Article
Biochemistry & Molecular Biology
Amita Pathak, B. Jayaram
Summary: The Seq2Enz method is a novel approach for predicting enzyme classes based on structural-chemical properties of proteins, outperforming conventional BLAST and ECPred in experimental evaluations. This methodology has been developed into a user-friendly web server and is freely accessible online.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2022)
Article
Computer Science, Software Engineering
Wenhai Wang, Enze Xie, Xiang Li, Deng-Ping Fan, Kaitao Song, Ding Liang, Tong Lu, Ping Luo, Ling Shao
Summary: This work presents the improved Pyramid Vision Transformer v2 (PVT v2) by adding three designs, achieving significant improvements in fundamental vision tasks. PVT v2 performs comparably or better than recent work such as the Swin transformer.
COMPUTATIONAL VISUAL MEDIA
(2022)
Article
Computer Science, Information Systems
Yang Zhou, Chunjiao Fu, Yuting Zhai, Jian Li, Ziqi Jin, Yanlei Xu
Summary: This paper proposes a classification and identification method based on an improved ShuffleNet V2 (GE-ShuffleNet) model. It replaces the 1 x 1 convolution in the basic unit modules of ShuffleNet V2 with the Ghost module and removes the unimportant 1 x 1 convolution. The Hardswish activation function is applied for better identification accuracy. An effective channel attention (ECA) module is added to avoid dimension reduction and extract channel correlations through 1D convolution. Experimental results show that GE-ShuffleNet outperforms other models in terms of model size, FLOPs, and parameters.
CMC-COMPUTERS MATERIALS & CONTINUA
(2023)
Article
Engineering, Electrical & Electronic
Nan Chen, Sisi Ma, Li Yang, Tingcun Wei
Summary: This article presents a digital V-2 controller integrated circuit (IC) for dc-dc switching converters to enhance transient response. The IC consists of two compensators, an analog-to-digital converter (ADC), and a digital pulsewidth modulator (DPWM). Experimental results show excellent transient response achieved with the prototype of the IC.
IEEE JOURNAL OF EMERGING AND SELECTED TOPICS IN POWER ELECTRONICS
(2022)
Article
Agronomy
Haixia Sun, Shujuan Zhang, Rui Ren, Liyang Su
Summary: The research improves the classification model of jujube maturity by using class balance loss and transfer learning, and develops a maturity detection system for Hupingzao jujubes, achieving good classification accuracy.
Article
Biochemical Research Methods
Zhen Cao, Yanting Huang, Ran Duan, Peng Jin, Zhaohui S. Qin, Shihua Zhang
Summary: CASAVA is an ensemble learning framework that predicts the risk of genomic loci for complex diseases using various genomics and epigenomics features. The study shows that CASAVA scores at a genomic locus provide reasonable predictions of the disease-specific and disease category-specific risk for non-coding variants located within the locus.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Physics, Mathematical
Archana Dixit, Priyanka Garg, Anirudh Pradhan
Summary: In this paper, the general behaviors of the Tsallic holographic dark energy (THDE) model in general relativity are investigated. The THDE models with the Hubble horizon and Granda-Oliveros (GO) cutoffs are studied using the Bianchi V I-0 metric, which is homogeneous and anisotropic. The behaviors and physical significances of quantities such as dark energy density (rho(D)), matter-energy density (rho(m)), and skewness parameter (gamma) are analyzed. Cosmographic parameters and the stability analysis of the THDE model are also discussed.
INTERNATIONAL JOURNAL OF GEOMETRIC METHODS IN MODERN PHYSICS
(2023)
Article
Multidisciplinary Sciences
Cheng Guo, You Duan, Weidong Ye, Wanting Zhang, Yingyin Cheng, Mijuan Shi, Xiao-Qin Xia
Summary: FishGET is an effort to collect and curate fish RNA-seq data in order to discover new RNAs and provide comprehensive transcriptome annotations. Through various steps including transcript assembly, meta-assembly, WGCNA, functional annotations, neighbor location annotation, lncRNA type annotation, and homology annotation, we obtained a total of 1362 RNA-seq paired-end data from 97 different studies of 8 fish species. To facilitate research on fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to access all information and utilize dynamic interactive visualization services.
Article
Chemistry, Applied
Yilun Weng, Supun Ranaweera, Da Zou, Anna P. Cameron, Xiaojing Chen, Hao Song, Chun-Xia Zhao
Summary: Enzymes are essential for industries, but their sensitivity to high temperatures can be problematic. Encapsulation with alginate microparticles has been shown to improve enzyme thermal stability, but other factors like enzyme loading and bioavailability also need to be considered. This study optimized the efficiency of enzyme encapsulation and achieved high enzyme loading and thermal stability, with excellent bioavailability demonstrated in an animal trial.
FOOD HYDROCOLLOIDS
(2023)
Article
Multidisciplinary Sciences
Ryan Lusk, Evan Stene, Farnoush Banaei-Kashani, Boris Tabakoff, Katerina Kechris, Laura M. Saba
Summary: aptardi is a novel machine learning algorithm that combines DNA sequence and RNA sequencing data to predict expressed polyadenylation sites with higher accuracy. The algorithm's average precision and recall are significantly better than traditional transcriptome assemblers, especially performing well on samples from different tissues and mammalian species.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Artificial Intelligence
Qing Ai, Fei Li, Xiangna Li, Ji Zhao, Wenhui Wang, Qingyun Gao, Fei Zhao
Summary: This paper proposes an improved multi-label twin support vector machine algorithm, which uses label-specific features with missing labels to address some drawbacks of the original algorithm. Experimental results demonstrate that the improved algorithm achieves better performance in multi-label classification tasks.
APPLIED INTELLIGENCE
(2023)
Article
Computer Science, Information Systems
Myasar Mundher Adnan, Mohd Shafry Mohd Rahim, Amjad Rehman Khan, Tanzila Saba, Suliman Mohamed Fati, Saeed Ali Bahaj
Summary: Every day, there is a growing number of photographs generated by websites and personal archives. The popularity of these digital image collections is attributed to their ease of use. However, not all databases provide appropriate indexing data, making it difficult to find specific information. Therefore, image annotation is necessary to classify and understand the content of images. This paper focuses on automatic feature extraction using a deep learning convolutional neural network to improve image coding and annotation capabilities. Experimental findings demonstrate the usefulness of this model for image annotation.
Article
Endocrinology & Metabolism
Kim Meredith-Jones, Rachael Taylor, Rachel Brown, Rebecca Cooke, Lara Vlietstra, Patrick Manning, Richie Poulton, Jillian Haszard
Summary: The study showed that DXA-measured visceral fat is related to traditional cardio-metabolic risk factors, especially high blood pressure in men over 40 and low HDL in men under 40. Four cut-offs for visceral fat mass were proposed, above which cardio-metabolic risk increased.
INTERNATIONAL JOURNAL OF OBESITY
(2021)
Article
Chemistry, Medicinal
Shimpei Iikuni, Yuta Tarumizu, Kazuma Nakashima, Yusuke Higaki, Hiroaki Ichikawa, Hiroyuki Watanabe, Masahiro Ono
Summary: The radioligand PSMA-DA1 shows promising potential as a PSMA-targeting radiotheranostic agent, with significant tumor uptake and retention capabilities in preclinical studies. PSMA-DA1 produced clear tumor images in mice and inhibited tumor growth, indicating its potential as an effective radiotherapeutic agent.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Andreia C. M. Rodrigues, Maria Vittoria Barbieri, Marco Chino, Giuseppe Manco, Ferdinando Febbraio
Summary: This study aimed to evaluate the applicability of Forster resonance energy transfer (FRET) as a sensitive and reliable method to quantify organophosphate (OP) pesticides at environmentally relevant concentrations. The results showed that fluorometric measurements using an enzyme-based biosensor with FRET can linearly quantify different concentrations of OP pesticides and are not interfered by changes in the pH of the medium or the addition of other organic components.
Article
Parasitology
Stefano Catalano, Manigandan Lejeune, Bradley van Paridon, Christopher A. Pagan, James D. Wasmuth, Paolo Tizzani, Padraig J. Duignan, Steven A. Nadler
JOURNAL OF PARASITOLOGY
(2015)
Article
Microbiology
Tomasz Blazejewski, Nirvana Nursimulu, Viviana Pszenny, Sriveny Dangoudoubiyam, Sivaranjani Namasivayam, Melissa A. Chiasson, Kyle Chessman, Michelle Tonkin, Lakshmipuram S. Swapna, Stacy S. Hung, Joshua Bridgers, Stacy M. Ricklefs, Martin J. Boulanger, Jitender P. Dubey, Stephen F. Porcella, Jessica C. Kissinger, Daniel K. Howe, Michael E. Grigg, John Parkinson
Article
Microbiology
Constance A. M. Finney, Shaden Kamhawi, James D. Wasmuth
Article
Biotechnology & Applied Microbiology
Aude Gilabert, David M. Curran, Simon C. Harvey, James D. Wasmuth
Article
Microbiology
James A. Cotton, Sasisekhar Bennuru, Alexandra Grote, Bhavana Harsha, Alan Tracey, Robin Beech, Stephen R. Doyle, Matthew Dunn, Julie C. Dunning Hotopp, Nancy Holroyd, Taisei Kikuchi, Olivia Lambert, Amruta Mhashilkar, Prudence Mutowo, Nirvana Nursimulu, Jose M. C. Ribeiro, Matthew B. Rogers, Eleanor Stanley, Lakshmipuram S. Swapna, Isheng J. Tsai, Thomas R. Unnasch, Denis Voronin, John Parkinson, Thomas B. Nutman, Elodie Ghedin, Matthew Berriman, Sara Lustigman
NATURE MICROBIOLOGY
(2017)
Article
Infectious Diseases
A. Chernick, A. Ambagala, K. Orsel, J. D. Wasmuth, G. van Marle, F. van der Meer
INFECTION GENETICS AND EVOLUTION
(2018)
Article
Multidisciplinary Sciences
David M. Curran, John S. Gilleard, James D. Wasmuth
Article
Genetics & Heredity
Sonja M. Dunemann, James D. Wasmuth
Article
Biology
David M. Curran, Alexandra Grote, Nirvana Nursimulu, Adam Geber, Dennis Voronin, Drew R. Jones, Elodie Ghedin, John Parkinson
Article
Immunology
Mia H. E. Kennedy, Tara P. Brosschot, Katherine M. Lawrence, Rachael D. FitzPatrick, Jenna M. Lane, Grace M. Mariene, James D. Wasmuth, Lisa A. Reynolds
Summary: The study revealed that H. polygyrus infection leads to an increase in isovaleric acid levels in the proximal small intestine of mice. Supplementing with isovaleric acid promoted helminth fecundity without affecting chronicity. The bacterial microbiota is necessary to support the elevated levels of isovaleric acid in the proximal small intestine during helminth infection.
INFECTION AND IMMUNITY
(2021)
Article
Infectious Diseases
Sara Roose, Russell W. Avramenko, Stephen M. J. Pollo, James D. Wasmuth, Shaali Ame, Mio Ayana, Martha Betson, Piet Cools, Daniel Dana, Ben P. Jones, Zeleke Mekonnen, Arianna Morosetti, Abhinaya Venkatesan, Johnny Vlaminck, Matthew L. Workentine, Bruno Levecke, John S. Gilleard, Peter Geldhof
Summary: This study characterized the beta-tubulin gene families in Ascaris worms and identified at least seven different beta-tubulin genes. Through deep amplicon sequencing, no known SNPs associated with BZ resistance were found in these genes in adult Ascaris populations. The study proposes a new nomenclature and discusses the prioritization of genes for future BZ resistance research in helminths.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biochemical Research Methods
Nirvana Nursimulu, Alan M. Moses, John Parkinson
Summary: Constraint-based modeling is a powerful framework for studying cellular metabolism. In this paper, the authors introduce Architect, a pipeline for automatic metabolic model reconstruction from protein sequences. Their method shows improved precision and recall compared to existing tools, and the resulting metabolic model is of high quality. Given the importance of metabolic models in various applications, this work contributes to the field and provides a valuable tool for researchers.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Kyle Lesack, Grace M. Mariene, Erik C. Andersen, James D. Wasmuth
Summary: The accurate characterization of structural variation is crucial for understanding phenotypic differences and genome evolution. The accuracy of popular tools for identifying structural variants using whole-genome sequencing remains unclear, and their performance for non-human genomes is uncertain.
