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https://www.readbyqxmd.com/read/28623075/thioflavin-t-fluorescence-to-analyse-amyloid-formation-kinetics-measurement-frequency-as-a-factor-explaining-irreproducibility
#1
Mathew Sebastiao, Noe Quittot, Steve Bourgault
The most frequent method to monitor amyloid formation relies on the fluorescence of thioflavin T (ThT). The present study reports a novel factor of irreproducibility in ThT kinetic assays performed in microplate. Discrepancies among kinetics of amyloid assembly, performed under quiescent conditions, were associated with the frequency of fluorescence measurement. Evaluating self-assembly of the islet amyloid polypeptide at short intervals hastened its fibrillization. This observation was confirmed by transmission electron microscopy, circular dichroism spectroscopy and 8-anilino-1-naphthalenesulfonic acid fluorescence...
June 13, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28620458/reproducibility2020-progress-and-priorities
#2
REVIEW
Leonard P Freedman, Gautham Venugopalan, Rosann Wisman
The preclinical research process is a cycle of idea generation, experimentation, and reporting of results. The biomedical research community relies on the reproducibility of published discoveries to create new lines of research and to translate research findings into therapeutic applications. Since 2012, when scientists from Amgen reported that they were able to reproduce only 6 of 53 "landmark" preclinical studies, the biomedical research community began discussing the scale of the reproducibility problem and developing initiatives to address critical challenges...
2017: F1000Research
https://www.readbyqxmd.com/read/28613855/distribution-of-catalytic-species-as-an-indicator-to-overcome-reproducibility-problems
#3
Xavier Companyó, Jordi Burés
Irreproducibility is a common issue in catalysis. The ordinary way to minimize it is by ensuring enhanced control over the factors that affect the reaction. When control is insufficient, some parameters can be used as indicators of the reaction performance. Herein we describe the use of the distribution of catalytic species as an indicator to map, track, and fine-tune the performance of catalytic reactions. This indicator is very sensitive and presents a quick response to variations in the reaction conditions...
June 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28596617/metaresearch-for-evaluating-reproducibility-in-ecology-and-evolution
#4
Fiona Fidler, Yung En Chee, Bonnie C Wintle, Mark A Burgman, Michael A McCarthy, Ascelin Gordon
Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of "positive" or "significant" results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices...
March 1, 2017: Bioscience
https://www.readbyqxmd.com/read/28534265/on-strong-inferences-and-irreproducibility-in-reproductive-medicine
#5
EDITORIAL
David F Albertini
No abstract text is available yet for this article.
June 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28515197/models-for-estimating-and-projecting-global-regional-and-national-prevalence-and-disease-burden-of-asthma-protocol-for-a-systematic-review
#6
Mohammad Romel Bhuia, Bright I Nwaru, Christopher J Weir, Aziz Sheikh
INTRODUCTION: Models that have so far been used to estimate and project the prevalence and disease burden of asthma are in most cases inadequately described and irreproducible. We aim systematically to describe and critique the existing models in relation to their strengths, limitations and reproducibility, and to determine the appropriate models for estimating and projecting the prevalence and disease burden of asthma. METHODS: We will search the following electronic databases to identify relevant literature published from 1980 to 2017: Medline, Embase, WHO Library and Information Services and Web of Science Core Collection...
May 17, 2017: BMJ Open
https://www.readbyqxmd.com/read/28480004/creating-multithemed-ecological-regions-for-macroscale-ecology-testing-a-flexible-repeatable-and-accessible-clustering%C3%A2-method
#7
Kendra Spence Cheruvelil, Shuai Yuan, Katherine E Webster, Pang-Ning Tan, Jean-François Lapierre, Sarah M Collins, C Emi Fergus, Caren E Scott, Emily Norton Henry, Patricia A Soranno, Christopher T Filstrup, Tyler Wagner
Understanding broad-scale ecological patterns and processes often involves accounting for regional-scale heterogeneity. A common way to do so is to include ecological regions in sampling schemes and empirical models. However, most existing ecological regions were developed for specific purposes, using a limited set of geospatial features and irreproducible methods. Our study purpose was to: (1) describe a method that takes advantage of recent computational advances and increased availability of regional and global data sets to create customizable and reproducible ecological regions, (2) make this algorithm available for use and modification by others studying different ecosystems, variables of interest, study extents, and macroscale ecology research questions, and (3) demonstrate the power of this approach for the research question-How well do these regions capture regional-scale variation in lake water quality? To achieve our purpose we: (1) used a spatially constrained spectral clustering algorithm that balances geospatial homogeneity and region contiguity to create ecological regions using multiple terrestrial, climatic, and freshwater geospatial data for 17 northeastern U...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28458808/of-faeces-and-sweat-how-much-a-mouse-is-willing-to-run-having-a-hard-time-measuring-spontaneous-physical-activity-in-different-mouse-sub-strains
#8
Dario Coletti, Sergio Adamo, Viviana Moresi
Invited Letter to the Editor. Physical activity has multiple beneficial effects in the physiology and pathology of the organism. In particular, we and other groups have shown that running counteracts cancer cachexia in both humans and rodents. The latter are prone to exercise in wheel-equipped cages even at advanced stages of cachexia. However, when we wanted to replicate the experimental model routinely used at the University of Rome in a different laboratory (i.e. at Paris 6 University), we had to struggle with puzzling results due to unpredicted mouse behavior...
February 24, 2017: European Journal of Translational Myology
https://www.readbyqxmd.com/read/28456268/note-manganin-foil-sensor-for-small-uniaxial-stress
#9
M K Frampton, N McLaughlin, Hu Jin, R J Zieve
We describe a simple manganin foil resistance manometer for uniaxial stress measurements. The manometer functions at low pressures and over a range of temperatures. In this design, no temperature seasoning is necessary although the manometer must be prestressed to the upper end of the desired pressure range. The prestress pressure cannot be increased arbitrarily; irreversibility arising from shear stress limits its range. Attempting larger pressures yields irreproducible resistance measurements.
April 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28455420/widespread-use-of-misidentified-cell-line-kb-hela-incorrect-attribution-and-its-impact-revealed-through-mining-the-scientific-literature
#10
Liwen Vaughan, Wolfgang Glänzel, Christopher Korch, Amanda Capes-Davis
Continuous cell lines are widely used, but can result in invalid, irreproducible research data. Cell line misidentification is a common problem that can be detected by authentication testing; however, misidentified cell lines continue to be used in publications. Here we explore the impact of one misidentified cell line, KB (HeLa), on the scientific literature. We identified 574 articles between 2000 and 2014 that provided an incorrect attribution for KB, in accordance with its false identity as oral epidermoid carcinoma, but only 57 articles that provided a correct attribution for KB, as HeLa or cervical adenocarcinoma...
April 28, 2017: Cancer Research
https://www.readbyqxmd.com/read/28430005/issues-in-current-microrna-target-identification-methods
#11
Hervé Seitz
microRNAs are currently believed to control a large diversity of physiologic processes, through the collective repression of thousands of target genes. Both experimental and computational analyses indeed suggest that each microRNA regulates tens or hundreds of genes. But some observations suggest that the phenotypic consequences of many published miRNA/mRNA interactions are dubious. For example, the reported amplitude of miRNA-guided repression is very small, while biologic processes tend to be robust to small changes in gene expression...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28414712/the-need-for-a-worldwide-consensus-for-cell-line-authentication-experience-implementing-a-mandatory-requirement-at-the-international-journal-of-cancer
#12
Norbert E Fusenig, Amanda Capes-Davis, Franca Bianchini, Sherryl Sundell, Peter Lichter
Cell lines are used in life science research worldwide as biological surrogates. All cell lines are subject to major limitations when used as research tools, including (i) cross-contamination with other cells cultured in the same laboratory environment and (ii) evolution in vitro that renders a given cell line inappropriate as a surrogate for a specific biological hypothesis. There is ample evidence that cross-contamination or phenotypic drift of cells in culture can generate irreproducible or misleading data...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28405182/a-standardized-protocol-for-stereotaxic-intrahippocampal-administration-of-kainic-acid-combined-with-electroencephalographic-seizure-monitoring-in-mice
#13
Pascal Bielefeld, Amanda Sierra, Juan M Encinas, Mirjana Maletic-Savatic, Anne Anderson, Carlos P Fitzsimons
Lack of scientific reproducibility is a growing concern and weak experimental practices may contribute to irreproducibility. Here, we describe an optimized and versatile protocol for stereotaxic intrahippocampal administration of Kainic Acid (KA) in mice with a C57Bl6 background. In this protocol, KA administration is combined with in vivo recording of neuronal activity with wired and wireless setups. Following our protocol, KA administration results in a robust dose-dependent induction of low-level epileptiform activity or Status Epilepticus (SE) and induces previously characterized hallmarks of seizure-associated pathology...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28373349/methodological-rigor-in-preclinical-cardiovascular-studies-targets-to-enhance-reproducibility-and-promote-research-translation
#14
F Daniel Ramirez, Pouya Motazedian, Richard G Jung, Pietro Di Santo, Zachary D MacDonald, Robert Moreland, Trevor Simard, Aisling A Clancy, Juan J Russo, Vivian A Welch, George A Wells, Benjamin Hibbert
RATIONALE: Methodological sources of bias and suboptimal reporting contribute to irreproducibility in preclinical science and may negatively affect research translation. Randomization, blinding, sample size estimation, and considering sex as a biological variable are deemed crucial study design elements to maximize the quality and predictive value of preclinical experiments. OBJECTIVE: To examine the prevalence and temporal patterns of recommended study design element implementation in preclinical cardiovascular research...
June 9, 2017: Circulation Research
https://www.readbyqxmd.com/read/28362402/evaporation-reducing-culture-condition-increases-the-reproducibility-of-multicellular-spheroid-formation-in-microtiter-plates
#15
Viswanath Das, Tomáš Fürst, Soňa Gurská, Petr Džubák, Marián Hajdúch
Tumor models that closely imitate in vivo conditions are becoming increasingly popular in drug discovery and development for the screening of potential anti-cancer drugs. Multicellular tumor spheroids (MCTSes) effectively mimic the physiological conditions of solid tumors, making them excellent in vitro models for lead optimization and target validation. Out of the various techniques available for MCTS culture, the liquid-overlay method on agarose is one of the most inexpensive methods for MCTS generation. However, the reliable transfer of MCTS cultures using liquid-overlay for high-throughput screening may be compromised by a number of limitations, including the coating of microtiter plates (MPs) with agarose and the irreproducibility of uniform MCTS formation across wells...
March 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28360252/state-of-reporting-of-primary-biomedical-research-a-scoping-review-protocol
#16
Guowei Li, Lawrence Mbuagbaw, Zainab Samaan, Yanling Jin, Ikunna Nwosu, Mitchell A H Levine, Jonathan D Adachi, Lehana Thabane
INTRODUCTION: Incomplete or inconsistent reporting remains a major concern in the biomedical literature. Incomplete or inconsistent reporting may yield the published findings unreliable, irreproducible or sometimes misleading. In this study based on evidence from systematic reviews and surveys that have evaluated the reporting issues in primary biomedical studies, we aim to conduct a scoping review with focuses on (1) the state-of-the-art extent of adherence to the emerging reporting guidelines in primary biomedical research, (2) the inconsistency between protocols or registrations and full reports and (3) the disagreement between abstracts and full-text articles...
March 29, 2017: BMJ Open
https://www.readbyqxmd.com/read/28350103/-retracted-nuclear-import-of-prototype-foamy-virus-transactivator-bel1-is-mediated-by-kpna1-kpna6-and-kpna7
#17
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/28343685/evaluation-of-sources-of-irreproducibility-of-retention-indices-under-programmed-temperature-gas-chromatography-conditions
#18
Liejun Wu, Ii Kyu Cho, Yanjie Li, Guangxiang Zhang, Qing X Li
Retention index under the programmed temperature gas chromatography (PTGC) conditions (I(T)) is widely accepted despite of its unsatisfactory reproducibility. Effects of heating rate (rT), stationary liquid film thickness (df), inlet pressure (pi), initial temperature (To) and polarity of stationary phase (sp) on I(T) reproducibility were studied in the present work. We found that excellent reproducibility and regularity of I(T) values are obtainable at conditions of relatively low To and relatively high rT and pi, as well as use of quality thick-film column under an operation in a single-retention behavior region (i...
April 28, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28342878/3d-printing-for-the-design-and-fabrication-of-polymer-based-gradient-scaffolds
#19
REVIEW
Laura G Bracaglia, Brandon T Smith, Emma Watson, Navein Arumugasaamy, Antonios G Mikos, John P Fisher
To accurately mimic the native tissue environment, tissue engineered scaffolds often need to have a highly controlled and varied display of three-dimensional (3D) architecture and geometrical cues. Additive manufacturing in tissue engineering has made possible the development of complex scaffolds that mimic the native tissue architectures. As such, architectural details that were previously unattainable or irreproducible can now be incorporated in an ordered and organized approach, further advancing the structural and chemical cues delivered to cells interacting with the scaffold...
March 22, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28328894/laboratory-environmental-factors-and-pain-behavior-the-relevance-of-unknown-unknowns-to-reproducibility-and-translation
#20
Jeffrey S Mogil
The poor record of basic-to-clinical translation in recent decades has led to speculation that preclinical research is "irreproducible", and this irreproducibility in turn has largely been attributed to deficiencies in reporting and statistical practices. There are, however, a number of other reasonable explanations of both poor translation and difficulties in one laboratory replicating the results of another. This article examines these explanations as they pertain to preclinical pain research. I submit that many instances of apparent irreproducibility are actually attributable to interactions between the phenomena and interventions under study and "latent" environmental factors affecting the rodent subjects...
March 22, 2017: Lab Animal
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