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https://www.readbyqxmd.com/read/29666754/empirical-evaluation-of-data-normalization-methods-for-molecular-classification
#1
Huei-Chung Huang, Li-Xuan Qin
Background: Data artifacts due to variations in experimental handling are ubiquitous in microarray studies, and they can lead to biased and irreproducible findings. A popular approach to correct for such artifacts is through post hoc data adjustment such as data normalization. Statistical methods for data normalization have been developed and evaluated primarily for the discovery of individual molecular biomarkers. Their performance has rarely been studied for the development of multi-marker molecular classifiers-an increasingly important application of microarrays in the era of personalized medicine...
2018: PeerJ
https://www.readbyqxmd.com/read/29663671/exposing-the-origins-of-irreproducibility-in-fluorine-nmr-spectroscopy
#2
Antonio Togni, Carl Philipp Rosenau, Benson J Jelier, Alvar D Gossert
Fluorine chemistry has taken a pivotal role in chemical reaction discovery, drug development, and chemical biology. NMR spectroscopy, arguably the most important technique for characterization of fluorinated compounds, is rife with highly inconsistent referencing of fluorine NMR chemical shifts, producing deviations larger than 1 ppm. Herein, we provide unprecedented evidence that both spectrometer design and the current unified scale system underpinning the calibration of heteronuclear NMR spectra has unintentionally led to widespread variation in the standardization of 19F NMR spectral data...
April 16, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29655874/differentiating-clearly-positive-from-indeterminate-results-a-review-of-irreproducible-hiv-1-pcr-positive-samples-from-south-africa-s-early-infant-diagnosis-program-2010-2015
#3
Ahmad Haeri Mazanderani, Faith Moyo, Tendesayi Kufa, Jean Maritz, Gayle G Sherman
We describe the extent of and variables associated with irreproducible HIV-1 PCR positive results within South Africa's Early Infant Diagnosis (EID) program from 2010 to 2015 and propose criteria for differentiating indeterminate from clearly positive results using the COBAS® AmpliPrep/COBAS® TaqMan HIV-1 Qualitative Test version 2.0 (CAP/CTM Qual v2.0). Fourteen percent of specimens with an instrument-positive result that were repeat-tested yielded a negative result for which cycle threshold (Ct) proved to be the only predictive variable...
March 3, 2018: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29643062/a-survey-on-data-reproducibility-and-the-effect-of-publication-process-on-the-ethical-reporting-of-laboratory-research
#4
Delphine R Boulbes, Tracy J Costello, Keith A Baggerly, Fan Fan, Rui Wang, Rajat Bhattacharya, Xiangcang Ye, Lee M Ellis
PURPOSE:  The successful translation of laboratory research into effective therapies is dependent upon the validity of peer-reviewed publications. However, several publications in recent years suggested that published scientific findings could only be reproduced 11-45% of the time. Multiple surveys attempted to elucidate the fundamental causes of data irreproducibility and underscored potential solutions; more robust experimental designs, better statistics, and better mentorship. However, no prior survey has addressed the role of the review and publication process on honest reporting...
April 11, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29608889/benign-and-malignant-scientific-irreproducibility
#5
EDITORIAL
Clare Fiala, Eleftherios P Diamandis
Irreproducibility is a widely recognized problem harming scientific progress. Here, we classify types of scientific irreproducibility based on deleteriousness using a cancer analogy: benign, pre-malignant and malignant. We discuss the difficulties of challenging potentially irreproducible papers, especially in high impact journals and/or by famous authors. We advocate for high impact journals publishing papers with large translation value, to implement mandatory author reflections on the reproducibility, utility and relevance of their work 5 to 10 years after publication...
March 30, 2018: Clinical Biochemistry
https://www.readbyqxmd.com/read/29574894/irreproducible-text-book-knowledge-the-effects-of-color-bands-on-zebra-finch-fitness
#6
Daiping Wang, Wolfgang Forstmeier, Malika Ihle, Mehdi Khadraoui, Sofia Jerónimo, Katrin Martin, Bart Kempenaers
Many fields of science-including behavioral ecology-currently experience a heated debate about the extent to which publication bias against null findings results in a misrepresentative scientific literature. Here, we show a case of an extreme mismatch between strong positive support for an effect in the literature and a failure to detect this effect across multiple attempts at replication. For decades, researchers working with birds have individually marked their study species with colored leg bands. For the zebra finch Taeniopygia guttata, a model organism in behavioral ecology, many studies over the past 35 years have reported effects of bands of certain colors on male or female attractiveness and further on behavior, physiology, life history, and fitness...
March 25, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29560831/spsnet-subpopulation-sensitive-network-based-analysis-of-heterogeneous-gene-expression-data
#7
Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong
BACKGROUND: Transcriptomic datasets often contain undeclared heterogeneity arising from biological variation such as diversity of disease subtypes, treatment subgroups, time-series gene expression, nested experimental conditions, as well as technical variation due to batch effects, platform differences in integrated meta-analyses, etc. However, current analysis approaches are primarily designed to handle comparisons between experimental conditions represented by homogeneous samples, thus precluding the discovery of underlying subphenotypes...
March 19, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29554998/contribution-of-the-breadth-and-depth-of-iacuc-membership-to-experimental-design-as-a-factor-in-research-reproducibility
#8
Swapna Mohan, Robert W Barbee, Susan B Silk
The IACUC comprises the key component of animal research oversight at any institution or facility and thus has the responsibility to review and approve proposed animal activities. As the primary oversight unit that ensures the quality of animal welfare and therefore contributes to overall research quality, the IACUC can support reproducibility in research by ensuring rigorous experimental design, standardization of care and management, and assessment of the validity of research. An IACUC that is constituted as required by the Animal Welfare Act and the PHS Policy incorporates a wide range of expertise...
March 1, 2018: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/29531095/scientific-progress-despite-irreproducibility-a-seeming-paradox
#9
Richard M Shiffrin, Katy Börner, Stephen M Stigler
It appears paradoxical that science is producing outstanding new results and theories at a rapid rate at the same time that researchers are identifying serious problems in the practice of science that cause many reports to be irreproducible and invalid. Certainly, the practice of science needs to be improved, and scientists are now pursuing this goal. However, in this perspective, we argue that this seeming paradox is not new, has always been part of the way science works, and likely will remain so. We first introduce the paradox...
March 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29531032/enhancing-primary-reports-of-randomized-controlled-trials-three-most-common-challenges-and-suggested-solutions
#10
Guowei Li, Meha Bhatt, Mei Wang, Lawrence Mbuagbaw, Zainab Samaan, Lehana Thabane
Evidence from a well-designed randomized controlled trial (RCT) is generally considered to be the gold standard that can inform clinical practice and guide decision-making. However, several deficiencies in the reporting of RCTs have frequently been identified, including incomplete, selective, and biased or inconsistent reporting. Such suboptimal reporting may lead to irreproducible results, substantial waste of resources, impaired study validity, erosion of public trust in science, and a high risk of research misconduct...
March 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29511367/while-it-is-not-deliberate-much-of-today-s-biomedical-research-contains-logical-and-technical-flaws-showing-a-need-for-corrective-action
#11
REVIEW
Yan He, Chengfu Yuan, Lichan Chen, Yanjie Liu, Haiyan Zhou, Ningzhi Xu, Dezhong Joshua Liao
Biomedical research has advanced swiftly in recent decades, largely due to progress in biotechnology. However, this rapid spread of new, and not always-fully understood, technology has also created a lot of false or irreproducible data and artifacts, which sometimes have led to erroneous conclusions. When describing various scientific issues, scientists have developed a habit of saying "on one hand… but on the other hand…", because discrepant data and conclusions have become omnipresent. One reason for this problematic situation is that we are not always thoughtful enough in study design, and sometimes lack enough philosophical contemplation...
2018: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/29490460/lab-on-a-valve-mesofluidic-platform-for-on-chip-handling-of-carbon-coated-titanium-dioxide-nanotubes-in-a-disposable-micro-solid-phase-extraction-mode
#12
María Teresa García-Valverde, Maria Rosende, Rafael Lucena, Soledad Cárdenas, Manuel Miró
Mesofluidic Lab-on-a-Valve (LOV) platforms have been proven suitable to accommodate automatic micro-solid-phase extraction approaches (µSPE) with on-chip handling of micrometer bead materials in a fully disposable mode to prevent sample cross-contamination and pressure drop effects. The efficiency of the extraction process notably depends upon the sorptive capacity of the material because the sorbent mass is usually down to 10 mg in LOV devices. Nanomaterials, capitalizing upon their enhanced surface to volume ratio and diversity of potential chemical moieties, are appealing alternates to microbead sorbents...
March 1, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29445172/rational-cell-culture-optimization-enhances-experimental-reproducibility-in-cancer-cells
#13
Marina Wright Muelas, Fernando Ortega, Rainer Breitling, Claus Bendtsen, Hans V Westerhoff
Optimization of experimental conditions is critical in ensuring robust experimental reproducibility. Through detailed metabolomic analysis we found that cell culture conditions significantly impacted on glutaminase (GLS1) sensitivity resulting in variable sensitivity and irreproducibility in data. Baseline metabolite profiling highlighted that untreated cells underwent significant changes in metabolic status. Both the extracellular levels of glutamine and lactate and the intracellular levels of multiple metabolites changed drastically during the assay...
February 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29410855/modelling-science-trustworthiness-under-publish-or-perish-pressure
#14
David Robert Grimes, Chris T Bauch, John P A Ioannidis
Scientific publication is immensely important to the scientific endeavour. There is, however, concern that rewarding scientists chiefly on publication creates a perverse incentive, allowing careless and fraudulent conduct to thrive, compounded by the predisposition of top-tier journals towards novel, positive findings rather than investigations confirming null hypothesis. This potentially compounds a reproducibility crisis in several fields, and risks undermining science and public trust in scientific findings...
January 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29378288/interleukins-and-their-signaling-pathways-in-the-reactome-biological-pathway-database
#15
Steven Jupe, Keith Ray, Corina Duenas Roca, Thawfeek Varusai, Veronica Shamovsky, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
BACKGROUND: There is a wealth of biological pathway information available in the scientific literature but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that have been dismissed as spurious, or found to be irreproducible, or are contradicted by later results and consequently now considered controversial. Many descriptions and images of pathways are incomplete, stylized representations that assume the reader is an expert, familiar with the established details of the process, which are consequently not fully explained...
January 25, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29351590/characteristics-and-evolution-of-the-ecosystem-of-software-tools-supporting-research-in-molecular-biology
#16
Florencio Pazos, Monica Chagoyen
Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model...
January 16, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29289306/integrated-platform-with-combination-of-on-line-protein-digestion-isotope-dimethyl-labeling-and-multidimensional-peptide-separation-for-high-throughput-proteome-quantification
#17
Shen Zhang, Huiming Yuan, Baofeng Zhao, Lihua Zhang, Yukui Zhang
In recent years, various enzymatic microreactors and on-line enzyme digestion strategies have been widely applied in high throughput proteome analysis. However, the incomplete and irreproducible digestion would introduce some unexpected variations in comparative proteome quantification when the samples are digested and then chemically isotope labeled in different aliquots. To address these problems, we developed an integrated platform for high throughput proteome quantification with combination of on-line low miss-cleavage protein digestion by an ultra-performance immobilized enzymatic reactor, on-line dimethyl labeling onto a C18 precolumn, peptide separation by two-dimensional nano liquid chromatography and MS detection...
February 13, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29248599/how-often-should-we-expect-to-be-wrong-statistical-power-p-values-and-the-expected-prevalence-of-false-discoveries
#18
REVIEW
Michael J Marino
There is a clear perception in the literature that there is a crisis in reproducibility in the biomedical sciences. Many underlying factors contributing to the prevalence of irreproducible results have been highlighted with a focus on poor design and execution of experiments along with the misuse of statistics. While these factors certainly contribute to irreproducibility, relatively little attention outside of the specialized statistical literature has focused on the expected prevalence of false discoveries under idealized circumstances...
December 14, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29188080/oxidation-characteristics-of-porous-nickel-prepared-by-powder-metallurgy-and-cast-nickel-at-1273-k-in-air-for-total-oxidation-time-of-100-h
#19
Lamiaa Z Mohamed, Wafaa A Ghanem, Omayma A El Kady, Mohamed M Lotfy, Hafiz A Ahmed, Fawzi A Elrefaie
The oxidation behavior of two types of inhomogeneous nickel was investigated in air at 1273 K for a total oxidation time of 100 h. The two types were porous sintered-nickel and microstructurally inhomogeneous cast-nickel. The porous-nickel samples were fabricated by compacting Ni powder followed by sintering in vacuum at 1473 K for 2 h. The oxidation kinetics of the samples was determined gravimetrically. The topography and the cross-section microstructure of each oxidized sample were observed using optical and scanning electron microscopy...
November 2017: Journal of Advanced Research
https://www.readbyqxmd.com/read/29182147/rapid-re-identification-of-human-samples-using-portable-dna-sequencing
#20
Sophie Zaaijer, Assaf Gordon, Daniel Speyer, Robert Piccone, Simon Cornelis Groen, Yaniv Erlich
DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited access. Here, we describe a rapid, inexpensive, and portable strategy to robustly re-identify human DNA called 'MinION sketching'. MinION sketching requires as few as 3 min of sequencing and 60-300 random SNPs to re-identify a sample enabling near real-time applications of DNA re-identification. Our method capitalizes on the rapidly growing availability of genomic reference data for cell lines, tissues in biobanks, and individuals...
November 28, 2017: ELife
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