An approach to predict and inhibit Amyloid Beta dimerization pattern in Alzheimer’s disease by Sreekanya Roy, Sima Biswas, Anirban Nandy, Dipanjan Guha, Rakhi Dasgupta, Angshuman Bagchi, Parames Chandra Sil

“…Several hypotheses are in the pipeline to establish the commencement of this disease; however, the amyloid hypothesis is one of the most widely accepted ones. …”
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Decoding the chicken gastrointestinal microbiome by PB. Burrows, F. Godoy-Santos, K. Lawther, A. Richmond, N. Corcionivoschi, SA. Huws

“…Specifically, bacterial 16S ribosomal DNA sequences from GIT samples associated with various breeds, differing in age, GIT sites (caecum, faeces, ileum and jejunum) and geographical location were obtained from the Sequence Read Archive and analysed using the MGnify pipeline. Metataxonomic profiles produced across the 602 datasets illustrated the presence of 3 phyla, 25 families and 30 genera, of which core genera (defined by presence in over 90% of datasets) belonged to Lactobacillus, Faecalibacterium, Butyricicoccus, Eisenbergiella, Subdoligranulum, Oscillibacter, Clostridium & Blautia. …”
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Fully automated segmentation and classification of renal tumors on CT scans via machine learning by Jang Hee Han, Byung Woo Kim, Taek Min Kim, Ji Yeon Ko, Seung Jae Choi, Minho Kang, Sang Youn Kim, Jeong Yeon Cho, Ja Hyeon Ku, Cheol Kwak, Young-Gon Kim, Chang Wook Jeong

“…After segmentation, the entire classification pipeline, including feature extraction and subtype classification, was conducted without any manual intervention. …”
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Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen by Kirsi Aaltonen, Ravi Kant, Marjut Eklund, Mirja Raunio-Saarnisto, Lars Paulin, Olli Vapalahti, Thomas Grönthal, Merja Rantala, Tarja Sironen

“…The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. …”
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A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance by Alexander Mazein, Marcio Luis Acencio, Irina Balaur, Adrien Rougny, Danielle Welter, Anna Niarakis, Anna Niarakis, Diana Ramirez Ardila, Ugur Dogrusoz, Piotr Gawron, Venkata Satagopam, Venkata Satagopam, Wei Gu, Wei Gu, Andreas Kremer, Reinhard Schneider, Reinhard Schneider, Marek Ostaszewski, Marek Ostaszewski

“…In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. …”
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Scalable information extraction from free text electronic health records using large language models by Bowen Gu, Vivian Shao, Ziqian Liao, Valentina Carducci, Santiago Romero Brufau, Jie Yang, Rishi J. Desai

“…Results LLMs outperformed the baseline pattern-matching approach, particularly for explicitly mentioned SDoH, achieving up to 40% higher Accuracymentioned. openchat_3.5 was the best-performing model, surpassing the baseline in overall accuracy across all nine SDoH aspects. The refined pipeline with prompt engineering reduced hallucinations and improved accuracy. …”
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High-Fidelity Depth Map Reconstruction System With RGB-Guided Super Resolution CNN and Cross-Calibrated Chaos LiDAR by Yu-Chun Ding, Chia-Yu Chang, Pei-Rong Li, Chao-Tsung Huang, Yung-Chen Lin, Tsung Chen, Wei-Lun Lin, Cheng-Ting Lee, Fan-Yi Lin, Yuan-Hao Huang

“…First, the misalignment across RGB-depth sensors is addressed using a two-stage calibration pipeline. Second, the lack of large-scale real-world LiDAR datasets is addressed by generating a large-scale synthetic dataset and adopting transfer learning. …”
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Embracing Generative Artificial Intelligence in Clinical Research and Beyond by Henry P. Foote, MD, Chuan Hong, PhD, Mohd Anwar, PhD, Maria Borentain, MD, Kevin Bugin, PhD, Nancy Dreyer, PhD, MPH, Josh Fessel, MD, PhD, Nitender Goyal, MD, Morgan Hanger, MPP, Adrian F. Hernandez, MD, Christoph P. Hornik, MD, PhD, MPH, Jennifer G. Jackman, PhD, MBA, Alistair C. Lindsay, MD, MPH, DPhil, Michael E. Matheny, MD, Kerem Ozer, MD, Jan Seidel, PhD, Norman Stockbridge, MD, PhD, Peter J. Embi, MD, Christopher J. Lindsell, PhD

“…Meeting insights point towards a future where, through collaboration and transparency, generative AI will help to shorten the translational pipeline and increase the inclusivity and equitability of clinical research.…”
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MicroVi: A Cost-Effective Microscopy Solution for Yeast Cell Detection and Count in Wine Value Chain by Ismael Benito-Altamirano, Sergio Moreno, David M. Vaz-Romero, Anna Puig-Pujol, Gemma Roca-Domènech, Joan Canals, Anna Vilà, Joan Daniel Prades, Ángel Diéguez

“…The technology relies on the top of state-of-the-art computer vision pipelines to post-process the images and count the cells. …”
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Complement inhibition targets a rich-club within the neuroinflammatory network after stroke to improve radiographic and functional outcomes by Youssef M. Zohdy, Tomas Garzon-Muvdi, Jonathan A. Grossberg, Daniel L. Barrow, Brian M. Howard, Gustavo Pradilla, Firas H. Kobeissy, Stephen Tomlinson, Ali M. Alawieh

“…This study’s approach, combining graph theory analysis along with in-silico modeling, offers a promising translational pipeline applicable to stroke and other complex diseases.…”
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Exoplanet Occurrence Rate with Age for FGK Stars in Kepler by Maryum Sayeed, Ruth Angus, Travis A. Berger, Yuxi(Lucy) Lu, Jessie L. Christiansen, Daniel Foreman-Mackey, Melissa K. Ness

“…We measure the exoplanet occurrence rate as a function of isochrone and gyrochronology ages using confirmed and candidate planets identified in Q1–17 DR25 Kepler data. We employ Kepler's pipeline detection efficiency to correct for the expected number of planets in each age bin. …”
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Chromosome-level and haplotype-resolved genome assembly of Bougainvillea glabra by Lan Lan, Haiyan Li, Shisong Xu, Yueting Xu, Qingyun Leng, Linbi Zhang, Linqiao Wu, Junmei Yin, Zhiqiang Wu, Junhai Niu

“…By combining the high-confidence different evidence of genome structure annotation pipeline we annotated each haplotype containing ~33,000 predicted genes, of which 86% were functionally annotated by different databases. …”
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Nanopore-based random genomic sampling for intraoperative molecular diagnosis by Francesco E. Emiliani, Abdol Aziz Ould Ismail, Edward G. Hughes, Gregory J. Tsongalis, George J. Zanazzi, Chun-Chieh Lin

“…Conclusions The iSCORED pipeline represents the first method capable of high-resolution CNV detection within the intraoperative timeframe. …”
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Digital twin-based modeling of natural gas leakage and dispersion in urban utility tunnels [version 2; peer review: 2 approved] by Jiansong Wu, Jitao Cai, Ziqi Han, Yanzhu Hu, Ming Fu, Yuefei Li, Xin Wang, Xiaofu Zou

“…Background Unexpected leakage accidents of the natural gas pipeline inside urban utility tunnels can pose great threats to public safety, property, and the environment. …”
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Multivariate description of gait changes in a mouse model of peripheral nerve injury and trauma. by Bilal A Naved, Shuling Han, Kyle M Koss, Mary J Kando, Jiao-Jing Wang, Craig Weiss, Maya G Passman, Jason A Wertheim, Yuan Luo, Zheng J Zhang

“…This study contributes a comprehensive, multivariate characterization pipeline for application in the study of any pathologies in which gait is a quantitative translational outcome metric.…”
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DR Loss-Free Dithering-Based Digital Background Linearity Calibration for SAR-Assisted Multi-Stage ADCs With Digital Input-Interference Cancellation by Lizhen Zhang, Bo Gao, Kun-Woo Park, Kent Edrian Lozada, Raymond Mabilangan, Hyeongjin Kim, Jianhui Wu, Seung-Tak Ryu

“…The simulation results are presented with a 12-bit SAR-assisted two-stage pipeline ADC model. Owing to our proposed calibration, the spurious-free dynamic range (SFDR) increased from 60.1 to 84.8 dB and the signal to noise and distortion ratio (SNDR) improved from 55.4 to 72.5 dB. …”
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Co-modulation of a circular form of PCDH11Y during neuroendocrine differentiation of prostate cancer by Giovanni Pecoraro, Ilaria Leone, Silvia Nuzzo, Santiago Negueruela, Giovanni Smaldone, Lorena Buono

“…To achieve that, we applied CirComPara2 pipeline to publicly available datasets to identify the differently expressed circRNAs in the LNCaP cell lines pre- and post-transdifferentiation. …”
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Expediated modeling of burn events results (EMBER): A screening-level dataset of 2023 ozone fire impacts in the USzenodo by Heather Simon, James Beidler, Kirk R. Baker, Barron H. Henderson, Loren Fox, Chris Misenis, Patrick Campbell, Jeff Vukovich, Norm Possiel, Alison Eyth

“…For emissions, these simulations utilized representative monthly and day-of-week anthropogenic emissions from a recent year and preliminary day-specific 2023 fire emissions derived using BlueSky pipeline. The base model run simulated ozone concentrations across the contiguous US during Apr 11-Sep 29, 2023. …”
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Vehicle Turn Pattern Counting and Short Term Forecasting Using Deep Learning for Urban Traffic Management System by Sundarakrishnan Narayanan, Sohan Varier, Tarun Bhupathi, Manaswini Simhadri Kavali, Mohana, P. Ramakanth Kumar, K. Sreelakshmi

“…A You Only Look Once (YOLOv8) and Auto-ARIMA based pipeline was deployed to address the challenge, which demonstrated robust detection capabilities, with an overall precision of 92.59% for vehicle detection. …”
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Bacterial interactions underpin worsening lung function in cystic fibrosis-associated infections by Damian W. Rivett, Lauren R. Hatfield, Helen Gavillet, Michelle Hardman, Christopher van der Gast

“…To confirm this, pooled samples from studies conducted by our laboratory, sequenced using the same pipeline, were used to assess microbiome-wide associations to lung function. …”
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