Article
Microbiology
Sada Egenriether, Robert Sanford, Wendy H. H. Yang, Angela D. Kent
Summary: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. The study compared heuristic OTU clustering and true hierarchical OTU clustering methods on two nitrogen cycling genes and found that hierarchical method outperformed heuristic method for a more diverse gene, nrfA. These findings suggest that care should be exercised in choosing clustering methods to ensure accurate analysis in microbiome studies.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Shadi Eshghi Sahraei, Brendan Furneaux, Kerri Kluting, Mustafa Zakieh, Hakan Rydin, Hakan Hytteborn, Anna Rosling
Summary: Long amplicon metabarcoding using PacBio SMRT sequencing was used to study the phylogenetic analysis of microeukaryotes in soil. Three different methods for generating operational taxonomic units (OTUs) were tested, and the effects on richness estimates, taxonomic identification, and ecological patterns were analyzed. The results showed that different OTU generation methods have significant impacts on richness estimates and the taxonomic and phylogenetic resolution of the characterized community.
ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Ze-Gang Wei, Xiao-Dan Zhang, Ming Cao, Fei Liu, Yu Qian, Shao-Wu Zhang
Summary: With the advancement of next-generation sequencing technology, researchers have the convenience and cost efficiency to thoroughly characterize microbial diversity and taxonomic composition in various environmental samples. The challenge lies in selecting appropriate clustering methods and parameter settings, which can be a daunting task for inexperienced users.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mikang Sim, Jongin Lee, Daehong Kwon, Daehwan Lee, Nayoung Park, Suyeon Wy, Younhee Ko, Jaebum Kim
Summary: RBRC is a new read-clustering algorithm that improves de novo microbial genome assembly by accurately estimating read proximity. It has shown excellent performance in simulation-based evaluation and application to real genomes, improving assembly quality without additional sequencing data. RBRC can be used to generate high-quality microbial strain genome assemblies when genome assemblies of related strains are available, and to upgrade existing microbial genome assemblies when additional sequencing data, such as long reads, are difficult to obtain.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Computer Science, Artificial Intelligence
Xiaobo Xia, Bo Han, Nannan Wang, Jiankang Deng, Jiatong Li, Yinian Mao, Tongliang Liu
Summary: This paper addresses the problem of learning with mixed closed-set and open-set noisy labels. It extends the traditional transition matrix to model mixed label noise and proposes a cluster-dependent transition matrix to combat instance-dependent label noise in real-world applications. Experimental results demonstrate that the proposed method can better cope with realistic label noise and outperform the prior state-of-the-art label-noise learning methods.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Plant Sciences
Jan Vondrak, Stanislav Svoboda, Jiri Kosnar, Jiri Malicek, Jaroslav Soun, Ivan Frolov, Mans Svensson, Petr Novotny, Zdenek Palice
Summary: This study presents a near-complete database of ITS and mtSSU barcodes for accurate molecular identification of epiphytic lichens in central Europe. The database includes 1,172 species, with newly sequenced ITS and mtSSU for a number of species. The study also reveals diverging genotypes and newly described species, contributing to the field of lichen taxonomy.
Article
Computer Science, Interdisciplinary Applications
Mohammad Mahdi Vali-Siar, Emad Roghanian, Armin Jabbarzadeh
Summary: This study addresses the problem of resilient mixed open and closed-loop supply chain network design and proposes a model with the objective of maximizing profit. To mitigate disruption risks, several resilience strategies are applied, and a two-stage stochastic programming approach is used. Constructive heuristic and metaheuristic methods (improved genetic algorithm and improved particle swarm optimization) are developed to deal with the problem's complexity. The results show the effectiveness of the proposed methods, and the analysis demonstrates the remarkable impact of resilient strategies on reducing risks and maintaining market share.
COMPUTERS & INDUSTRIAL ENGINEERING
(2022)
Article
Mathematics, Applied
Ashok Kumar Das, Rajkamal Sahu
Summary: This article introduces interval graphs and unit interval graphs, and characterizes the intersection graphs and interval bigraphs of open and closed intervals of unit length.
DISCRETE APPLIED MATHEMATICS
(2024)
Article
Automation & Control Systems
Sveinung Johan Ohrem, Christian Holden
Summary: This article presents an output feedback controller and observer design approach for linear time-invariant systems with unknown dynamics, using an open-loop reference model to generate desired trajectory and a closed-loop reference model as an observer. Stability proofs based on Lyapunov show that error states converge asymptotically to zero and all other signals are uniformly stable, with bounds proven on the transient behavior.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2021)
Article
Cardiac & Cardiovascular Systems
P. Elliott Miller, Fouad Chouairi, Alexander Thomas, Yukiko Kunitomo, Faisal Aslam, Maureen E. Canavan, Christa Murphy, Krishna Daggula, Thomas Metkus, Saraschandra Vallabhajosyula, Anthony Carnicelli, Jason N. Katz, Nihar R. Desai, Tariq Ahmad, Eric J. Velazquez, Joseph Brennan
Summary: The study found lower in-hospital and CICU mortality rates after transitioning to a closed cardiac intensive care unit. Additionally, cases of cardiac arrest and respiratory insufficiency in the closed unit showed lower in-hospital mortality rates.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2021)
Article
Biochemistry & Molecular Biology
Martin W. Hahn, Andrea Huemer, Alexandra Pitt, Matthias Hoetzinger
Summary: The study utilized a protein-encoding gene to reveal hidden ecological patterns within a single operational taxonomic unit, leading to the detection of 600 species-like taxa in 99 freshwater habitats. It showed how environmental conditions shape bacterial communities and identified a surprising compositional separation of Polynucleobacter communities in habitats with different levels of calcium ions. This new approach opens up a window to explore the incredible diversity of free-living bacteria and investigate the impact of environmental conditions on bacterial evolution.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Environmental Sciences
Shuaibin Liu, Fen Lin, Zhongkai Fan, Tao Hu, Yixiang Mo, Shuai Yuan, Ruomei Xie, Huiying Li, Jiale Sun, Haibo Yi, Linquan Cheng, Zhipeng Liu, Jiulin Wu, Xinyi Zhang, Hongzhi Yuan, Yanliang Tan
Summary: The radon-222 (Rn-222) exhalation rate is crucial for assessing radiation risk from various materials. AlphaGUARD is a recognized instrument for measuring radon concentration based on the ionization chamber principle. In China, measurements of radon exhalation rate are performed using AlphaGUARD in flow-through mode to ensure accuracy. The device can quickly detect changes in radon concentration, tightly pressing against the medium surface to accumulate exhaled radon. The obtained radon exhalation rates through nonlinear data fitting are similar to the reference values, with minimal differences among six measurements.
RADIATION PROTECTION DOSIMETRY
(2023)