Measurement quality metrics to improve absolute microbial cell counting by Kirsten Parratt, David Newton, Joy Dunkers, Jennifer Dootz, Monique Hunter, Alshae' Logan-Jackson, Laura Pierce, Sumona Sarkar, Stephanie L. Servetas, Nancy J. Lin

“…In the absence of a ground-truth reference material for cell count, one cannot quantify the accuracy of any cell counting method, which limits method performance assessments and comparisons. …”
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Cell-type annotation with accurate unseen cell-type identification using multiple references. by Yi-Xuan Xiong, Meng-Guo Wang, Luonan Chen, Xiao-Fei Zhang

“…But it relies on the diversity of cell types in the reference, which may not capture all the cell types present in the query data of interest. …”
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Reference-informed evaluation of batch correction for single-cell omics data with overcorrection awareness by Xiaoyue Hu, He Li, Ming Chen, Junbin Qian, Hangjin Jiang

“…Abstract Batch effect correction (BEC) is fundamental to integrate multiple single-cell RNA sequencing datasets, and its success is critical to empower in-depth interrogation for biological insights. …”
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Reference-Free Assessment of Speech Intelligibility Using Bispectrum of an Auditory Neurogram. by Mohammad E Hossain, Wissam A Jassim, Muhammad S A Zilany

“…In this study, a new reference-free speech intelligibility metric is proposed using 2-D neurograms constructed from the output of a computational model of the auditory periphery. …”
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Changes in the Erythrogram Parameters and in the Erythrocyte Sizes of Adult <i>Pelophylax ridibundus</i> (Pallas 1771) (Anura: Ranidae) Inhabiting the Sedimentation Lake of Brikel... by Zhivko Zhelev, Tihomir Vachev, Danail Minchev

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Biomaterial-driven regenerative drug delivery: a vicennial bibliometric landscape by Xin Shen, Haobin Deng, Jing Lin, Jianhua Wang, Yilun Liu, Shikun Mo

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Prognostic score models for acquired resistance to frontline anti-programmed cell death protein 1/programmed death-ligand 1 therapy in metastatic non-small-cell lung cancer by J.C. Murray, Q. Huang, Y.-C. Chen, C. Hu, R.L. DiSantostefano, C. Wong, L. Glatz, E. Curran, L.C. Villaruz, A.N. Hasan, A.J. Schoenfeld

“…Background: Acquired resistance (AR) to immunotherapy following initial response occurs frequently in metastatic non-small-cell lung cancer (mNSCLC). We developed and validated easy-to-apply prognostic score models to identify patients with mNSCLC at greater risk of AR to frontline (1L) anti-programmed cell death protein 1/programmed death-ligand 1 [anti-PD-(L)1] therapy. …”
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Protocol for predicting suppressors of cell-death pathways based on transcriptomic and vulnerability data by Yaron Vinik, Avi Maimon, Sima Lev

“…This protocol enables the identification of several experimentally validated cell death repressors.For complete details on the use and execution of this protocol, please refer to Vinik et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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A cell type and state specific gene regulation network inference method for immune regulatory analysis by Xiong Li, Kun Rao, Chuang Chen, Yuejin Zhang, Juan Zhou, Xu Meng, Yi Hua, Jie Li, Haowen Chen

“…Then, a sparse regression model, combined with reference network information, is used to construct a cell type-specific regulatory network (CSN) for each window. …”
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Protocol for achieving enhanced snRNA-seq data quality using Quality Clustering by Paavo J. Tavi, Johannes Ojanen, Pia Laitinen, Suvi Linna-Kuosmanen

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A machine learning model with crude estimation of property strategy for performance prediction of perovskite solar cells based on process optimization by Dan Li, Ernie Che Mid, Shafriza Nisha Basah, Xiaochun Liu, Jian Tang, Hongyan Cui, Huilong Su, Qianliang Xiao, Shiyin Gong

“…Perovskite solar cells (PSCs) have attracted significant attention due to their high power conversion efficiency (PCE) and affordability. …”
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Intestinal Microbiota Transplant Prior to Allogeneic Stem Cell Transplant (MAST) trial: study protocol for a multicentre, double-blinded, placebo-controlled, phase IIa trial by Julian R Marchesi, Emma Nicholson, Benjamin H Mullish, Renuka Palanicawandar, Graham Wheeler, Francesca Kinsella, Andrew J Innes, Lauren A Roberts, Shian Anim-Burton, Lee Webber, Nicholas A Johnson, Rohma Ghani, Pakhshan Farshi, Anjum B Khan, Panagiotis Kottaridis, Pramila Krishnamurthy, Frances Davies, Jiří Pavlů

“…Secondary outcomes will include tolerability, the dynamics of gut microbiome diversity metrics and taxonomy over all time points assessed, as well as clinical outcomes (including burden of invasive infections, days of fever, admission to intensive care, development of graft-vs-host disease and mortality).Ethics and dissemination This study was approved by a UK Research Ethics Committee (REC reference: 23/NE/0105). …”
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Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset by Mei R. M. Du, Changqing Wang, Charity W. Law, Daniela Amann-Zalcenstein, Casey J. A. Anttila, Ling Ling, Peter F. Hickey, Callum J. Sargeant, Yunshun Chen, Lisa J. Ioannidis, Pradeep Rajasekhar, Raymond K. H. Yip, Kelly L. Rogers, Diana S. Hansen, Rory Bowden, Matthew E. Ritchie

“…Our analysis of replicate samples extends to explore spatially variable gene detection, the outcomes of clustering and cell deconvolution using matched single-cell RNA-sequencing data and publicly available reference data to identify cell types and tissue regions expected in the spleen. …”
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Comparing non-machine learning vs. machine learning methods for Ki67 scoring in gastrointestinal neuroendocrine tumors by Nazanin Mola, Hrafn Weishaupt, Valentin Krasontovitsch, Erlend Hodneland, Sabine Leh

“…Manual scoring by an experienced pathologist was used as the reference standard. The ML compared to the non-ML tool showed better performance metrics (F-score 0.90 vs. 0.74) in detecting the tumor cells. …”
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Detecting Flooded Areas Using Sentinel-1 SAR Imagery by Francisco Alonso-Sarria, Carmen Valdivieso-Ros, Gabriel Molina-Pérez

“…Sentinel-1 SAR metrics are used as predictors and irrigation ponds as training areas. …”
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InP-on-GaAs engineered substrates: A pathway toward low-cost, high-efficiency optoelectronic device fabrication by Carmine Pellegrino, Frank Dimroth, Jens Ohlmann, Henning Helmers, David Lackner

“…The performances are on par with that of reference devices fabricated on a prime InP wafer. …”
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Animal and cellular models of atrial fibrillation: a review by Qiuying Wu, Xize Wu, Teng Feng, Feiyu Chen, Jiaqi Ren, Shan Gao, Bo Wang, Yue Li, Lihong Gong

“…Cellular models commonly use primary cultured cardiomyocytes, the HL-1 cell line, hiPSC-CMs, and H9c2 cells as subjects of study. …”
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Fundus changes in healthy adults after high altitude exposure by Jiaxin Li, Yunzhu Kong, Peiyu Wang, Chen Chen, Juping Liu, Xiaorong Li, Yan Shao

“…Swept-source optical coherence tomography/Swept-source optical coherence tomography angiography (SS-OCT/SS-OCTA) was used to analyze fundus changes in participants before and after plateau exposure. Fundus metrics included best corrected visual acuity (BCVA), the thickness of the retina (ReT), Inner ReT, Outer ReT, nerve fiber layer thickness (RNFLT), and ganglion cell internal plexiform layer thickness (GCIPLT), vascular density (VD), the size of the perfusion area (PA), choroidal vessel volume (CVV), and choroidal vascularity index (CVI) in all quadrants of the macula. …”
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Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis by Alison S. Devonshire, Jordi Morata, Claire Jubin, Rui Pedro Abreu Pereira, Laura Hernandez-Hernandez, Dilek Yener, Eric Cabannes, Steven McGinn, Marc Delepine, Cédric Fund, Raúl Tonda, Simon Heath, Marc Dabad, Javier Gutierrez-Cuesta, Ignacio Sanchez Escudero, Maria Cristina Frias-Lopez, Simon Cowen, Alexandra Whale, Thorsten Voss, Jean-François Deleuze, Ivo Gut, Marta Gut, Carole A. Foy

“…The interlaboratory study described here tested four commonly used methods: Fire Monkey, Nanobind, Puregene and Genomic-tip with a reference cell line containing known chromosomal alterations. …”
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Performance of the BD-FACS Presto for CD4 count and hemoglobin measurement in a district hospital and rural laboratory in Ghana. by Zelda Moran, Jilian A Sacks, Francis Kwabena Frimpong, Atta Boahen Frimpong, Yanis Ben Amor

“…<h4>Introduction</h4>In Ghana, initiation of Antiretroviral Therapy (ART) is recommended for all patients with an HIV diagnosis, regardless of CD4+ T-cell count. However, measurement of CD4 count remains an important metric for identifying patients with advanced HIV disease, and assessing a person's overall immune status, which informs the decision to offer opportunistic infection screening and prophylaxis. …”
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