Article
Operations Research & Management Science
Peter Tea, Tim B. Swartz
Summary: Anticipating opponents' serve and being aware of one's own serve tendencies are essential skills in tennis. Using Bayesian hierarchical models, this paper investigates the intended serve direction of professional tennis players at Roland Garros and reveals discernible differences between men's and women's tennis, as well as individual players.
ANNALS OF OPERATIONS RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
Didier Nibbering, Trevor J. Hastie
Summary: This study introduces a multinomial logistic regression model that penalizes the number of class-specific parameters, showing improved performance in both in-sample and out-of-sample situations compared to a standard model. The model clusters parameters by penalizing differences between class-specific parameter vectors, providing interpretable parameter estimates.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2022)
Article
Biochemical Research Methods
Ayyuce Begum Bektas, Cigdem Ak, Mehmet Gonen
Summary: With the increasing sizes of computational biology datasets, previous kernel-based machine learning algorithms have failed to provide satisfactory interpretability. To address this issue, we propose a fast and efficient multiple kernel learning algorithm that can extract significant information from genomic data. Our experiments demonstrate that the algorithm outperforms baseline methods while using only a small fraction of input features, and it has the potential to discover new biomarkers and therapeutic guidelines.
Article
Computer Science, Interdisciplinary Applications
Kei Hirose, Kanta Miura, Atori Koie
Summary: This article proposes a cluster-based LDA method that improves prediction accuracy through hierarchical clustering and cross-validation, while addressing computational efficiency.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2023)
Article
Water Resources
Chandrashekarayya G. Hiremath, Lakshman Nandagiri
Summary: This study utilized hierarchical cluster analysis to delineate hydrologically homogeneous regions in 50 basins in South India, and used multiple linear regression models to derive flow duration curves. The developed models showed excellent performance in different hydrologically homogeneous regions, but exhibited mixed reliability for high and low flow quantiles.
JOURNAL OF WATER AND CLIMATE CHANGE
(2023)
Article
Biochemical Research Methods
Shaojing Wang, Guoqiang Li, Zitong Liao, Yunke Cao, Yuan Yun, Zhaoying Su, Xuefeng Tian, Ziyu Gui, Ting Ma
Summary: Temperature is crucial for microbial growth, and suitable conditions can improve the isolation possibility of uncultured microorganisms. CnnPOGTP is a deep learning-based predictor that uses k-mers distribution from genomic sequences to infer the optimal growth temperature of prokaryotes.
Article
Environmental Sciences
G. Shenbagalakshmi, A. Shenbagarajan, S. Thavasi, M. Gomathy Nayagam, R. Venkatesh
Summary: The past decade has witnessed an increase in the impact of human activities on the environment, particularly due to population growth, urbanization, and agricultural practices. This paper focuses on studying the groundwater characteristics in industrial zones around Chennai and determining the water quality index (WQI) by analyzing the influencing factors. The hierarchical cluster analysis (HCA) is used to categorize the water quality data into hydrochemical groups. The results show that the suggested strategy accurately classifies the water quality samples in the industrial zones.
Article
Agriculture, Dairy & Animal Science
Wei-Tse Hsu, Peter Williamson, Mehar Singh Khatkar
Summary: A study identified genomic regions that differentiate the Bullmastiff breed, suggesting genetic drift or the effects of selective breeding as possible factors.
Article
Computer Science, Information Systems
Joelson Antonio dos Santos, Talat Iqbal Syed, Murilo C. Naldi, Ricardo J. G. B. Campello, Joerg Sander
Summary: Hierarchical density-based clustering is a powerful tool for data analysis, but its applicability to large datasets is limited by computational complexity. MapReduce is a programming model used to speed up data mining and machine learning algorithms, however, parallelizing hierarchical clustering algorithms with MapReduce is inherently difficult.
IEEE TRANSACTIONS ON BIG DATA
(2021)
Article
Computer Science, Interdisciplinary Applications
Diogo Ferrari
Summary: The existence of latent clusters with different responses to treatment is a significant concern in scientific research. This article discusses the implementation of a novel hierarchical Dirichlet process approach using the R package hdpGLM. The methods provided in the package make it easier for researchers to investigate heterogeneity in treatment effects and identify clusters of subjects with differential effects.
JOURNAL OF STATISTICAL SOFTWARE
(2023)
Article
Energy & Fuels
Geng Niu, Yu Ji, Zhihui Zhang, Wenbo Wang, Jikai Chen, Peng Yu
Summary: Scenario analysis is important in the planning and operation of island power supply systems. This paper proposes a cohesive hierarchical clustering based K-means clustering method for clustering analysis of typical scenarios, effectively categorizing different islands and analyzing their typical scenario features.
Article
Biochemistry & Molecular Biology
Ryan J. Weaver, Samantha Rabinowitz, Kiley Thueson, Justin C. Havird
Summary: Mitonuclear coevolution is strongly supported across mammalian evolution, although nuclear compensation is not the major mode of mitonuclear coevolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Clinical Neurology
Dana Pisica, Ruben Dammers, Eric Boersma, Victor Volovici
Summary: This article provides a theoretical and practical tutorial on regression analysis, including data preparation, univariable and multivariable analysis, and model selection. It also demonstrates the application of regression analysis to real-world data and emphasizes the importance of multidisciplinary collaborations with professionals.
WORLD NEUROSURGERY
(2022)
Article
Biology
Fei Deng, Haijun Zhou, Yong Lin, John A. Heim, Lanlan Shen, Yuan Li, Lanjing Zhang
Summary: This study predicted 5-category causes of death among lung cancer patients and showed that the random forests model outperformed multinomial logistic regression in prediction accuracy. Factors such as sex, chemotherapy status, age, radiotherapy status played important roles in the prediction accuracy.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Engineering, Environmental
Samira Ziyadidegan, Moein Razavi, Homa Pesarakli, Amir Hossein Javid, Madhav Erraguntla
Summary: This paper analyzes county-level factors to determine the key factors affecting the risk of COVID-19 infection and death. Results show that population density, percentage of population, percentage of people in poverty, percentage of elderly population, number of ICU beds per 10,000 people, and percentage of smokers are the most significant attributes.
STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT
(2022)
Article
Microbiology
Trudy M. Wassenaar, Se-Ran Jun, Michael Robeson, David W. Ussery
Article
Fisheries
Ragnar Thorarinsson, Jeffrey C. Wolf, Makoto Inami, Lisa Phillips, Ginny Jones, Alicia M. Macdonald, Jose F. Rodriguez, Hilde Sindre, Eystein Skjerve, Espen Rimstad, Oystein Evensen
Summary: The DNA vaccine group showed significantly higher SAV3 neutralizing antibody titers after the immunization period, lower SAV3 viremia levels at 19 days post-challenge, reduced transmission of SAV3 to naive fish, higher weight gain, and reduced prevalence/severity of SAV-induced morphological changes in target organs. Additionally, the DNA vaccine group had significantly higher post-challenge survival compared to the Saline group.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
J. F. Johnsen, I. H. Holmoy, C. M. Mejdell, K. Ellingsen-Dalskau, O. Osteras, A. Dosen, E. Skjerve, A. Nodtvedt
Summary: The study aimed to investigate the associations between management factors, compliance with legislation, and calf mortality rates. The results showed that a lack of water access was associated with higher calf mortality rates, and herds with registered calf disease events had a higher mortality rate ratio.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Polymer Science
Bikram Gautam, Gaumani Gyanwali, David Wayne Ussery
Summary: The study shows that pH values of most bottled water samples do not meet standards, while electrical conductivity and total dissolved solids concentrations may affect the bacterial load. Some extremophiles present may degrade the PET material.
INTERNATIONAL JOURNAL OF POLYMER SCIENCE
(2021)
Article
Biology
Kaleb Abram, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Michael S. Robeson, David W. Ussery
Summary: In this study, over 100,000 publicly available Escherichia coli and Shigella genome sequences were analyzed using Mash-based analysis to identify 14 unique phylogroups. The results revealed that most of the sequenced E. coli genomes belong to four distinct phylogroups.
COMMUNICATIONS BIOLOGY
(2021)
Article
Food Science & Technology
Gunvor Elise Nagel Gravning, Ole-Johan Rotterud, Solfrid Bjorkoy, Merete Forseth, Eystein Skjerve, Ann-Katrin Llarena, Astrid Lian, Gro S. Johannessen, Sigrun J. Hauge
Summary: This study evaluated four different sampling methods for quantification of bacterial contamination of broiler carcasses and found that the whole-carcass rinse sampling method provided the best reflection of the extent of carcass contamination.
Article
Multidisciplinary Sciences
Siri E. Haberg, Christian M. Page, Yunsung Lee, Haakon E. Nustad, Maria C. Magnus, Kristine L. Haftorn, Ellen O. Carlsen, William R. P. Denault, Jon Bohlin, Astanand Jugessur, Per Magnus, Hakon K. Gjessing, Robert Lyle
Summary: Assisted reproductive technology (ART) may affect fetal development through epigenetic mechanisms, leading to widespread differences in DNA methylation and variations in genes related to growth, neurodevelopment, and other health outcomes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jon Bohlin, Christian M. Page, Yunsung Lee, John H-O Pettersson, Astanand Jugessur, Per Magnus, Siri E. Haberg
Summary: Male sex and advanced age are associated with severe symptoms of COVID-19 and exhibit substantial associations with genome-wide DNA methylation differences. The study found wide-spread associations between sex and age in DNAm linked to genes implicated with SARS-CoV-2 host cell entry and severe COVID-19, but the effect from these CpGs was not stronger than randomly sampled CpGs; age was significantly less associated with the CpGs.
Article
Biotechnology & Applied Microbiology
Trudy M. Wassenaar, Visanu Wanchai, David W. Ussery
Summary: This study compared the genome sequences of Monkeypox virus isolates from the current outbreak to those from previous outbreaks. It identified consistent differences in the 2022 isolates, including variations in repeat units and single nucleotide polymorphisms. Some of these polymorphisms caused amino acid substitutions that may affect the virus's virulence. This bioinformatic analysis provides guidance for further wet-lab research.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
William R. P. Denault, Jon Bohlin, Christian M. Page, Stephen Burgess, Astanand Jugessur
Summary: This article introduces a new approach called Cross-Fitted Instrument (CFI) to handle bias from weak instruments in instrumental variable regression (IVR). The CFI method splits the data randomly and estimates the impact of the instrument on exposure in each partition, enabling an IVR on each partition. When applied to Mendelian randomization (MR) setting, the adapted Cross-Fitting for Mendelian Randomization (CFMR) approach remains biased towards the null even with weak instruments, making it a conservative one-sample MR approach. CFMR also maximizes statistical power by using all available data to select genetic instruments, addresses ethnic heterogeneity in meta-analyses, and allows analysis of rare or difficult to measure exposures.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Trudy M. Wassenaar, David W. Ussery, Adriana Cabal Rosel
Summary: Omics research involves the collection and analysis of big data, which requires automated approaches. In the field of genomics, specialized software, quality control of input data, and simplification for visualization of results are necessary. Clear communication of big data analyses can be enhanced by novel visualization strategies. The interpretation of findings may be hindered by lack of understanding of analytical tools by microbiologists and limited knowledge of the biology of the microbes under study by researchers.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Review
Microbiology
Trudy M. Wassenaar, Visanu Wanchai, Gregory Buzard, David W. Ussery
Summary: With over 6 million SARS-CoV-2 genomes sequenced, researchers have identified only 15 significant mutations along the viral genome and observed several global waves of variant lineages. However, dividing and redefining variant lineages does not contribute to describing the epidemic waves, and only about 5% of the SARS-CoV-2 genome is found to be variable.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Microbiology
Piroon Jenjaroenpun, Visanu Wanchai, Kikumi D. Ono-Moore, Jennifer Laudadio, Laura P. James, Sean H. Adams, Fred Prior, Intawat Nookaew, David W. Ussery, Thidathip Wongsurawat
Summary: Two coding-complete sequences of SARS-CoV-2 were obtained from samples of two patients in Arkansas, United States, located in the southeastern region. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Sangam Kandel, Supaphen Sripiboon, Piroon Jenjaroenpun, David W. Ussery, Intawat Nookaew, Michael S. Robeson, Thidathip Wongsurawat
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Piroon Jenjaroenpun, Thidathip Wongsurawat, Zulema Udaondo, Courtney Anderson, James Lopez, Meera Mohan, Ruslana Tytarenko, Brian Walker, Intawat Nookaew, David Ussery, Atul Kothari, Se-Ran Jun
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)