biomarker-panel-for-subjects-with-psychological-suboptimal-health-state-using-1-h-nmr-based-metabolomics-profiles
#19
Jun-Sheng Tian, Xiao-Tao Xia, Yan-Fei Wu, Lei Zhao, Huan Xiang, Guan-Hua Du, Xiang Zhang, Xue-Mei Qin
Individuals in the state of psychological suboptimal health keep increasing, only scales and questionnaires were used to diagnose in clinic under current conditions, and symptoms of high reliability and accuracy are destitute. Therefore, the noninvasive and precise laboratory diagnostic methods are needed. This study aimed to develop an objective method through screen potential biomarkers or a biomarker panel to facilitate the diagnosis in clinic using plasma metabolomics. Profiles were based on H-nuclear magnetic resonance ((1)H-NMR) metabolomics techniques combing with multivariate statistical analysis...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27647713/an-integrated-chemical-cytometry-method-shining-a-light-on-akt-activity-in-single-cells
#20
Emilie R Mainz, Qunzhao Wang, David S Lawrence, Nancy L Allbritton
Tools to evaluate oncogenic kinase activity in small clinical samples have the power to guide precision medicine in oncology. Existing platforms have demonstrated impressive insights into the activity of protein kinases, but these technologies are unsuitable for the study of kinase behavior in large numbers of primary human cells. To address these limitations, we developed an integrated analysis system that utilizes a light-programmable, cell-permeable reporter deliverable simultaneously to many cells. The reporter's ability to act as a substrate for Akt, a key oncogenic kinase, was masked by a 2-4,5-dimethoxy 2-nitrobenzyl (DMNB) moiety...
October 10, 2016: Angewandte Chemie
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