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https://www.readbyqxmd.com/read/28207468/significant-differences-in-the-bone-of-an-isogenic-inbred-versus-nonisogenic-outbred-murine-mandible-a-study-in-rigor-and-reproducibility
#1
Edward G Carey, Sagar S Deshpande, Kevin M Urlaub, Alexander R Zheutlin, Noah S Nelson, Alexis Donneys, Stephen Y Kang, Kathleen K Gallagher, Peter A Felice, Catherine N Tchanque-Fossuo, Steven R Buchman
Inattention to differences between animal strains is a potential cause of irreproducibility of basic science investigations. Accordingly, the authors' laboratory sought to ensure that cross-comparisons of results generated from studies of mandibular physiology utilizing the Sprague Dawley and Lewis rat strains are valid. The authors specifically investigated baseline histomorphometrics, bone mineral density, and biomechanical strength of the unaltered endogenous mandibles of the inbred, isogenic Lewis rat, and the outbred, nonisogenic Sprague Dawley rat to determine if they are indeed equal...
February 15, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28151827/ethics-of-research-for-patients-in-pain
#2
David B Waisel
PURPOSE OF REVIEW: This review describes advances in rising and continuing ethical issues in research in patients in pain. Although some of the issues focus directly on pain research, such as research in neonatal pain management, others focus on widespread ethical issues that are relevant to pain research, such as scientific misconduct, deception, placebo use and genomics. RECENT FINDINGS: Scientific misconduct is more widespread than realized and requires greater awareness of the markers of misconduct like irreproducibility...
February 1, 2017: Current Opinion in Anaesthesiology
https://www.readbyqxmd.com/read/28144217/subtle-scientific-fallacies-undermine-the-validity-of-neuroendocrinological-research-do-not-draw-premature-conclusions-on-the-role-of-female-sex-hormones
#3
Michael P Hengartner
Major scientific flaws such as reporting and publication biases are well documented, even though acknowledgment of their importance appears to be lacking in various psychological and medical fields. Subtle and less obvious biases including selective reviews of the literature and empirically unsupported conclusions and recommendations have received even less attention. Using the literature on the association between transition to menopause, hormones and the onset of depression as a guiding example, I outline how such scientific fallacies undermine the validity of neuroendocrinological research...
2017: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/28123930/irreproducibility-of-published-bioscience-research-diagnosis-pathogenesis-and-therapy
#4
Jeffrey S Flier
No abstract text is available yet for this article.
January 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28121685/predatory-publishing-an-emerging-threat-to-the-medical-literature
#5
H Benjamin Harvey, Debra F Weinstein
The quality of medical literature is increasingly threatened by irresponsible publishing, leading to rising retraction rates, irreproducible results, and a flood of inconsequential publications that distract readers from more meaningful scholarship. "Predatory publishers" offer rapid publication with loose peer review, exploiting a system in which faculty seek longer bibliographies to achieve academic promotion. In this Commentary, the authors highlight some of the evidence that this problem exists and suggest actions to address it...
February 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28117563/patent-law-s-reproducibility-paradox
#6
Jacob S Sherkow
Clinical research faces a reproducibility crisis. Many recent clinical and preclinical studies appear to be irreproducible--their results cannot be verified by outside researchers. This is problematic for not only scientific reasons but also legal ones: patents grounded in irreproducible research appear to fail their constitutional bargain of property rights in exchange for working disclosures of inventions. The culprit is likely patent law’s doctrine of enablement. Although the doctrine requires patents to enable others to make and use their claimed inventions, current difficulties in applying the doctrine hamper or even actively dissuade reproducible data in patents...
January 2017: Duke Law Journal
https://www.readbyqxmd.com/read/28098867/-retracted-nuclear-import-of-prototype-foamy-virus-transactivator-bel1-is-mediated-by-kpna1-kpna6-and-kpna7
#7
Jihui Duan, Zhiqin Tang, Hong Mu, Guojun Zhang
We would like to retract the article entitled "Nuclear import of prototype foamy virus transactivator Bel1 is mediated by KPNA1, KPNA6 and KPNA7" published in International Journal of Molecular Medicine 38: 339-406, 2016. The results presented in Fig. 6 have been demonstrated to be unreproducible, and we cannot provide an explanation for this. Furthermore, we have recently identified that the cell cultures used in our experiments were partly contaminated with Mycoplasma, which could have contributed to the irreproducibility of the results...
January 17, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28088185/igc-an-integrated-analysis-package-of-gene-expression-and-copy-number-alteration
#8
Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang
BACKGROUND: With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28061006/confirmation-of-promise-a-simple-genomics-based-clinical-classifier-for-endometrial-cancer
#9
Aline Talhouk, Melissa K McConechy, Samuel Leung, Winnie Yang, Amy Lum, Janine Senz, Niki Boyd, Judith Pike, Michael Anglesio, Janice S Kwon, Anthony N Karnezis, David G Huntsman, C Blake Gilks, Jessica N McAlpine
BACKGROUND: Classification of endometrial carcinomas (ECs) by morphologic features is irreproducible and imperfectly reflects tumor biology. The authors developed the Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE), a molecular classification system based on The Cancer Genome Atlas genomic subgroups, and sought to confirm both feasibility and prognostic ability in a new, large cohort of ECs. METHODS: Immunohistochemistry (IHC) for the presence or absence of mismatch repair (MMR) proteins (to identify MMR deficiency [MMR-D]), sequencing for polymerase-ɛ (POLE) exonuclease domain mutations (POLE EDMs), and IHC for tumor protein 53 (p53) (wild type vs null/missense mutations; p53 wt and p53 abn, respectively) were performed on 319 new EC samples...
January 6, 2017: Cancer
https://www.readbyqxmd.com/read/28009490/exploring-the-chemical-reaction-space-at-the-formation-of-chalcogenidometalate-superspheres-in-ionic-liquids
#10
Silke Santner, Sivathmeehan Yogendra, Jan J Weigand, Stefanie Dehnen
The synthesis of anionic chalcogenidometalate superspheres can be achieved from [Ge4 Se10 ](4-) salts and SnCl4 in ionic liquids with 1-alkyl-(2,)3-(di)methylimidazolium cations, denoted as (Cn (C1 )C1 Im)(+) (alkyl = butyl for n=4, hexyl for n=6, octyl for n=8). Their formation is apparently independent from the lengths of the Cn chain, and the presence or absence of a second methyl group at the ionic liquid cation (that are exchanged for alkali metal cations in precursor compounds during the reactions), although this may appear counterintuitive...
December 23, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27990689/resetting-the-bar-statistical-significance-in-whole-genome-sequencing-based-association-studies-of-global-populations
#11
Sara L Pulit, Sera A J de With, Paul I W de Bakker
Genome-wide association studies (GWAS) of common disease have been hugely successful in implicating loci that modify disease risk. The bulk of these associations have proven robust and reproducible, in part due to community adoption of statistical criteria for claiming significant genotype-phenotype associations. As the cost of sequencing continues to drop, assembling large samples in global populations is becoming increasingly feasible. Sequencing studies interrogate not only common variants, as was true for genotyping-based GWAS, but variation across the full allele frequency spectrum, yielding many more (independent) statistical tests...
December 18, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27988499/the-effect-of-storage-temperature-fluctuations-on-the-stability-of-biochemical-analytes-in-blood-serum
#12
Helmuth Haslacher, Thomas Szekeres, Marlene Gerner, Elisabeth Ponweiser, Manuela Repl, Oswald F Wagner, Thomas Perkmann
BACKGROUND: Irreproducibility of scientific results constitutes an undesirably onerous economic burden and is in many cases caused by low-quality materials. Therefore, researchers are increasingly devoting their attention to the bioresources they use. In turn, those bioresources are required to validate their preanalytical processes in order to ensure best possible quality. The present study thus aimed to evaluate the impact of repeated temperature fluctuations, as they occur in most research biobanks due to repetitive opening and closing of freezer doors, on the stability of 26 biochemical analytes...
December 19, 2016: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/27988358/feature-selection-in-clinical-proteomics-with-great-power-comes-great-reproducibility
#13
REVIEW
Wei Wang, Andrew C-H Sue, Wilson W B Goh
In clinical proteomics, reproducible feature selection is unattainable given the standard statistical hypothesis-testing framework. This leads to irreproducible signatures with no diagnostic power. Instability stems from high P-value variability (p_var), which is inevitable and insolvable. The impact of p_var can be reduced via power increment, for example increasing sample size and measurement accuracy. However, these are not realistic solutions in practice. Instead, workarounds using existing data such as signal boosting transformation techniques and network-based statistical testing is more practical...
December 15, 2016: Drug Discovery Today
https://www.readbyqxmd.com/read/27959516/interlaboratory-reproducibility-of-a-targeted-metabolomics-platform-for-analysis-of-human-serum-and-plasma
#14
Alexandros P Siskos, Pooja Jain, Werner Römisch-Margl, Mark Bennett, David Achaintre, Yasmin Asad, Luke Marney, Larissa Richardson, Albert Koulman, Julian L Griffin, Florence Raynaud, Augustin Scalbert, Jerzy Adamski, Cornelia Prehn, Hector C Keun
A critical question facing the field of metabolomics is whether data obtained from different centers can be effectively compared and combined. An important aspect of this is the interlaboratory precision (reproducibility) of the analytical protocols used. We analyzed human samples in six laboratories using different instrumentation but a common protocol (the AbsoluteIDQ p180 kit) for the measurement of 189 metabolites via liquid chromatography (LC) or flow injection analysis (FIA) coupled to tandem mass spectrometry (MS/MS)...
December 13, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27907145/training-to-improve-precision-and-accuracy-in-the-measurement-of-fiber-morphology
#15
Nathan A Hotaling, Jun Jeon, Mary Beth Wade, Derek Luong, Xavier-Lewis Palmer, Kapil Bharti, Carl G Simon
An estimated $7.1 billion dollars a year is spent due to irreproducibility in pre-clinical data from errors in data analysis and reporting. Therefore, developing tools to improve measurement comparability is paramount. Recently, an open source tool, DiameterJ, has been deployed for the automated analysis of scanning electron micrographs of fibrous scaffolds designed for tissue engineering applications. DiameterJ performs hundreds to thousands of scaffold fiber diameter measurements from a single micrograph within a few seconds, along with a variety of other scaffold morphological features, which enables a more rigorous and thorough assessment of scaffold properties...
2016: PloS One
https://www.readbyqxmd.com/read/27855167/assessment-of-olfactory-function-in-mapt-associated-neurodegenerative-disease-reveals-odor-identification-irreproducibility-as-a-non-disease-specific-general-characteristic-of-olfactory-dysfunction
#16
Katerina Markopoulou, Bruce A Chase, Piotr Robowski, Audrey Strongosky, Ewa Narożańska, Emilia J Sitek, Mariusz Berdynski, Maria Barcikowska, Matt C Baker, Rosa Rademakers, Jarosław Sławek, Christine Klein, Katja Hückelheim, Meike Kasten, Zbigniew K Wszolek
Olfactory dysfunction is associated with normal aging, multiple neurodegenerative disorders, including Parkinson's disease, Lewy body disease and Alzheimer's disease, and other diseases such as diabetes, sleep apnea and the autoimmune disease myasthenia gravis. The wide spectrum of neurodegenerative disorders associated with olfactory dysfunction suggests different, potentially overlapping, underlying pathophysiologies. Studying olfactory dysfunction in presymptomatic carriers of mutations known to cause familial parkinsonism provides unique opportunities to understand the role of genetic factors, delineate the salient characteristics of the onset of olfactory dysfunction, and understand when it starts relative to motor and cognitive symptoms...
2016: PloS One
https://www.readbyqxmd.com/read/27814676/q-nexus-a-comprehensive-and-efficient-analysis-pipeline-designed-for-chip-nexus
#17
Peter Hansen, Jochen Hecht, Jonas Ibn-Salem, Benjamin S Menkuec, Sebastian Roskosch, Matthias Truss, Peter N Robinson
BACKGROUND: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data...
November 4, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27797406/the-impact-of-fraudulent-and-irreproducible-data-to-the-translational-research-crisis-solutions-and-implementation
#18
Jörg B Schulz, Mark R Cookson, Laura Hausmann
One of the aims of basic neuroscience research is ultimately the development of therapeutics to cure diseases. Funders granting money to research institutions increasingly express interest into how their financial resources are used and look for successful translation in clinical practice. Disappointingly, many findings that started out promising in basic research projects and phase I trials did not live up to the promise of therapeutic efficacy in later phase II or III trials. An inordinately high amount of time and money is thus spent on research that does not always have the required human impact...
October 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/27781023/quality-assurance-in-biobanking-for-pre-clinical-research
#19
REVIEW
Daniel Simeon-Dubach, Steffen M Zeisberger, Simon P Hoerstrup
It is estimated that not less than USD 28 billion are spent each year in the USA alone on irreproducible pre-clinical research, which is not only a fundamental loss of investment and resources but also a strong inhibitor of efficiency for upstream processes regarding the translation towards clinical applications and therapies. The issues and cost of irreproducibility has mainly been published on pre-clinical research. In contrast to pre-clinical research, test material is often being transferred into humans in clinical research...
September 2016: Transfusion Medicine and Hemotherapy
https://www.readbyqxmd.com/read/27773339/liquid-liquid-and-liquid-solid-phase-separation-in-protein-polyelectrolyte-systems
#20
Fatih Comert, Paul L Dubin
The coacervation of systems containing colloids (e.g. proteins or micelles) and polyelectrolytes (notably ionic polysaccharides) is often accompanied by precipitation. This can introduce inhomogeneity, irreversibility and irreproducible kinetics in applications in food science and bioengineering, with negative impact on texture and stability of food products, and unpredictable delivery of active "payloads." The relationship between coacervation and precipitation is obscure in that coacervates might be intermediates in the formation of precipitates, or else the two phenomena might proceed by different but possibly simultaneous mechanisms...
August 10, 2016: Advances in Colloid and Interface Science
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