keyword
https://read.qxmd.com/read/37453100/promise-and-perils-of-microrna-discovery-research-working-toward-quality-over-quantity
#41
REVIEW
Emma K McIlwraith, Wenyuan He, Denise D Belsham
Since the first microRNA (miRNA) was described in 1993 in the humble worm Caenorhabditis elegans, the miRNA field has boomed, with more than 100 000 related patents filed and miRNAs now in ongoing clinical trials. Despite an advanced understanding of the biogenesis and action of miRNAs, applied miRNA research faces challenges and irreproducibility due to a lack of standardization. This review provides guidelines regarding miRNA investigation, while focusing on the pitfalls and considerations that are often overlooked in prevailing applied miRNA research...
August 1, 2023: Endocrinology
https://read.qxmd.com/read/37449901/cytocipher-determines-significantly-different-populations-of-cells-in-single-cell-rna-seq-data
#42
JOURNAL ARTICLE
Brad Balderson, Michael Piper, Stefan Thor, Mikael Boden
MOTIVATION: Identification of cell types using single cell RNA-seq (scRNA-seq) is revolutionising the study of multicellular organisms. However, typical scRNA-seq analysis often involves post hoc manual curation to ensure clusters are transcriptionally distinct, which is time-consuming, error-prone, and irreproducible. RESULTS: To overcome these obstacles, we developed Cytocipher, a bioinformatics method and scverse compatible software package that statistically determines significant clusters...
July 14, 2023: Bioinformatics
https://read.qxmd.com/read/37449884/beta-binomial-statistical-model-for-validation-studies-of-analytes-with-a-binary-response
#43
JOURNAL ARTICLE
Robert A LaBudde, Paul Wehling
BACKGROUND: The probability of detection or 'POD' model has had widespread application for statistically analyzing single and multiple collaborator validations studies with binary outcome data for a wide range of analytes over the last decade. OBJECTIVE: The POD model is placed on a firm theoretical foundation, and extended to a more generalized beta-binomial model. METHODS: The POD model is revisited and embedded in the beta-binomial model...
July 14, 2023: Journal of AOAC International
https://read.qxmd.com/read/37417475/a-new-look-at-an-old-classic-implementation-of-a-sers-based-water-hardness-titration
#44
JOURNAL ARTICLE
Ngoc Mai Duong, Angélina Noclain, Victoria E Reichel, Pierre de Cordovez, Jean-Marc Di Meglio, Pascal Hersen, Gaëlle Charron
The routine use of SERS as an analytical technique has been hindered by practical considerations among which the irreproducibility of its signals and the lack of robustness of its calibration. In the present work, we examine a strategy to perform quantitative SERS without the need for calibration. The method reinvests a colorimetric volumetric titration procedure to determine water hardness but involves monitoring the progression of the titration through the SERS signal of a complexometric indicator. Upon reaching the equivalence between the chelating titrant and the metal analytes, the SERS signal abruptly jumps, which conveniently serves as an end-point marker...
July 7, 2023: Analyst
https://read.qxmd.com/read/37413663/practical-strategies-for-robust-and-inexpensive-imaging-of-aqueous-cleared-tissues
#45
JOURNAL ARTICLE
Rebecca M Williams, Jordana C Bloom, Cara M Robertus, Andrew K Recknagel, David Putnam, John C Schimenti, Warren R Zipfel
Lightsheet microscopy offers an ideal method for imaging of large (mm-cm scale) biological tissues rendered transparent via optical clearing protocols. However the diversity of clearing technologies and tissue types, and how these are adapted to the microscope can make tissue mounting complicated and somewhat irreproducible. Tissue preparation for imaging can involve glues and or equilibration in a variety of expensive and/or proprietary formulations. Here we present practical advice for mounting and capping cleared tissues in optical cuvettes for macroscopic imaging, providing a standardized 3D cell that can be imaged routinely and relatively inexpensively...
July 6, 2023: Journal of Microscopy
https://read.qxmd.com/read/37370808/a-weakly-supervised-deep-learning-model-and-human-machine-fusion-for-accurate-grading-of-renal-cell-carcinoma-from-histopathology-slides
#46
JOURNAL ARTICLE
Qingyuan Zheng, Rui Yang, Huazhen Xu, Junjie Fan, Panpan Jiao, Xinmiao Ni, Jingping Yuan, Lei Wang, Zhiyuan Chen, Xiuheng Liu
(1) Background: The Fuhrman grading (FG) system is widely used in the management of clear cell renal cell carcinoma (ccRCC). However, it is affected by observer variability and irreproducibility in clinical practice. We aimed to use a deep learning multi-class model called SSL-CLAM to assist in diagnosing the FG status of ccRCC patients using digitized whole slide images (WSIs). (2) Methods: We recruited 504 eligible ccRCC patients from The Cancer Genome Atlas (TCGA) cohort and obtained 708 hematoxylin and eosin-stained WSIs for the development and internal validation of the SSL-CLAM model...
June 15, 2023: Cancers
https://read.qxmd.com/read/37350016/reproducibility-in-modeling-and-simulation-of-the-knee-academic-industry-and-regulatory-perspectives
#47
REVIEW
Carl W Imhauser, Andrew P Baumann, Xiangyi Cheryl Liu, Jeffrey E Bischoff, Nico Verdonschot, Benjamin J Fregly, Shady S Elmasry, Neda N Abdollahi, Donald R Hume, Nynke B Rooks, Marco T-Y Schneider, William Zaylor, Thor F Besier, Jason P Halloran, Kevin B Shelburne, Ahmet Erdemir
Stakeholders in the modeling and simulation (M&S) community organized a workshop at the 2019 Annual Meeting of the Orthopaedic Research Society (ORS) entitled "Reproducibility in Modeling and Simulation of the Knee: Academic, Industry, and Regulatory Perspectives". The goal was to discuss efforts among these stakeholders to address irreproducibility in M&S focusing on the knee joint. An academic representative from a leading orthopaedic hospital in the United States described a multi-institutional, open effort funded by the National Institutes of Health to assess model reproducibility in computational knee biomechanics...
June 22, 2023: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://read.qxmd.com/read/37345117/biomarker-reproducibility-challenge-a-review-of-non-nucleotide-biomarker-discovery-protocols-from-body-fluids-in-breast-cancer-diagnosis
#48
REVIEW
Fatemeh Safari, Cheka Kehelpannala, Azadeh Safarchi, Amani M Batarseh, Fatemeh Vafaee
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection...
May 16, 2023: Cancers
https://read.qxmd.com/read/37341121/robust-fully-controlled-nanometer-liquid-layers-for-high-resolution-liquid-cell-electron-microscopy
#49
JOURNAL ARTICLE
Tyler S Lott, Ariel A Petruk, Nicolette A Shaw, Natalie Hamada, Carmen M Andrei, Yibo Liu, Juewen Liu, Germán Sciaini
Liquid cell electron microscopy (LCEM) has long suffered from irreproducibility and its inability to confer high-quality images over a wide field of view. LCEM demands the encapsulation of the in-liquid sample between two ultrathin membranes (windows). In the vacuum environment of the electron microscope, the windows bulge, drastically reducing the achievable resolution and the usable viewing region. Herein, we introduce a shape-engineered nanofluidic cell architecture and an air-free drop-casting sample loading technique, which combined, provide robust bulgeless imaging conditions...
June 21, 2023: Lab on a Chip
https://read.qxmd.com/read/37289659/teaching-students-to-r3eason-not-merely-to-solve-problem-sets-the-role-of-philosophy-and-visual-data-communication-in-accessible-data-science-education
#50
JOURNAL ARTICLE
Ilinca I Ciubotariu, Gundula Bosch
Much guidance on statistical training in STEM fields has been focused largely on the undergraduate cohort, with graduate education often being absent from the equation. Training in quantitative methods and reasoning is critical for graduate students in biomedical and science programs to foster reproducible and responsible research practices. We argue that graduate student education should more center around fundamental reasoning and integration skills rather than mainly on listing 1 statistical test method after the other without conveying the bigger context picture or critical argumentation skills that will enable student to improve research integrity through rigorous practice...
June 2023: PLoS Computational Biology
https://read.qxmd.com/read/37189359/sctranssort-transformers-for-intelligent-annotation-of-cell-types-by-gene-embeddings
#51
JOURNAL ARTICLE
Linfang Jiao, Gan Wang, Huanhuan Dai, Xue Li, Shuang Wang, Tao Song
Single-cell transcriptomics is rapidly advancing our understanding of the composition of complex tissues and biological cells, and single-cell RNA sequencing (scRNA-seq) holds great potential for identifying and characterizing the cell composition of complex tissues. Cell type identification by analyzing scRNA-seq data is mostly limited by time-consuming and irreproducible manual annotation. As scRNA-seq technology scales to thousands of cells per experiment, the exponential increase in the number of cell samples makes manual annotation more difficult...
March 28, 2023: Biomolecules
https://read.qxmd.com/read/37116766/highlight-results-don-t-hide-them-enhance-interpretation-reduce-biases-and-improve-reproducibility
#52
JOURNAL ARTICLE
Paul A Taylor, Richard C Reynolds, Vince Calhoun, Javier Gonzalez-Castillo, Daniel A Handwerker, Peter A Bandettini, Amanda F Mejia, Gang Chen
Most neuroimaging studies display results that represent only a tiny fraction of the collected data. While it is conventional to present "only the significant results" to the reader, here we suggest that this practice has several negative consequences for both reproducibility and understanding. This practice hides away most of the results of the dataset and leads to problems of selection bias and irreproducibility, both of which have been recognized as major issues in neuroimaging studies recently. Opaque, all-or-nothing thresholding, even if well-intentioned, places undue influence on arbitrary filter values, hinders clear communication of scientific results, wastes data, is antithetical to good scientific practice, and leads to conceptual inconsistencies...
April 26, 2023: NeuroImage
https://read.qxmd.com/read/37113645/trends-in-subcutaneous-tumour-height-and-impact-on-measurement-accuracy
#53
JOURNAL ARTICLE
Daniel Brough, Hope Amos, Karl Turley, Jake Murkin
Tumour volume is typically calculated using only length and width measurements, using width as a proxy for height in a 1:1 ratio. When tracking tumour growth over time, important morphological information and measurement accuracy is lost by ignoring height, which we show is a unique variable. Lengths, widths, and heights of 9522 subcutaneous tumours in mice were measured using 3D and thermal imaging. The average height:width ratio was found to be 1:3 proving that using width as a proxy for height overestimates tumour volume...
2023: Cancer Informatics
https://read.qxmd.com/read/37091456/the-myth-of-reproducibility-a-review-of-event-tracking-evaluations-on-twitter
#54
REVIEW
Nicholas Mamo, Joel Azzopardi, Colin Layfield
Event tracking literature based on Twitter does not have a state-of-the-art. What it does have is a plethora of manual evaluation methodologies and inventive automatic alternatives: incomparable and irreproducible studies incongruous with the idea of a state-of-the-art. Many researchers blame Twitter's data sharing policy for the lack of common datasets and a universal ground truth-for the lack of reproducibility-but many other issues stem from the conscious decisions of those same researchers. In this paper, we present the most comprehensive review yet on event tracking literature's evaluations on Twitter...
2023: Frontiers in big data
https://read.qxmd.com/read/37033093/addressing-the-environmental-impact-of-science-through-a-more-rigorous-reproducible-and-sustainable-conduct-of-research
#55
JOURNAL ARTICLE
Susan M Meyn, Kathryn A Ramirez-Aguilar, Christopher W Gregory, Sheenah Mische, Andrew W Ott, Katia Sol-Church, Michael Sturges, Douglas J Taatjes
The pervasiveness of irreproducible research remains a thorny problem for the progress of scientific endeavor, spawning an abundance of opinion, investigation, and proposals for improvement. Irreproducible research has negative consequences beyond the obvious impact on achieving new scientific discoveries that can advance healthcare and enable new technologies. The conduct of science is resource intensive, resulting in a large environmental impact from even the smallest research programs. There is value in making explicit connections between the conduct of more rigorous, reproducible science and commitments to environmental sustainability...
December 31, 2022: Journal of Biomolecular Techniques: JBT
https://read.qxmd.com/read/36986779/a-review-of-quantitative-systems-pharmacology-models-of-the-coagulation-cascade-opportunities-for-improved-usability
#56
REVIEW
Douglas Chung, Suruchi Bakshi, Piet H van der Graaf
Despite the numerous therapeutic options to treat bleeding or thrombosis, a comprehensive quantitative mechanistic understanding of the effects of these and potential novel therapies is lacking. Recently, the quality of quantitative systems pharmacology (QSP) models of the coagulation cascade has improved, simulating the interactions between proteases, cofactors, regulators, fibrin, and therapeutic responses under different clinical scenarios. We aim to review the literature on QSP models to assess the unique capabilities and reusability of these models...
March 11, 2023: Pharmaceutics
https://read.qxmd.com/read/36845599/influence-of-the-crystallographic-texture-of-ito-on-the-electrodeposition-of-silver-nanoparticles
#57
JOURNAL ARTICLE
Yorick Bleiji, Mees Dieperink, Imme Schuringa, Hongyu Sun, Esther Alarcon-Llado
The electrochemical control over nucleation and growth of metal nanoparticles on foreign substrates is an active field of research, where the surface properties of the substrate have a key role in nucleation dynamics. Polycrystalline indium tin oxide (ITO) films are highly desired substrates for many optoelectronic applications, for which the only parameter that is often specified is the sheet resistance. As a result, growth on ITO is highly irreproducible. Here, we show that ITO substrates with same technical specifications ( i...
February 21, 2023: RSC Advances
https://read.qxmd.com/read/36812653/full-control-of-solid-state-electrolytes-for-electrostatic-gating
#58
JOURNAL ARTICLE
Chuanwu Cao, Margherita Melegari, Marc Philippi, Daniil Domaretskiy, Nicolas Ubrig, Ignacio Gutiérrez-Lezama, Alberto F Morpurgo
Ionic gating is a powerful technique to realize field-effect transistors (FETs) enabling experiments not possible otherwise. So far, ionic gating has relied on the use of top electrolyte gates, which pose experimental constraints and make device fabrication complex. Promising results obtained recently in FETs based on solid-state electrolytes remain plagued by spurious phenomena of unknown origin, preventing proper transistor operation, and causing limited control and reproducibility. Here we explore a class of solid-state electrolytes for gating (Lithium-ion conducting glass-ceramics, LICGCs), identify the processes responsible for the spurious phenomena and irreproducible behavior, and demonstrate properly functioning transistors exhibiting high density ambipolar operation with gate capacitance of ≈20 - 50 µF/cm2 (depending on the polarity of the accumulated charges)...
February 22, 2023: Advanced Materials
https://read.qxmd.com/read/36769134/from-the-catastrophic-objective-irreproducibility-of-cancer-research-and-unavoidable-failures-of-molecular-targeted-therapies-to-the-sparkling-hope-of-supramolecular-targeted-strategies
#59
REVIEW
Irina Alekseenko, Liya Kondratyeva, Igor Chernov, Eugene Sverdlov
The unprecedented non-reproducibility of the results published in the field of cancer research has recently come under the spotlight. In this short review, we try to highlight some general principles in the organization and evolution of cancerous tumors, which objectively lead to their enormous variability and, consequently, the irreproducibility of the results of their investigation. This heterogeneity is also extremely unfavorable for the effective use of molecularly targeted medicine. Against the seemingly comprehensive background of this heterogeneity, we single out two supramolecular characteristics common to all tumors: the clustered nature of tumor interactions with their microenvironment and the formation of biomolecular condensates with tumor-specific distinctive features...
February 1, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/36671881/ultrasensitive-optical-fingerprinting-of-biorelevant-molecules-by-means-of-sers-mapping-on-nanostructured-metasurfaces
#60
JOURNAL ARTICLE
Elizaveta Kozhina, Sergey Bedin, Alexander Martynov, Stepan Andreev, Alexey Piryazev, Yuri Grigoriev, Yulia Gorbunova, Andrey Naumov
The most relevant technique for portable (on-chip) sensors is Surface Enhanced Raman Scattering (SERS). This strategy crashes in the case of large (biorelevant) molecules and nano-objects, whose SERS spectra are irreproducible for "homeopathic" concentrations. We suggested solving this problem by SERS-mapping. We analyzed the distributions of SERS parameters for relatively "small" (malachite green (MG)) and "large" (phthalocyanine, H2 Pc*) molecules. While fluctuations of spectra for "small" MG were negligible, noticeable distribution of spectra was observed for "large" H2 Pc*...
December 28, 2022: Biosensors
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