MultiTax-human: an extensive and high-resolution human-related full-length 16S rRNA reference database and taxonomy by Zhiwei Bao, Bin Zhang, Jianhua Yao, Ming D. Li

“…In this study, we developed an automatic system, named MultiTax pipeline, for generating de novo taxonomy from full-length 16S rRNA sequences using the Genome Taxonomy Database and other existing reference databases. …”
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Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics by Claudio Neidhöfer, Claudio Neidhöfer, Niklas Klein, Niklas Klein, Aylin Yürüktümen, Tessa Hattenhauer, Rebekka Mispelbaum, Christian Bode, Tobias A. W. Holderried, Achim Hoerauf, Marijo Parčina

“…Noscendo GmbH (Duisburg, Germany) has developed the CE/IVD pipeline DISQVER for clinical metagenomics testing based on cell-free DNA (cfDNA) from blood samples to address this issue.MethodsWe conducted a retrospective study to evaluate the diagnostic utility of this methodological setup in improving treatment decisions since it was introduced into our clinical setting. …”
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Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals by Dimitrios V. Vavoulis, Anthony Cutts, Nishita Thota, Jordan Brown, Robert Sugar, Antonio Rueda, Arman Ardalan, Kieran Howard, Flavia Matos Santo, Thippesh Sannasiddappa, Bronwen Miller, Stephen Ash, Yibin Liu, Chun-Xiao Song, Brian D. Nicholson, Helene Dreau, Carolyn Tregidgo, Anna Schuh

“…Additionally, we successfully track tumour burden and ctDNA shedding from precancerous lesions post-treatment without requiring matched tumour biopsies. This pipeline is ready for further clinical evaluation to extend cancer screening and improve patient triage and monitoring.…”
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Methionine-driven methylation modification overcomes plasmid-mediated high-level tigecycline resistance by Dan Fang, Tianqi Xu, Fulei Li, Yue Sun, Jingyi Sun, Yanqing Yin, Haijie Zhang, Zhiqiang Wang, Yuan Liu

“…Novel antimicrobial strategies not limited to new antibiotics in pharmaceutical pipeline are urgently needed. Herein, we reveal the metabolic disparities between tet(X)-negative and -positive E. coli, including distinct energy demand patterns under tigecycline exposure. …”
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Deep R-gene discovery in HLB resistant wild Australian limes uncovers evolutionary features and potentially important loci for hybrid breeding by Jianyang Liu, Khushwant Singh, Matthew Huff, Christopher Gottschalk, Michael Do, Margaret Staton, Manjunath L. Keremane, Robert Krueger, Chandrika Ramadugu, Chris Dardick

“…Our results indicate up to 70% of the R-genes were identified in the unannotated regions in the original genome annotation of each species, owing to the use of a R-gene specific pipeline. Surprisingly, the two cultivated species harbored 15.8 to 104% more R-genes than the Australian limes. …”
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Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci by Natasha Berthold, Silvana Gaudieri, Sean Hood, Monika Tschochner, Allison L. Miller, Jennifer Jordan, Laura M. Thornton, Cynthia M. Bulik, Patrick Anthony Akkari, Martin A. Kennedy

“…To test this hypothesis, we implemented a novel approach with targeted nanopore sequencing (Oxford Nanopore Technologies) for 200 kb regions centred on each of the eight AN-associated loci in 10 AN case samples. Our bioinformatics pipeline entailed base-calling and alignment with Dorado and minimap2 software, followed by variant calling with four separate tools, Sniffles2, Clair3, Straglr, and NanoVar. …”
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A Population Analysis of 20 Exoplanets Observed from Optical to Near-infrared Wavelengths with the Hubble Space Telescope: Evidence for Widespread Stellar Contamination by Arianna Saba, Alexandra Thompson, Kai Hou Yip, Sushuang Ma, Angelos Tsiaras, Ahmed Faris Al-Refaie, Giovanna Tinetti

“…To obtain spectral information from the near-ultraviolet to the near-infrared, we reanalyzed 16 WFC3 and over 50 STIS archival data sets with our dedicated HST pipeline. We also include 24 WFC3 data sets previously reduced with the same software. …”
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A morphometric signature to identify ductal carcinoma in situ with a low risk of progression by Marcelo Sobral-Leite, Simon P. Castillo, Shiva Vonk, Hendrik A. Messal, Xenia Melillo, Noomie Lam, Brandi de Bruijn, Yeman B. Hagos, Myrna van den Bos, Joyce Sanders, Mathilde Almekinders, Lindy L. Visser, Emma J. Groen, Petra Kristel, Caner Ercan, Leyla Azarang, Jacco van Rheenen, E. Shelley Hwang, Yinyin Yuan, Grand Challenge PRECISION Consortium, Renee Menezes, Esther H. Lips, Jelle Wesseling

“…To identify features associated with progression, we developed an artificial intelligence-based DCIS morphometric analysis pipeline (AIDmap) on hematoxylin-eosin-stained (H&E) tissue sections. …”
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Experimental Study on the Influence of Buried Geothermal Pipes on the Temperature Field of Concrete Roads by Yan Tan, Jun Song, Zhi Chen, Henglin Xiao

“…The model experiments are carried out under the conditions of 0.8 m/s, 0.85 m/s, and 0.9 m/s of pipeline flow velocity, 15 cm and 25 cm of buried pipe depth, and 10 cm and 15 cm of pipe space. …”
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Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain by Abimel Salazar, Navin Sreng, Chanthol Peng, Yehzi Fu, Erin M. Nawrocki, Taejung Chung, Jessie Vipham, Edward G. Dudley, Jasna Kovac

“…Isolates’ relatedness was assessed based on high-quality single nucleotide polymorphisms (hqSNPs) identified within each serotype using the CFSAN SNP pipeline. Among 29 detected serotypes, Paratyphi B var. …”
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Teknik Identifikasi Fitur Berdasarkan Kalimat Pernyataan Kebutuhan dalam Konteks Pengembangan Software Product Line by M Syauqi Haris, Tri Astoto Kurniawan

“…In this research, 4 (four) dependency parser rules are proposed, which is one of the pipelines in NLP. The success rate of the method in this study is between 65% to 88% for the 5 groups of sentences that were tested. …”
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MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data by Katarzyna Arturi, Eliza J. Harris, Lilian Gasser, Beate I. Escher, Georg Braun, Robin Bosshard, Juliane Hollender

“…Abstract MLinvitroTox is an automated Python pipeline developed for high-throughput hazard-driven prioritization of toxicologically relevant signals detected in complex environmental samples through high-resolution tandem mass spectrometry (HRMS/MS). …”
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Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample by Catherine Prattico, Emmanuel Gonzalez, Lharbi Dridi, Shiva Jazestani, Kristin E. Low, D. Wade Abbott, Corinne F. Maurice, Bastien Castagner

“…Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. …”
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Protein identification using Cryo-EM and artificial intelligence guides improved sample purification by Kenneth D. Carr, Dane Evan D. Zambrano, Connor Weidle, Alex Goodson, Helen E. Eisenach, Harley Pyles, Alexis Courbet, Neil P. King, Andrew J. Borst

“…Here, we used an automated structure-to-sequence pipeline to first identify an unknown co-purifying protein found in several purified designed protein samples. …”
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A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission by Benjamin Sobkowiak, Patrick Cudahy, Melanie H. Chitwood, Taane G. Clark, Caroline Colijn, Louis Grandjean, Katharine S. Walter, Valeriu Crudu, Ted Cohen

“…Building upon our previous tool, MixInfect, we increased the accuracy of classifying in vitro mixed samples through multiple improvements to the bioinformatic pipeline. Major and minor proportion constituent strains were reconstructed using three approaches and assessed by comparing the estimated sequence to the known constituent strain sequence. …”
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Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC by William Boulton, Asaf Salamov, Igor V. Grigoriev, Sara Calhoun, Kurt LaButti, Robert Riley, Kerrie Barry, Allison A. Fong, Clara J. M. Hoppe, Katja Metfies, Kersten Oetjen, Sarah Lena Eggers, Oliver Müller, Jessie Gardner, Mats A. Granskog, Anders Torstensson, Marc Oggier, Aud Larsen, Gunnar Bratbak, Andrew Toseland, Richard M. Leggett, Vincent Moulton, Thomas Mock

“…This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. …”
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Reducing gas pressure pulsations in the suction line of a piston compressor when using throttle washers by S. S. Busarov, A. A. Kapelyukhovskaya, V. V. Voronin, K. A. Bakulin, N. G. Sinitsin

“…Therefore, special attention must be paid to the layout of pipelines and equipment, while avoiding resonance phenomena. …”
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SpecPCM: A Low-Power PCM-Based In-Memory Computing Accelerator for Full-Stack Mass Spectrometry Analysis by Keming Fan, Ashkan Moradifirouzabadi, Xiangjin Wu, Zheyu Li, Flavio Ponzina, Anton Persson, Eric Pop, Tajana Rosing, Mingu Kang

“…We leverage a robust hyperdimensional computing (HD) algorithm with a novel dimension-packing method and develop specialized hardware for the end-to-end MS pipeline to overcome the nonideal behavior of PCM devices. …”
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SVM directed machine learning classifier for human action recognition network by Dharmanna Lamani, Pramod Kumar, A Bhagyalakshmi, J. Maria Shanthi, Lakshmana Phaneendra Maguluri, Mohammad Arif, C Dhanamjayulu, Sathish Kumar. K, Baseem Khan

“…The suggested method presents an innovative pipeline for creating spatial motion data from raw video inputs, which makes successful latent representation learning of human motions easier to accomplish. …”
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DeepCERES: A deep learning method for cerebellar lobule segmentation using ultra-high resolution multimodal MRI by Sergio Morell-Ortega, Marina Ruiz-Perez, Marien Gadea, Roberto Vivo-Hernando, Gregorio Rubio, Fernando Aparici, Maria de la Iglesia-Vaya, Gwenaelle Catheline, Boris Mansencal, Pierrick Coupé, José V. Manjón

“…Finally, a new online pipeline, named DeepCERES, has been developed to make available the proposed method to the scientific community requiring as input only a single T1 MR image at standard resolution.…”
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