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https://www.readbyqxmd.com/read/27907145/training-to-improve-precision-and-accuracy-in-the-measurement-of-fiber-morphology
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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%)...
September 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27642309/in-vitro-characterization-and-oral-bioavailability-of-organic-solvent-free-solid-dispersions-containing-telmisartan
#13
Yue Cao, Li-Li Shi, Qing-Ri Cao, Mingshi Yang, Jing-Hao Cui
Poorly water-soluble drugs often suffer from limited or irreproducible clinical response due to their low solubility and dissolution rate. In this study, organic solvent-free solid dispersions (OSF-SDs) containing telmisartan (TEL) were prepared using polyvinylpyrrolidone K30 (PVP K30) and polyethylene glycol 6000 (PEG 6000) as hydrophilic polymers, sodium hydroxide (NaOH) as an alkalizer, and poloxamer 188 as a surfactant by a lyophilization method. In-vitro dissolution rate and physicochemical properties of the OSF-SDs were characterized using the USP I basket method, differential scanning calorimetry (DSC), X-ray diffractometry (XRD) and fourier transform-infrared (FT-IR) spectroscopy...
2016: Iranian Journal of Pharmaceutical Research: IJPR
https://www.readbyqxmd.com/read/27637315/specific-detection-of-tetanus-toxoid-using-an-aptamer-based-matrix
#14
Harshvardhan B Modh, Ankan K Bhadra, Kinjal A Patel, Rajeev K Chaudhary, Nishant K Jain, Ipsita Roy
Batch-to-batch variation of therapeutic proteins produced by biological means requires rigorous monitoring at all stages of the production process. A large number of animals are employed for risk assessment of biologicals, which has low ethical and economic acceptability. Research is now focussed on the validation of in vitro and ex vivo tests to replace live challenges. Among in vitro methods, enzyme-linked immunosorbent assay (ELISA) is considered to be the gold standard for estimation of integrity of tetanus toxoid...
November 20, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27628177/development-of-separation-technology-for-the-removal-of-radium-223-from-targeted-thorium-conjugate-formulations-part-i-purification-of-decayed-thorium-227-on-cation-exchange-columns
#15
Janne Olsen Frenvik, Knut Dyrstad, Solveig Kristensen, Olav B Ryan
Targeted Thorium Conjugates (TTCs) are being explored as a potential future platform for specific tumour targeting pharmaceuticals. In TTCs the alpha emitting radionuclide thorium-227 ((227)Th) with a half-life of 18.697 days is labelled to targeting moieties, such as monoclonal antibodies (mAbs). The amount of daughter nuclide radium-223 ((223)Ra, t1/2 = 11.435 days) will increase during manufacture and distribution, and so a technology for purification is required to assure an acceptable level of (223)Ra is administrated to the patient...
September 15, 2016: Drug Development and Industrial Pharmacy
https://www.readbyqxmd.com/read/27604569/coupling-of-strain-stress-and-oxygen-non-stoichiometry-in-thin-film-pr0-1ce0-9o2-%C3%AE
#16
J Sheth, D Chen, J J Kim, W J Bowman, P A Crozier, H L Tuller, S T Misture, S Zdzieszynski, B W Sheldon, S R Bishop
Stress and strain in thin films of Pr0.1Ce0.9O2-δ, supported on yttria stabilized zirconia (YSZ) and sapphire substrates, induced by large deviations from oxygen stoichiometry (δ = 0) were investigated by in situ high temperature X-ray diffraction and wafer curvature studies. The measured stresses and strains were correlated with change in δ, measured in situ using optical transmission spectroscopy of defect centers in the films and compared with prior chemical capacitance studies. The coefficient of chemical expansion and elastic modulus values for the films were found to be 18% less than, and 16% greater than in the bulk, respectively...
September 28, 2016: Nanoscale
https://www.readbyqxmd.com/read/27558212/reproducibility-in-chemical-research
#17
EDITORIAL
Robert G Bergman, Rick L Danheiser
"… To what extent is reproducibility a significant issue in chemical research? How can problems involving irreproducibility be minimized? … Researchers should be aware of the dangers of unconscious investigator bias, all papers should provide adequate experimental detail, and Reviewers have a responsibility to carefully examine papers for adequacy of experimental detail and support for the conclusions …" Read more in the Editorial by Robert G. Bergman and Rick L. Danheiser.
October 4, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27538512/reproducible-detection-of-disease-associated-markers-from-gene-expression-data
#18
Katsuhiro Omae, Osamu Komori, Shinto Eguchi
BACKGROUND: Detection of disease-associated markers plays a crucial role in gene screening for biological studies. Two-sample test statistics, such as the t-statistic, are widely used to rank genes based on gene expression data. However, the resultant gene ranking is often not reproducible among different data sets. Such irreproducibility may be caused by disease heterogeneity. RESULTS: When we divided data into two subsets, we found that the signs of the two t-statistics were often reversed...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27537554/the-impact-of-grape-seed-extract-treatment-on-blood-pressure-changes-a-meta-analysis-of-16-randomized-controlled-trials
#19
Haili Zhang, Shuang Liu, Lan Li, Shisong Liu, Shuqi Liu, Jia Mi, Geng Tian
BACKGROUNDS AND OBJECTIVE: Several clinical trials have shown that grape seed extract can reduce blood pressure, but the results are often irreproducible. We therefore sought to systematically evaluate the impact of grape seed extract treatment on the changes of systolic/diastolic blood pressure (SBP/DBP) by meta-analyzing available randomized controlled trials. METHODS: Trial selection and data extraction were completed independently by 2 investigators. Effect-size estimates were expressed as weighted mean difference (WMD) and 95% confidence interval (CI)...
August 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27485340/membrane-protein-solubilization-and-composition-of-protein-detergent-complexes
#20
Katia Duquesne, Valérie Prima, James N Sturgis
Membrane proteins are typically expressed in heterologous systems with a view to in vitro characterization. A critical step in the preparation of membrane proteins after expression in any system is the solubilization of the protein in aqueous solution, typically using detergents and lipids, to obtain the protein in a form suitable for purification, structural or functional analysis. This process is particularly difficult as the objective is to prepare the protein in an unnatural environment, a protein detergent complex, separating it from its natural lipid partners while causing the minimum destabilization or modification of the structure...
2016: Methods in Molecular Biology
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