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https://www.readbyqxmd.com/read/29445172/rational-cell-culture-optimization-enhances-experimental-reproducibility-in-cancer-cells
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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%C3%A2-k-in-air-for-total-oxidation-time-of-100%C3%A2-h
#7
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
#8
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
https://www.readbyqxmd.com/read/29171034/retrospective-estimation-of-the-electric-and-magnetic-field-exposure-conditions-in-in-vitro-experimental-reports-reveal-considerable-potential-for-uncertainty
#9
Lucas A Portelli, Karsten Falldorf, György Thuróczy, Jan Cuppen
Experiments on cell cultures exposed to extremely low frequency (ELF, 3-300 Hz) magnetic fields are often subject to multiple sources of uncertainty associated with specific electric and magnetic field exposure conditions. Here we systemically quantify these uncertainties based on exposure conditions described in a group of bioelectromagnetic experimental reports for a representative sampling of the existing literature. The resulting uncertainties, stemming from insufficient, ambiguous, or erroneous description, design, implementation, or validation of the experimental methods and systems, were often substantial enough to potentially make any successful reproduction of the original experimental conditions difficult or impossible...
November 24, 2017: Bioelectromagnetics
https://www.readbyqxmd.com/read/29167737/make-researchers-revisit-past-publications-to-improve-reproducibility
#10
Clare Fiala, Eleftherios P Diamandis
Scientific irreproducibility is a major issue that has recently increased attention from publishers, authors, funders and other players in the scientific arena.  Published literature suggests that 50-80% of all science performed is irreproducible.  While various solutions to this problem have been proposed, none of them are quick and/or cheap.  Here, we propose one way of reducing scientific irreproducibility by asking authors to revisit their previous publications and provide a commentary after five years...
2017: F1000Research
https://www.readbyqxmd.com/read/29159012/robust-planning-for-a-patient-treated-in-decubitus-position-with-proton-pencil-beam-scanning-radiotherapy
#11
Shikui Tang, Limin Song, Jared D Sturgeon, Chang Chang
A challenging case was reported for a patient treated in decubitus position with proton pencil beam scanning. A regular robust plan with the consideration of the uncertainties of translational alignment and range accuracy cannot ensure the target coverage as revealed in two verification computed tomography (CT) scans during the first week of the treatment. The irreproducibility of daily alignment and anatomical variations in such a position is mainly due to patient's roll. To mitigate the interfractional effect on the target coverage, a novel robust optimization against the patient's angular setup uncertainties was implemented to improve the plan quality by introducing two artificial CT image sets by rolling the planning CT three degrees in both clockwise and counter-clockwise directions and adding them into robust optimization scenarios, which was shown to be an effective and simple way to mitigate target dose degradation with respect to interfractional variations...
September 20, 2017: Curēus
https://www.readbyqxmd.com/read/29117541/dealing-with-consequences-of-irreproducibility-and-modifying-the-published-literature-retractions-versus-revisions
#12
David J Glass, Jeffrey S Flier
One of the barriers to revising the literature when new data are produced, demonstrating the lack of reproducibility of particular published findings, is the stigma associated with the current tools available, most notably the use of retractions. We suggest an additional tool: revisions, which could be linked to prior manuscripts by the original authors and by others (upon peer review). We hope new approaches such as the ability to revise prior reports will help to keep the literature up-to-date and representative of the most complete understanding of an issue...
November 7, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/29116214/bioinspired-synthesis-of-mesoporous-gold-silica-hybrid-microspheres-as-recyclable-colloidal-sers-substrates
#13
Ho Yeon Son, Kyeong Rak Kim, Jun Bae Lee, Trang Huyen Le Kim, Jihui Jang, Su Ji Kim, Moung Seok Yoon, Jin Woong Kim, Yoon Sung Nam
Noble metal nanostructures have been intensively investigated as active substrates for surface-enhanced Raman spectroscopy (SERS) from visible to near-IR wavelengths. However, metal nanoparticle-based SERS analysis in solutions is very challenging due to uncontrollable and irreproducible colloid aggregation. Here we report the templated synthesis of porous gold-silica hybrid microspheres and their application as reusable colloidal SERS substrates. Mesoporous polymer microspheres are synthesized and used as templates for the synthesis of non-aggregated gold nanoparticles, followed by polydopamine-mediated silicification to fabricate mesoporous gold-silica hybrid microspheres...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29108435/irreproducible-data-problems-and-solutions-for-psychiatry
#14
Brian Dean
No abstract text is available yet for this article.
November 1, 2017: Australian and New Zealand Journal of Psychiatry
https://www.readbyqxmd.com/read/29100752/chelatable-trace-zinc-causes-low-irreproducible-kdac8-activity
#15
Tasha B Toro, Samantha A Edenfield, Brandon J Hylton, Terry J Watt
Acetylation is an important regulatory mechanism in cells, and emphasis is being placed on identifying substrates and small molecule modulators of this post-translational modification. However, the reported in vitro activity of the lysine deacetylase KDAC8 is inconsistent across experimental setups, even with the same substrate, complicating progress in the field. We detected trace levels of zinc, a known inhibitor of KDAC8 when present in excess, even in high-quality buffer reagents, at concentrations that are sufficient to significantly inhibit the enzyme under common reaction conditions...
October 31, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29099758/the-hypothalamic-pituitary-axis-and-autoantibody-related-disorders
#16
REVIEW
Cristina Cocco, Carla Brancia, Giulia Corda, Gian-Luca Ferri
This review summarized different studies reporting the presence of autoantibodies reacting against cells of the pituitary (APAs) and/or hypothalamus (AHAs). Both APAs and AHAs have been revealed through immunofluorescence using different kinds of substrates. Autoantibodies against gonadotropic cells were mainly found in patients affected by cryptorchidism and hypogonadotropic hypogonadism while those against prolactin cells were found in different kinds of patients, the majority without pituitary abnormalities...
November 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29069353/concurrent-lactic-and-volatile-fatty-acid-analysis-of-microbial-fermentation-samples-by-gas-chromatography-with-heat-pre-treatment
#17
Darwin, WipaCharles, Ralf Cord-Ruwisch
Organic acid analysis of fermentation samples can be readily achieved by gas chromatography (GC), which detects volatile organic acids. However, lactic acid, a key fermentation acid is non-volatile and can hence not be quantified by regular GC analysis. However the addition of periodic acid to organic acid samples has been shown to enable lactic acid analysis by GC, as periodic acid oxidizes lactic acid to the volatile acetaldehyde. Direct GC injection of lactic acid standards and periodic acid generated inconsistent and irreproducible peaks, possibly due to incomplete lactic acid oxidation to acetaldehyde...
October 23, 2017: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/29046846/bi-layer-sandwich-film-for-antibacterial-catheters
#18
Gerhard Franz, Florian Schamberger, Hamideh Heidari Zare, Sara Felicitas Bröskamp, Dieter Jocham
Background: Approximately one quarter of all nosocomial infections can be attributed to the urinary tract. The infections are supposed to be mainly caused by implantations of urethral catheters and stents. A new catheter design is introduced with the aim to lower the high number of nosocomial urethral infections. In order to avoid limitations to use, the design is first applied to conventional commercially available balloon catheters. Results: The main feature of the design is a sandwich layer on both sides of the catheter wall, which is composed of a fragmented base layer of silver capped by a thin film of poly(p-xylylene)...
2017: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/29043336/on-verdigris-part-i-synthesis-crystal-structure-solution-and-characterisation-of-the-1-2-0-phase-cu3-ch3coo-2-oh-4
#19
Sebastian Bette, Reinhard K Kremer, Gerhard Eggert, Chiu C Tang, Robert E Dinnebier
Known synthesis approaches for basic copper(ii) acetates, the main components of historic verdrigis pigments were reinvestigated and revealed to be partially irreproducible. A modification of the reaction conditions led to the successful and reproducible synthesis of the 1-2-0 phase (Cu3(CH3COO)2(OH)4 = 1Cu(CH3COO)2·2Cu(OH)2·0H2O). The phase composition was derived from elemental and thermal analysis and confirmed by the crystal structure solution using synchrotron X-ray powder diffraction (XRPD) data. The 1-2-0 phase crystallises in space group Pbca with lattice parameters of a = 20...
November 7, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29031017/how-to-reduce-scientific-irreproducibility-the-5-year-reflection
#20
Clare Fiala, Eleftherios P Diamandis
We discuss in depth six causes of scientific irreproducibility and their ramifications for the clinical sciences: fraud, unfounded papers published by prominent authorities, bias, technical deficiencies, fragmented science and problems with big data. Some proposed methods to combat this problem are briefly described, including an effort to replicate results from some high impact papers and a proposal that authors include detailed preclinical data in papers with supposedly high translational value. We here advocate for a 5-year reflection on papers with seemingly high clinical/translational potential, published alongside the original paper where authors reflect on the quality, reproducibility and impact of their findings...
October 26, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
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