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https://www.readbyqxmd.com/read/28098867/-retracted-nuclear-import-of-prototype-foamy-virus-transactivator-bel1-is-mediated-by-kpna1-kpna6-and-kpna7
#1
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
#2
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
#3
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
#4
Stefanie Dehnen, Silke Santner, Jan J Weigand, Sivathmeehan Yogendra
The synthesis of anionic chalcogenidometalate superspheres can be achieved from [Ge4Se10]4- salts and SnCl4 in ionic liquids with (Cn(C1)C1Im)+ cations (n = 4, 6, 8). Its 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 during the reactions, although this may appear counterintuitive. In contrast, and equally counterintuitive, the ionic liquid anion was found to play a crucial role for both the general observability as well as the crystal yield and quality of the products, although they are not part of the product: a minimum content of chloride is needed, while ionic liquids with [BF4]- anions alone do not support the product formation/crystallization...
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27764123/the-importance-of-medical-students-attitudes-regarding-cognitive-competence-for-teaching-applied-statistics-multi-site-study-and-meta-analysis
#15
Natasa M Milic, Srdjan Masic, Jelena Milin-Lazovic, Goran Trajkovic, Zoran Bukumiric, Marko Savic, Nikola V Milic, Andja Cirkovic, Milan Gajic, Mirjana Kostic, Aleksandra Ilic, Dejana Stanisavljevic
BACKGROUND: The scientific community increasingly is recognizing the need to bolster standards of data analysis given the widespread concern that basic mistakes in data analysis are contributing to the irreproducibility of many published research findings. The aim of this study was to investigate students' attitudes towards statistics within a multi-site medical educational context, monitor their changes and impact on student achievement. In addition, we performed a systematic review to better support our future pedagogical decisions in teaching applied statistics to medical students...
2016: PloS One
https://www.readbyqxmd.com/read/27735003/mito-magneto-a-tool-for-nanoparticle-mediated-mitochondria-isolation
#16
Bhabatosh Banik, Brett W Askins, Shanta Dhar
The field of intracellular organelle targeting using nanoparticle (NP) is mushrooming rapidly. Thus, the area of nanotechnology-enabled targeting of mitochondrion, the cellular powerhouse, for diseases characterized by mitochondrial dysfunctions such as cancer, diseases of the central nervous system, and cardiovascular diseases is also growing at a rapid pace. Optimization of a NP's ability to target the mitochondria requires quantification of the particles in this subcellular organelle and isolation of mitochondria from the cells...
December 1, 2016: Nanoscale
https://www.readbyqxmd.com/read/27731798/eco-hab-as-a-fully-automated-and-ecologically-relevant-assessment-of-social-impairments-in-mouse-models-of-autism
#17
Alicja Puścian, Szymon Łęski, Grzegorz Kasprowicz, Maciej Winiarski, Joanna Borowska, Tomasz Nikolaev, Paweł M Boguszewski, Hans-Peter Lipp, Ewelina Knapska
Eco-HAB is an open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. The system closely follows murine ethology. It requires no contact between a human experimenter and tested animals, overcoming the confounding factors that lead to irreproducible assessment of murine social behavior between laboratories. In Eco-HAB, group-housed animals live in a spacious, four-compartment apparatus with shadowed areas and narrow tunnels, resembling natural burrows...
October 12, 2016: ELife
https://www.readbyqxmd.com/read/27727246/data-from-a-pre-publication-independent-replication-initiative-examining-ten-moral-judgement-effects
#18
MULTICENTER STUDY
Warren Tierney, Martin Schweinsberg, Jennifer Jordan, Deanna M Kennedy, Israr Qureshi, S Amy Sommer, Nico Thornley, Nikhil Madan, Michelangelo Vianello, Eli Awtrey, Luke Lei Zhu, Daniel Diermeier, Justin E Heinze, Malavika Srinivasan, David Tannenbaum, Eliza Bivolaru, Jason Dana, Clintin P Davis-Stober, Christilene du Plessis, Quentin F Gronau, Andrew C Hafenbrack, Eko Yi Liao, Alexander Ly, Maarten Marsman, Toshio Murase, Michael Schaerer, Christina M Tworek, Eric-Jan Wagenmakers, Lynn Wong, Tabitha Anderson, Christopher W Bauman, Wendy L Bedwell, Victoria Brescoll, Andrew Canavan, Jesse J Chandler, Erik Cheries, Sapna Cheryan, Felix Cheung, Andrei Cimpian, Mark A Clark, Diana Cordon, Fiery Cushman, Peter H Ditto, Alice Amell, Sarah E Frick, Monica Gamez-Djokic, Rebecca Hofstein Grady, Jesse Graham, Jun Gu, Adam Hahn, Brittany E Hanson, Nicole J Hartwich, Kristie Hein, Yoel Inbar, Lily Jiang, Tehlyr Kellogg, Nicole Legate, Timo P Luoma, Heidi Maibeucher, Peter Meindl, Jennifer Miles, Alexandra Mislin, Daniel C Molden, Matt Motyl, George Newman, Hoai Huong Ngo, Harvey Packham, P Scott Ramsay, Jennifer L Ray, Aaron M Sackett, Anne-Laure Sellier, Tatiana Sokolova, Walter Sowden, Daniel Storage, Xiaomin Sun, Jay J Van Bavel, Anthony N Washburn, Cong Wei, Erik Wetter, Carlos T Wilson, Sophie-Charlotte Darroux, Eric Luis Uhlmann
We present the data from a crowdsourced project seeking to replicate findings in independent laboratories before (rather than after) they are published. In this Pre-Publication Independent Replication (PPIR) initiative, 25 research groups attempted to replicate 10 moral judgment effects from a single laboratory's research pipeline of unpublished findings. The 10 effects were investigated using online/lab surveys containing psychological manipulations (vignettes) followed by questionnaires. Results revealed a mix of reliable, unreliable, and culturally moderated findings...
October 11, 2016: Scientific Data
https://www.readbyqxmd.com/read/27698924/long-non-coding-rnas-in-urologic-malignancies-functional-roles-and-clinical-translation
#19
Jiajia Chen, Zhijun Miao, Boxin Xue, Yuxi Shan, Guobin Weng, Bairong Shen
Early diagnosis and surveillance for metastasis and recurrences are critical issues of urologic cancer. Deregulation of long non-coding RNAs (lncRNAs) has been implicated in urologic malignancies and represents potential markers or therapeutic targets. However, the utility of lncRNA as biomarkers appears to be overstated due to heterogeneous or irreproducible results from different studies. Thus, a critical and cautious review on the biomarker potential of lncRNAs is needed. This review provides an update on new findings of lncRNA-based markers for urologic cancer...
2016: Journal of Cancer
https://www.readbyqxmd.com/read/27683123/the-changing-50-inhibitory-concentration-ic50-of-cisplatin-a-pilot-study-on-the-artifacts-of-the-mtt-assay-and-the-precise-measurement-of-density-dependent-chemoresistance-in-ovarian-cancer
#20
Yifeng He, Qiujing Zhu, Mo Chen, Qihong Huang, Wenjing Wang, Qing Li, Yuting Huang, Wen Di
Inconsistencies in the half-maximal (50%) inhibitory concentration (IC50) data for anticancer chemotherapeutic agents have yielded irreproducible experimental results and thus reciprocally contradictory theories in modern cancer research. The MTT assay is currently the most extensively used method for IC50 measurements. Here, we dissected the critical reasons behind MTT-dependent IC50 inconsistencies. We showed that IC50 errors caused by the technical deficiencies of the MTT assay are large and not adjustable (range: 300-11,000%)...
October 25, 2016: Oncotarget
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