Article
Biochemistry & Molecular Biology
Vadim Elisseev, Laura-Jayne Gardiner, Ritesh Krishna
Summary: The article presents a proof of concept implementation of the in-memory computing paradigm for analyzing metagenomic sequencing reads. By comparing different file systems and key-value storage for omics data, the researchers demonstrate the potential for integrating high-performance computing and cloud native technologies. In-memory key value storage is shown to offer improved handling of omics data through faster and more flexible data processing. The researchers envision fully containerized workflows with multiple instances working concurrently with distributed in-memory storage.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Virology
Colin Young, Sarah Meng, Niema Moshiri
Summary: The use of viral sequence data to inform public health intervention in epidemiology is becoming more common, but the evaluation of the accuracy and runtime of such methods is lacking. In this study, we evaluated commonly used viral phylogenetic analysis methods on simulated viral sequence data and found that MAFFT outperformed other tools in multiple sequence alignment in terms of accuracy and runtime, while RAxML-NG provided the most accurate branch lengths and pairwise distances in phylogenetic inference.
Article
Dermatology
Bharti Sharma, Skarma Nonzom
Summary: This study investigated the prevalence of cutaneous mycosis in Jammu district, India, and isolated and identified the recovered causal agents. Three new cases of cutaneous phaeohyphomycosis from Jammu district were reported, with the recovered etiological agents being Alternaria alstromeriae, Epicoccum tritici, and Phialemonium obovatum. Careful microscopic and mycological examination are important for correct diagnosis of such fungal infections.
Article
Energy & Fuels
Xiaobing Yu, Yansong Shen
Summary: Ironmaking blast furnace (BF) is an energy-intensive chemical process. This study investigates the dynamic behaviors of BF under different scenarios of blast temperature (BT) decrease using a transient-state BF model. The responses of different BF regions to the BT change are found to be different, with the regions near BF gas inlet responding more promptly and significantly. This research provides a cost-effective tool to study time-related behaviors in the BF domain when BT changes occur.
Review
Oncology
Paula Carrillo-Rodriguez, Frode Selheim, Maria Hernandez-Valladares
Summary: Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a powerful technology for discovering new cancer biomarkers. This review highlights the methodological features that cancer researchers must consider before executing an LC-MS-based proteomics project. Based on these features, researchers can use straightforward and complex workflows to discover new molecules or therapeutic pathways to combat oncological diseases.
Article
Materials Science, Multidisciplinary
E. Eshed, D. Choudhuri, S. Osovski
Summary: In this study, the hexagonal structure of M7C3-type carbides and the occupancy of a previously considered vacant site by a carbon atom in its atomic structure were experimentally confirmed. Co-existence of two variants in the atomic structure, which explains the preference for this structure over the orthorhombic one, was also discovered. This research is significant for controlling the growth, stability, and performance of (Cr,Fe)(7)C-3 carbides.
Review
Chemistry, Multidisciplinary
Prithvijit Mukherjee, So Hyun Park, Nibir Pathak, Cesar A. Patino, Gang Bao, Horacio D. Espinosa
Summary: The field of cell therapy has the potential to treat a wide range of diseases with limited treatment options. Recent advancements in micro and nanotechnology have enabled the development of single cell analysis methods and precise manipulation of cells. This review explores how these technologies have influenced the understanding of disease pathophysiology and the development of cell-based therapeutics.
Article
Biochemical Research Methods
Frank Koopmans, Ka Wan Li, Remco V. Klaassen, August B. Smit
Summary: This article introduces a mass spectrometry downstream analysis pipeline (MS-DAP) that integrates popular and recently developed algorithms for data normalization and statistical analysis. It generates extensive data visualizations and quality reporting in standardized PDF reports, promoting transparent and reproducible proteome science.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Medicine, General & Internal
Chao Liu, Bin Tang, Can Gao, Jianjun Deng, Min Shen, Chaolin Li, Zekun Fu, Zhan Gao, Qi Jiang, Hao Shi, Miao He, Huaiwu Jiang, Xu Jia
Summary: This study reported the first case of asymptomatic SARS-CoV-2 infection imported from Spain into Sichuan Province, China on March 11, 2020. The identified sequence was closely related to the evolution of the SARS-CoV-2 D614G mutant strain circulating in Spain.
FRONTIERS IN MEDICINE
(2021)
Article
Energy & Fuels
Xiongbo Duan, Banglin Deng, Yiqun Liu, Yangyang Li, Jingping Liu
Summary: This study investigated the impacts of key operating and design parameters on the cycle-to-cycle variations in a high compression ratio SI natural gas engine under lean mixture conditions. The results showed that with increasing engine speed, there were fewer incomplete combustion cycles and the in-cylinder pressure distribution became more concentrated. Increasing load led to more concentrated pressure distribution and peak combustion pressure. Additionally, the relationship between peak combustion pressure and load was nearly linear, but increasing load caused the in-cylinder pressure traces to disperse slightly. Under low-load conditions, increasing compression ratio led to more concentrated pressure traces and fewer incomplete combustion cycles, while the effects were slight under high-load conditions.
Article
Computer Science, Software Engineering
Douglas de Oliveira, Fabio Porto, Cristina Boeres, Daniel de Oliveira
Summary: Apache Spark has become the standard framework for big data systems, used in various fields for compute- and data-intensive workflows. To efficiently execute Spark-based workflows, users need to fine-tune a large number of Spark and workflow parameters. By generating predictive machine learning models and extracting useful rules, the proposed approach can help non-expert users configure parameters effectively.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2021)
Review
Agronomy
Oswaldo Guzman-Lopez, Celeste Ricano-Rodriguez, Daniela Luis-Yong, Jorge Ricano-Rodriguez
Summary: The National Center for Biotechnology Information (NCBI) provides computational resources and repositories for genomic and protein sequences, citations, and scientific abstracts. This study compiles an overview of NCBI, focusing on the Entrez system, information sources, literature updates, taxonomy database, metadata management, genetic expression, nucleotide sequences, and genomic and protein processing. It also discusses useful tools and research results in plant genetics, including genomic annotations, metadata organization, transcriptomics, nucleotide alignments, and protein modeling.
REVISTA FITOTECNIA MEXICANA
(2023)
Article
Plant Sciences
Ciro Cabal
Summary: Fine root density is a crucial plant functional trait with significant implications for plant ecology and agriculture. The root tragedy of the commons (RToC) is a behavioral strategy predicted by game theory models, which reflects plants' inefficient foraging for soil resources. This opinion challenges the conventional idea that RToC is a proactive competition strategy induced by non-self roots, suggesting an alternative perspective based solely on soil resource information. This alternative perspective has important implications for experimental designs investigating the physiological mechanisms underlying observable plant root responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Yaohua Hu, Huanbo Yang, Bingru Hou, Ziting Xi, Zidong Yang
Summary: The efficiency of orchard plant protection machinery in China is low. This study analyzed the effects of control parameters on the spray performance of air-blast sprayers, and established a regression model to obtain the optimum parameter values.
Article
Engineering, Civil
Bin Feng, Li Chen, Haoyang Li, Dapeng Chen, Donglei Zhou
Summary: This study analyzed the propagation of blast waves in an enclosed blast wall (EBWS) at a hazardous chemical storage yard through scaled field tests and numerical simulations. It was found that the commonly adopted assumptions underestimated the peak overpressure in the access passage and could not predict the following multiple overpressure peaks.
ENGINEERING STRUCTURES
(2023)
Article
Biochemical Research Methods
Vladimir Smirnov, Tandy Warnow
Summary: MAGUS is a new technique for computing large-scale alignments, similar to PASTA but faster and more accurate. It utilizes a divide-and-conquer approach and merges subset alignments using a Graph Clustering Merger.
Article
Microbiology
Jay Noboru Worley, Kiran Javkar, Maria Hoffmann, Kristen Hysell, Amanda Garcia-Williams, Kaitlin Tagg, Sanjat Kanjilal, Errol Strain, Mihai Pop, Marc Allard, Louise Francois Watkins, Lynn Bry
Summary: MDR Shigella infections are a global concern among MSM, with new macrolide-resistant strains complicating treatment. Genomic analyses reveal resistant genes in US Shigella isolates and the receptivity of certain strains to plasmid acquisition. Leveraging integrated genomic-epidemiologic analyses can guide targeted clinical actions and public health efforts to combat the spread of multidrug-resistant Shigella.
Article
Microbiology
Harihara Subrahmaniam Muralidharan, Nidhi Shah, Jacquelyn S. Meisel, Mihai Pop
Summary: High-throughput sequencing has transformed microbiology, but reconstructing complete genomes from metagenomic data is still challenging due to the fragmented nature. Scientists use binning to cluster contigs from the same organism, and this study suggests using assembly graphs to improve binning strategies. The Binnacle tool extracts information from assembly graphs to cluster scaffolds into comprehensive bins, enhancing the quality and contiguity of the resulting bins.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Evolutionary Biology
James Willson, Mrinmoy Saha Roddur, Baqiao Liu, Paul Zaharias, Tandy Warnow
Summary: Gene tree heterogeneity poses a challenge for species tree inference, but the introduction of DISCO, a new approach that decomposes multi-copy gene family trees into single copy trees, improves the accuracy of species tree estimation.
SYSTEMATIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Chengze Shen, Paul Zaharias, Tandy Warnow
Summary: Multiple sequence alignment is a key step in bioinformatics pipelines, but it is challenging to estimate alignments on datasets with fragmentary sequences. This paper examines a new MSA method called MAGUS, which is robust to fragmentary sequences under many conditions, and shows that using a two-stage approach improves alignment accuracy.
Article
Biochemical Research Methods
Yasamin Tabatabaee, Kowshika Sarker, Tandy Warnow
Summary: This article presents Quintet Rooting (QR), a method for rooting species trees based on a proof of identifiability of the rooted species tree under the multi-species coalescent model. The method is shown to be generally more accurate than other rooting methods, except under extreme levels of gene tree estimation error.
Article
Pharmacology & Pharmacy
Domenick J. Braccia, Glory Minabou Ndjite, Ashley Weiss, Sophia Levy, Stephenie Abeysinghe, Xiaofang Jiang, Mihai Pop, Brantley Hall
Summary: The human gut microbiome contains numerous azoreductases that play a vital role in modifying orally administered drugs. Through analyzing bacterial azoreductases and genome sequences, this study identified putative azo-reducing species and hypothesized the presence of uncharacterized azoreductases in prominent strains of the human gut microbiome.
DRUG METABOLISM AND DISPOSITION
(2023)
Review
Biology
Paul Zaharias, Tandy Warnow
Summary: This article introduces some recent advances in highly accurate phylogeny estimation on large datasets, including divide-and-conquer techniques, methods for estimating species trees from multi-locus datasets and addressing heterogeneity, and methods for adding sequences into large gene trees or species trees.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemical Research Methods
Paul Zaharias, Vladimir Smirnov, Tandy Warnow
Summary: MAGUS is an accurate multiple sequence alignment method that uses divide-and-conquer and the Graph Clustering Method (GCM) for merging alignments. The study shows that GCM is a good heuristic for the NP-hard MWT-AM problem and suggests a new direction for large-scale MSA estimation based on improved divide-and-conquer strategies. MAGUS and its enhanced versions can be found at https://github.com/vlasmirnov/MAGUS.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Eleanor Wedell, Yirong Cai, Tandy Warnow
Summary: SCAMPP is a technique that extends the scalability of likelihood-based phylogenetic placement methods to ultra-large backbone trees, achieving accurate evolutionary tree classification. It can handle ultra-large backbone trees with 50,000 or more leaves and has higher accuracy compared to other fast phylogenetic placement methods.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, Tandy Warnow
Summary: UPP2 is an improvement on UPP, with a fast technique for selecting HMMs in the ensemble, achieving the same accuracy as UPP but with reduced runtime.
Article
Information Science & Library Science
Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy Warnow, George Chacko
Summary: Clustering and community detection in networks are widely studied topics, we focus on detecting communities of scientific publications linked by citations, and have developed a modular pipeline based on the k-core algorithm to find publication communities. Through quantitative and qualitative evaluation on a citation network of over 14 million publications in the extracellular vesicles field, we compare our approach with the widely used Leiden algorithm for community detection.
QUANTITATIVE SCIENCE STUDIES
(2022)
Article
Biochemical Research Methods
Chengze Shen, Minhyuk Park, Tandy Warnow
Summary: Accurate multiple sequence alignment is challenging, especially for data sets with sequence length heterogeneity. Existing methods have made progress in addressing the first two challenges, but sequence length heterogeneity remains a significant issue. This study introduces a new method, WITCH, which improves alignment accuracy by weighting and ranking HMMs, using multiple HMMs, and using a consensus algorithm that considers the weights.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Baqiao Liu, Tandy Warnow
Summary: This study introduces two new methods, NJst-J and FASTRAL-J, for estimating the species tree based on partial knowledge. The results show that both NJst-J and FASTRAL-J are faster than ASTRAL-J, and all three methods are statistically consistent under the given constraint.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Paul Zaharias, Martin Grosshauser, Tandy Warnow
Summary: This study evaluated the accuracy of recently trained DNNs in comparison to standard phylogeny estimation methods on simulated datasets with similar and higher rates of evolution. The results showed that DNNs were less accurate than standard methods for quartet accuracy, and global methods had higher accuracy on large datasets.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
