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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
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...
October 18, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
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 14, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
Alexey A Pakhomov, Vladimir I Martynov, Alexander N Orsa, Alena A Bondarenko, Rita V Chertkova, Konstantin A Lukyanov, Alexander G Petrenko, Igor E Deyev
Fluorescent protein Dendra2 is a monomeric GFP-like protein that belongs to the group of Kaede-like photoconvertible fluorescent proteins with irreversible photoconversion from a green- to red-emitting state when exposed to violet-blue light. In an acidic environment, photoconverted Dendra2 turns green due to protonation of the phenolic group of the chromophore with pKa of about 7.5. Thus, photoconverted form of Dendra2 can be potentially used as a ratiometric pH-sensor in the physiological pH range. However, incomplete photoconversion makes ratiometric measurements irreproducible when using standard filter sets...
October 3, 2017: Biochemical and Biophysical Research Communications
Joshua I Warrick
Pathologists have identified many "histologic variants" of bladder cancer (BCA): histologic patterns that differ from conventional urothelial carcinoma (transitional cell carcinoma). Several of these are biologically aggressive, and their identification may aid in clinical decision-making. This article reviews several histologic variants and their value in deciding management of cT1 disease and predicting response to neoadjuvant chemotherapy (NAC). Diagnostic issues are also addressed, such as interobserver variability among pathologists...
October 2017: Journal of the National Comprehensive Cancer Network: JNCCN
Sabrina M Hodgson, Stuart A McNelles, Leonora Abdullahu, Ian A Marozas, Kristi S Anseth, Alex Adronov
A common issue with hydrogel formulations is batch-to-batch irreproducibility, originating from poorly-defined polymer precursors. Here, we report the use of dendritic polymer end-groups to address this issue and maintain reproducibility between batches of poly(ethylene glycol) (PEG) hydrogels. Specifically, we synthesized two end-functionalized PEG chains, one with azide-terminated first- and second-generation dendrons, and the other with strained cyclooctynes. The two complementary azide and alkyne polymers react via the Strain-Promoted Alkyne-Azide Cycoladdition (SPAAC) to produce hydrogels quickly in the absence of additional reagents or catalyst, at low polymer concentrations...
October 2, 2017: Biomacromolecules
Gaorui Bian, Gregory B Gloor, Aihua Gong, Changsheng Jia, Wei Zhang, Jun Hu, Hong Zhang, Yumei Zhang, Zhenqing Zhou, Jiangao Zhang, Jeremy P Burton, Gregor Reid, Yongliang Xiao, Qiang Zeng, Kaiping Yang, Jiangang Li
The microbiota of the aged is variously described as being more or less diverse than that of younger cohorts, but the comparison groups used and the definitions of the aged population differ between experiments. The differences are often described by null hypothesis statistical tests, which are notoriously irreproducible when dealing with large multivariate samples. We collected and examined the gut microbiota of a cross-sectional cohort of more than 1,000 very healthy Chinese individuals who spanned ages from 3 to over 100 years...
September 2017: MSphere
Nathalie Percie du Sert, Ian Bamsey, Simon T Bate, Manuel Berdoy, Robin A Clark, Innes Cuthill, Derek Fry, Natasha A Karp, Malcolm Macleod, Lawrence Moon, S Clare Stanford, Brian Lings
Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, providing automated feedback on the proposed design and generating a graphical summary that aids communication with colleagues, funders, regulatory authorities, and the wider scientific community...
September 2017: PLoS Biology
Michael V Cohen, James M Downey
Scientists and clinicians have been concerned by the lack of a clinically suitable strategy for cardioprotection in patients with acute myocardial infarction despite decades of intensive pre-clinical investigations and a surprising number of clinical trials based on those observations which have uniformly been disappointing. However, it would be a mistake to abandon this search. Rather it would be useful to examine these past efforts and determine reasons for the multiple failures. It appears that earlier clinical trials were often based on results from a single experimental laboratory, thus minimizing the importance of establishing reproducibility in multiple laboratories by multiple scientists and in multiple models...
September 26, 2017: Basic Research in Cardiology
Brahmajee K Nallamothu, Joseph A Hill
Medical journals currently find themselves in the throes of 2 powerful trends: (1) a growing concern for the irreproducibility of scientific reports, and (2) a rising imperative to accelerate dissemination of new knowledge in the digital era. Without question, the individual merit of tackling each issue is readily apparent. Irreproducibility of scientific reports is surprisingly common and contributes to an overall loss of confidence in research by the public and other stakeholders. And who could argue with efforts to leverage new online technologies to distribute information as rapidly and widely as possible?...
September 14, 2017: Circulation
SeungHye Han, Tolani F Olonisakin, John P Pribis, Jill Zupetic, Joo Heung Yoon, Kyle M Holleran, Kwonho Jeong, Nader Shaikh, Doris M Rubio, Janet S Lee
Irreproducibility of preclinical biomedical research has gained recent attention. It is suggested that requiring authors to complete a checklist at the time of manuscript submission would improve the quality and transparency of scientific reporting, and ultimately enhance reproducibility. Whether a checklist enhances quality and transparency in reporting preclinical animal studies, however, has not been empirically studied. Here we searched two highly cited life science journals, one that requires a checklist at submission (Nature) and one that does not (Cell), to identify in vivo animal studies...
2017: PloS One
Shunbo Li, Muling Zeng, Thembaninkosi Gaule, Michael J McPherson, Fiona C Meldrum
Segmented flow microfluidic devices offer an attractive means of studying crystallization processes. However, while they are widely employed for protein crystallization, there are few examples of their use for sparingly soluble compounds due to problems with rapid device fouling and irreproducibility over longer run-times. This article presents a microfluidic device which overcomes these issues, as this is constructed around a novel design of "picoinjector" that facilitates direct injection into flowing droplets...
September 5, 2017: Small
Oh Joo Kweon, Mi-Kyung Lee, Hye Ryoun Kim
CONTEXT: - In the XN series of hematology analyzers (Sysmex, Kobe, Japan), the probability of the presence of abnormal cells is indicated by flags based on Q values. OBJECTIVE: - To evaluate the Q values performance of the Sysmex XN-20 modular analyzer. DESIGN: - The interinstrumental concordance, intrainstrumental precision, and diagnostic accuracy of Q values, with tested flags of "blasts/abnormal lymphocytes," "atypical lymphocytes," and "blasts," were investigated...
August 31, 2017: Archives of Pathology & Laboratory Medicine
Leonid Hanin
One area of biomedical research where the replication crisis is most visible and consequential is clinical trials. Why do outcomes of so many clinical trials contradict each other? Why is the effectiveness of many drugs and other medical interventions so low? Why have prescription medications become the third leading cause of death in the US and Europe after cardiovascular diseases and cancer? In answering these questions, the main culprits identified so far have been various biases and conflicts of interest in planning, execution and analysis of clinical trials as well as reporting their outcomes...
August 22, 2017: BMC Medical Research Methodology
Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu, Yuefeng Lu
BACKGROUND: High-throughput assays are widely used in biological research to select potential targets. One single high-throughput experiment can efficiently study a large number of candidates simultaneously, but is subject to substantial variability. Therefore it is scientifically important to performance quantitative reproducibility analysis to identify reproducible targets with consistent and significant signals across replicate experiments. A few methods exist, but all have limitations...
August 11, 2017: BMC Systems Biology
Peggy Barschke, Patrick Oeckl, Petra Steinacker, Albert Ludolph, Markus Otto
Amyotrophic lateral sclerosis (ALS) is a progressive degenerative motor neuron disease, which usually leads to death within a few years. The diagnosis is mainly based on clinical symptoms and there is a need for ALS-specific biomarkers to make an early and precise diagnosis, for development of disease-modifying drugs and to gain new insights into pathophysiology. Areas covered: In the present review, we summarize studies using mass spectrometric (MS) approaches to identify protein alterations in the cerebrospinal fluid (CSF) of ALS patients...
September 2017: Expert Review of Proteomics
Carlos Guzman, Iván D'Orso
BACKGROUND: Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. RESULTS: We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data...
August 8, 2017: BMC Bioinformatics
Georg Ramer, Florian Reisenbauer, Benedikt Steindl, Wolfgang Tomischko, Bernhard Lendl
Photothermal-induced resonance (PTIR) is a method for optical spectroscopy that allows for infrared (IR) chemical imaging at spatial resolution below the limit of diffraction. By using the mechanical resonance of the cantilever for amplification the technique has been shown to allow sensitivity down to single monolayers. In this work, we discuss the challenges that must be overcome for performing stable resonant PTIR measurements and how imprecise experimental procedures can lead to irreproducible or even erroneous results...
August 2017: Applied Spectroscopy
Jennifer L A Shaw, Jonathan D Judy, Anupama Kumar, Paul Bertsch, Ming-Bo Wang, Jason K Kirby
Chronic exposure to environmental contaminants can induce heritable "transgenerational" modifications to organisms, potentially affecting future ecosystem health and functionality. Incorporating transgenerational epigenetic heritability into risk assessment procedures has been previously suggested. However, a critical review of existing literature yielded numerous studies claiming transgenerational impacts, with little compelling evidence. Therefore, contaminant-induced epigenetic inheritance may be less common than is reported in the literature...
August 14, 2017: Environmental Science & Technology
M Berger, Y Xia, W Aichinger, K Mentl, M Unberath, A Aichert, C Riess, J Hornegger, R Fahrig, A Maier
In cone-beam CT, involuntary patient motion and inaccurate or irreproducible scanner motion substantially degrades image quality. To avoid artifacts this motion needs to be estimated and compensated during image reconstruction. In previous work we showed that Fourier consistency conditions (FCC) can be used in fan-beam CT to estimate motion in the sinogram domain. This work extends the FCC to [Formula: see text] cone-beam CT. We derive an efficient cost function to compensate for [Formula: see text] motion using [Formula: see text] detector translations...
August 21, 2017: Physics in Medicine and Biology
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