Yuan-Yuan Zhang, Qi-Liang Chen, Qiong Wang, Shan-Shan Ding, Shu-Nan Li, Shu-Jiao Chen, Xue-Juan Lin, Can-Dong Li, Tetsuya Asakawa
Acupuncture is an ancient therapeutic method based on the theory of Chinese medicine (CM). Traditional acupuncture has many limitations; it is subjective and relies more on the experience of an acupuncturist, and the efficacy is sometimes irreproducible. In contrast, electroacupuncture (EA) has special characteristics in terms of objectivity and stability, thereby gaining considerable attention. Parameter setting plays a crucial role in EA practice. The current paper summarizes the current situation and limitations of parameter setting in EA practice...
July 20, 2020: Chinese Journal of Integrative Medicine
Emily G Facchine, Richard J Spontak, Orlando J Rojas, Saad A Khan
Cellulosic nanomaterials constitute a topic of growing commercial interest for numerous applications, many of which demand a working knowledge of the rheology of the materials. We demonstrate here that aqueous suspensions of micro/nanofibrillated cellulose (MNFC) exhibit complex shear behavior governed primarily by fibrillar floc dynamics. Regimes corresponding to structure formation, persistence and breakdown are quantitatively differentiated. We assess the recovery of the network structure as a function of the applied breakdown conditions and identify critical conditions that characterize the floc dynamics as isotropic or anisotropic...
July 20, 2020: Biomacromolecules
Chang-Hyuk Yoo, Jae-Kyoung Yu, Yeju Seong, Jun-Kyu Choi
Protein microarrays are miniaturized two-dimensional arrays, incorporating thousands of immobilized proteins, typically printed in minute amounts on functionalized solid substrates, which can be analyzed in a high-throughput fashion. Irreproducibility of the printing techniques adopted, resulting in inconsistently and nonuniformly deposited microscopic spots, nonuniform signal intensities from the printed microspots, and significantly high background noise are some of the critical issues that affect protein analysis using traditional protein microarrays...
July 14, 2020: ACS Omega
Thyago Leal-Calvo, Milton Ozório Moraes
Due to multiple hypothesis testing with often limited sample size, microarrays and other-omics technologies can sometimes produce irreproducible findings. Complementary to better experimental design, reanalysis and integration of gene expression datasets may help overcome reproducibility issues by identifying consistent differentially expressed genes from independent studies. In this work, after a systematic search, nine microarray datasets evaluating host gene expression in leprosy were reanalyzed and the information was integrated to strengthen evidence of differential expression for several genes...
July 13, 2020: Molecular Genetics and Genomics: MGG
Ann Borda, Kathleen Gray, Yuqing Fu
Background: Public engagement in health and biomedical research is being influenced by the paradigm of citizen science. However, conventional health and biomedical research relies on sophisticated research data management tools and methods. Considering these, what contribution can citizen science make in this field of research? How can it follow research protocols and produce reliable results? Objective: The aim of this article is to analyze research data management practices in existing biomedical citizen science studies, so as to provide insights for members of the public and of the research community considering this approach to research...
April 2020: JAMIA Open
John R Erb-Downward, Nicole R Falkowski, Jennifer C D'Souza, Lisa M McCloskey, Roderick A McDonald, Christopher A Brown, Kerby Shedden, Robert P Dickson, Christine M Freeman, Kathleen A Stringer, Betsy Foxman, Gary B Huffnagle, Jeffrey L Curtis, Sara D Adar
The bacterial microbiome of human body sites, previously considered sterile, remains highly controversial because it can be challenging to isolate signal from noise when low-biomass samples are being analyzed. We tested the hypothesis that stochastic sequencing noise, separable from reagent contamination, is generated during sequencing on the Illumina MiSeq platform when DNA input is below a critical threshold. We first purified DNA from serial dilutions of Pseudomonas aeruginosa and from negative controls using three DNA purification kits, quantified input using droplet digital PCR, and then sequenced the 16S rRNA gene in four technical replicates...
June 9, 2020: MBio
Radosław Gocoł, Marcin Malinowski, Jarosław Bis, Damian Hudziak, Joanna Ciosek, Wojciech Wojakowski, Ewa Gaszewska-Żurek, Marek Jasiński, Marek A Deja
BACKGROUND: Over the last years aortic valve repair has evolved from being a random and irreproducible procedure to a standardized technique yielding durable long-term results. AIMS: Long-term outcome of aortic valve repair and aortic valve sparing procedures. METHODS: We analyzed the outcomes of all consecutive patients who underwent aortic valve repair and/or aortic valve sparing root replacement till the end of 2019. We assessed mortality, freedom from reoperation and freedom from at least moderate aortic valve regurgitation...
June 2, 2020: Kardiologia Polska
Tian-Xing Zhang, Zhan-Zhan Zhang, Yu-Xin Yue, Xin-Yue Hu, Fan Huang, Linqi Shi, Yang Liu, Dong-Sheng Guo
Enhanced drug delivery can improve the therapeutic efficacy of drugs and help overcome side effects. However, many reported drug-delivery systems are too complex and irreproducible for practical use. In this work, the design of a hypoxia-responsive molecular container based on calixarene, called CAC4A, which presents a significant advance in practical, hypoxia-targeted drug-delivery, is reported. CAC4A enables a wide variety of clinical drugs to be quantitatively loaded to improve their solubility and stability, as well as enable the administration of reduced doses...
May 27, 2020: Advanced Materials
Hanfei Shen, Tony Liu, Jesse Cui, Piyush Borole, Ari Benjamin, Konrad Kording, David Issadore
Liquid biopsy (LB) technologies continue to improve in sensitivity, specificity, and multiplexing and can measure an ever growing library of disease biomarkers. However, clinical interpretation of the increasingly large sets of data these technologies generate remains a challenge. Machine learning is a popular approach to discover and detect signatures of disease. However, limited machine learning expertise in the LB field has kept the discipline from fully leveraging these tools and risks improper analyses and irreproducible results...
May 18, 2020: Lab on a Chip
Jinyang Zhang, Chao Su, Fergus J M Rogers, Nadim Darwish, Michelle L Coote, Simone Ciampi
Here, we investigate the development and relaxation of static charges on the surface of plastic materials that are first brought in contact, and then macroscopically separated. Experimentalists dealing with the static electrification of insulators are aware of difficulties predictably attaining, and precisely reproducing, a given charging magnitude. Here we have observed for the first time that in homo-systems (e.g. PTFE rubbed against PTFE) charge densities reach the maximum value after a material-specific contact time...
May 14, 2020: Physical Chemistry Chemical Physics: PCCP
Jenna E Gallegos, Neil R Adames, Mark F Rogers, Pavel Kraikivski, Aubrey Ibele, Kevin Nurzynski-Loth, Eric Kudlow, T M Murali, John J Tyson, Jean Peccoud
Over the last 30 years, computational biologists have developed increasingly realistic mathematical models of the regulatory networks controlling the division of eukaryotic cells. These models capture data resulting from two complementary experimental approaches: low-throughput experiments aimed at extensively characterizing the functions of small numbers of genes, and large-scale genetic interaction screens that provide a systems-level perspective on the cell division process. The former is insufficient to capture the interconnectivity of the genetic control network, while the latter is fraught with irreproducibility issues...
May 6, 2020: NPJ Systems Biology and Applications
Lisa-Katrin Schätzle, Ali Hadizadeh Esfahani, Andreas Schuppert
Translational models directly relating drug response specific processes that can be observed in vitro to their in vivo role in cancer patients constitute a crucial part of the development of personalized medication. Unfortunately, current studies often focus on the optimization of isolated model characteristics instead of examining the overall modeling workflow and the interplay of the individual model components. Moreover, they are often limited to specific data sets only. Therefore, they are often confined by the irreproducibility of the results and the non-transferability of the approaches into other contexts...
April 20, 2020: PLoS Computational Biology
Verena M Prade, Thomas Kunzke, Annette Feuchtinger, Maria Rohm, Birgit Luber, Florian Lordick, Achim Buck, Axel Walch
BACKGROUND: Imaging mass spectrometry enables in situ label-free detection of thousands of metabolites from intact tissue samples. However, automated steps for multi-omics analyses and interpretation of histological images have not yet been implemented in mass spectrometry data analysis workflows. The characterization of molecular properties within cellular and histological features is done via time-consuming, non-objective, and irreproducible definitions of regions of interest, which are often accompanied by a loss of spatial resolution due to mass spectra averaging...
February 14, 2020: Molecular Metabolism
Georg Tscheuschner, Timm Schwaar, Michael G Weller
Thousands of antibodies for diagnostic and other analytical purposes are on the market. However, it is often difficult to identify duplicates, reagent changes, and to assign the correct original publications to an antibody. This slows down scientific progress and might even be a cause of irreproducible research and a waste of resources. Recently, activities were started to suggest the sole use of recombinant antibodies in combination with the open communication of their sequence. In this case, such uncertainties should be eliminated...
March 26, 2020: Antibodies
Anatoly L Buchachenko, Alexander A Bukhvostov, Kirill V Ermakov, Dmitry A Kuznetsov
The great diversity of molecular processes in chemistry, physics, and biology exhibits universal property: they are controlled by powerful factor, angular momentum. Conservation of angular momentum (electron spin) is a fundamental and universal principle: all molecular processes are spin selective, they are allowed only for those spin states of reactants whose total spin is identical to that of products. Magnetic catalysis induced by magnetic interactions is a powerful and universal means to overcome spin prohibition and to control physical, chemical and biochemical processes...
March 26, 2020: Progress in Biophysics and Molecular Biology
Habib Rahman, Stephen Ankier
While there has been much discussion of how the scientific establishment's culture can engender research misconduct and scientific irreproducibility, this has been discussed much less frequently with respect to the medical profession. Here the authors posit that a lack of self-criticism, an encouragement of novel scientific research generated by the recruitment policies of the UK Royal Training Colleges along with insufficient training in the sciences are core reasons as to why research misconduct and dishonesty prevail within the medical community...
March 18, 2020: BMC Medical Ethics
Oliver Braganza
Several systematic studies have suggested that a large fraction of published research is not reproducible. One probable reason for low reproducibility is insufficient sample size, resulting in low power and low positive predictive value. It has been suggested that insufficient sample-size choice is driven by a combination of scientific competition and 'positive publication bias'. Here we formalize this intuition in a simple model, in which scientists choose economically rational sample sizes, balancing the cost of experimentation with income from publication...
2020: PloS One
Haiyan Huang, Yi Zou, Huarong Zhang, Xiang Li, Yawei Li, Xusheng Deng, Huaqin Sun, Zheng Guo, Lu Ao
Accurately prognostic evaluation of patients with stage I-II pancreatic ductal adenocarcinoma (PDAC) is of importance to treatment decision and patient management. Most previously reported prognostic signatures were based on risk scores summarized from quantitative expression measurements of signature genes, which are susceptible to experimental batch effects and impractical for clinical applications. Based on the within-sample relative expression orderings of genes, we developed a robust qualitative transcriptional prognostic signature, consisting of 64 gene pairs (64-GPS), to predict the overall survival (OS) of 161 stage I-II PDAC patients in the training dataset who were treated with surgery only...
February 13, 2020: Translational Research: the Journal of Laboratory and Clinical Medicine
Alexander Mendoza, Thomas Asrat, Favian Liu, Pauline Wonnenberg, Alexander G Zestos
Carbon fiber-microelectrodes (CFMEs) have been the standard for neurotransmitter detection for over forty years. However, in recent years, there have been many advances of utilizing alternative nanomaterials for neurotransmitter detection with fast scan cyclic voltammetry (FSCV). Recently, carbon nanotube (CNT) yarns have been developed as the working electrode materials for neurotransmitter sensing capabilities with fast scan cyclic voltammetry. Carbon nanotubes are ideal for neurotransmitter detection because they have higher aspect ratios enabling monoamine adsorption and lower limits of detection, faster electron transfer kinetics, and a resistance to surface fouling...
February 20, 2020: Sensors
Tsuyoshi Miyakawa
A reproducibility crisis is a situation where many scientific studies cannot be reproduced. Inappropriate practices of science, such as HARKing, p-hacking, and selective reporting of positive results, have been suggested as causes of irreproducibility. In this editorial, I propose that a lack of raw data or data fabrication is another possible cause of irreproducibility.As an Editor-in-Chief of Molecular Brain, I have handled 180 manuscripts since early 2017 and have made 41 editorial decisions categorized as "Revise before review," requesting that the authors provide raw data...
February 21, 2020: Molecular Brain
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