Article
Computer Science, Interdisciplinary Applications
Lin-Sen Zhang, Shi-Qi Liu, Xiao-Liang Xie, Xiao-Hu Zhou, Zeng-Guang Hou, Chao-Nan Wang, Xin-Kai Qu, Wen-Zheng Han, Xi-Yao Ma, Meng Song
Summary: This article proposes a novel 3D spatial predictive positioning navigation (SPPN) technique for predicting the real-time location of surgical instruments in intravascular interventional surgery. Extensive experiments demonstrate the outstanding performance of this method, improving the accuracy of interventional surgery.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Materials Science, Multidisciplinary
Teng Sun, Jianan Hui, Bo Lin, Hebin Sun, Lin Zhou, Jianlong Zhao, Hongju Mao
Summary: Wearable sweat sensors have immense potential for non invasively monitoring physiological parameters continuously. Iontophoresis-induced sweat analysis is a more attractive option for easy-sampling in daily life, despite challenges such as analyte concentration being affected by sweat rate variance and dilution. This study developed a multi-sensing patch for iontophoresis-stimulated sweat detection under sedentary conditions, significantly improving signal stability at low sweat rate.
APPLIED MATERIALS TODAY
(2023)
Article
Biochemical Research Methods
Mohammad Neamul Kabir, Limsoon Wong
Summary: This study presents a novel method called EnsembleFam that aims to improve function prediction for proteins in the twilight zone. By extracting core characteristics and using SVM classifiers, EnsembleFam achieves better accuracy in identifying proteins with low sequence homology compared to existing methods.
BMC BIOINFORMATICS
(2022)
Article
Engineering, Biomedical
Huy Phan, Oliver Y. Chen, Philipp Koch, Zongqing Lu, Ian McLoughlin, Alfred Mertins, Maarten De Vos
Summary: The study introduces a deep transfer learning approach to address data-variability and data-inefficiency issues in automatic sleep staging for small cohorts, demonstrating significant performance improvement on target domains.
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
(2021)
Article
Engineering, Electrical & Electronic
Diogo J. F. Reis, Jose Eduardo O. Pessanha
Summary: This paper presents an improved version of Hamiltonian Monte Carlo (HMC) method for voltage sags studies in power systems. By incorporating coefficient of variation and optimization strategy, the algorithm outperforms existing techniques in terms of average performance.
INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS
(2023)
Article
Biochemical Research Methods
Jun Hu, Lin-Lin Zheng, Yan-Song Bai, Ke-Wen Zhang, Dong-Jun Yu, Gui-Jun Zhang
Summary: DeepATPseq is a novel method for predicting protein-ATP binding residues without using protein three-dimensional structure or sequence-derived structural information. It achieves an accuracy of 77.71% and demonstrates the advantage of combining DCNN and SVM for extracting more discriminative information from PSFM profiles.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Omer Ali, Amna Farooq, Mingyi Yang, Victor X. Jin, Magnar Bjoras, Junbai Wang
Summary: The abc4pwm tool efficiently clusters PWMs from multiple sources, generates representative motifs for each cluster, evaluates clustering quality automatically, and filters out incorrectly clustered PWMs. It can also automatically update the human DNA-Binding Domain (DBD) family database, classify known human TF PWMs to the respective DBD family, and conduct TF motif searching and motif discovery using a new ensemble learning approach.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Hani M. Samawi, Ding-Geng Chen
Summary: The paper introduces a new ranked simulated resampling approach that is more accurate and efficient than Efron's bootstrap resampling approach. Simulation studies and real data applications support this comparison.
JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION
(2021)
Article
Biochemical Research Methods
Changyong Yu, Yuhai Zhao, Chu Zhao, Haitao Ma, Guoren Wang
Summary: This article introduces a more accurate and efficient pre-alignment algorithm called DiagAF for sequence alignment. DiagAF uses a new lower bound of edit distance based on shift hamming masks and can handle alignments of sequence pairs with different lengths. It also allows for early termination of alignments. The experiment shows that DiagAF achieves a lower error rate and requires less time compared to state-of-the-art methods, making it a potential improvement for sequence alignment software.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Orthopedics
Penglei Chen, Wangxin Liu, Cong Wu, Pengfei Ruan, Jicheng Zeng, Weifeng Ji
Summary: The study suggests that the fluoroscopy-guided direct anterior approach in the supine position (S-DAA) is more helpful in improving the position of acetabular and femoral components compared to the lateral decubitus position (L-DAA), with higher accuracy in adjustment after surgery. Additionally, there was no significant difference in hip joint function and activity between the two groups at follow-up.
BMC MUSCULOSKELETAL DISORDERS
(2023)
Article
Biochemical Research Methods
Wen-Xin Zheng, Shu-Xuan Wang, Hong Liu
Summary: By using an algorithm based on sequence features, we improved the accuracy of gene essentiality prediction in the Saccharomyces cerevisiae genome, with the best AUC of 0.944 for 5-fold cross-validation.
CURRENT BIOINFORMATICS
(2021)
Article
Zoology
Scott Y. S. Chui, Leszek Karczmarski
Summary: Reliable identification of individuals is crucial for behavioral studies of free-ranging animal populations. In the case of elephants, ear markings and facial wrinkle patterns can be used for individual identification. The facial wrinkle pattern method, with its high consistency and reliability, improves data robustness and reduces analytical errors. It also allows for a more representative sample of the elephant population across all age classes.
Article
Engineering, Electrical & Electronic
Thierry Tambe, En-Yu Yang, Glenn G. Ko, Yuji Chai, Coleman Hooper, Marco Donato, Paul N. Whatmough, Alexander M. Rush, David Brooks, Gu-Yeon Wei
Summary: The proliferation of personal AI assistant technologies is driving the growth in the consumer IoT market. This study presents a system-on-chip that executes speech-enhancing ASR and NLP workloads, providing uncompromising performance for context learning in long sequences and seamless operation in polyphonic environments.
IEEE JOURNAL OF SOLID-STATE CIRCUITS
(2023)
Article
Acoustics
Roberto San Millan-Castillo, Luca Martino, Eduardo Morgado, Fernando Llorente
Summary: In the last decade, soundscapes have become a popular research topic in Acoustics, with a focus on emotion recognition and variable selection. The study suggests that simple linear models can be used to describe soundscape emotions, and these models perform well.
IEEE-ACM TRANSACTIONS ON AUDIO SPEECH AND LANGUAGE PROCESSING
(2022)
Proceedings Paper
Electrochemistry
Ghadir Razaz, Torbjorn Carlberg
Summary: The study addresses the issue of accuracy in chemical composition analysis of as-cast aluminum alloys using sampling methods, as well as the research on a novel insulated periphery mold for sampling tests. Results from samples made with the new mold show more accurate analyses and good reproducibility in segregation profiles.
LIGHT METALS 2021, 50TH EDITION
(2021)
Article
Biochemical Research Methods
Chencheng Xu, Qiao Liu, Jianyu Zhou, Minzhu Xie, Jianxing Feng, Tao Jiang
Article
Multidisciplinary Sciences
Chuzhong Li, Weiyan Xie, Jared S. Rosenblum, Jianyu Zhou, Jing Guo, Yazhou Miao, Yutao Shen, Hongyun Wang, Lei Gong, Mingxuan Li, Sida Zhao, Sen Cheng, Haibo Zhu, Tao Jiang, Shiying Ling, Fei Wang, Hongwei Zhang, Mingshan Zhang, Yanming Qu, Qi Zhang, Guilin Li, Junmei Wang, Jun Ma, Zhengping Zhuang, Yazhuo Zhang
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng
Article
Biochemical Research Methods
Dipan Shaw, Hao Chen, Minzhu Xie, Tao Jiang
Summary: The DeepLPI method uses a hybrid framework that integrates sequence, structure, and expression data to predict interactions between lncRNAs and protein isoforms. By combining multimodal deep learning neural network and conditional random field, along with using multiple instance learning approach, DeepLPI has improved prediction performance significantly. Further correlation analyses also demonstrated the effectiveness of co-expression information in predicting interactions.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Hailin Hu, Xianggen Liu, An Xiao, YangYang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song, Jianyang Zeng
Summary: Riboexp is a novel deep reinforcement learning-based framework that successfully models the uneven distribution of ribosomes on mRNA during translation elongation, outperforming existing methods in predicting ribosome density. The application of Riboexp in codon optimization significantly increases protein production, while also providing meaningful biological insights through in-depth analyses.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Xuan He, Sai Zhang, Yanqing Zhang, Zhixin Lei, Tao Jiang, Jianyang Zeng
Summary: The study introduced a model named PULSE based on convolutional neural network for analyzing large-scale Psi site data and characterizing the sequence features of pseudouridylation. The validation tests showed that PULSE outperformed other prediction methods, providing novel insights into the functional roles of pseudouridylation and enabling further research on the transcriptome-wide landscape of Psi sites.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Yuanpeng Xiong, Xuan He, Dan Zhao, Tingzhong Tian, Lixiang Hong, Tao Jiang, Jianyang Zeng
Summary: N-6-methyladenosine (m(6)A) is the most prevalent modification in eukaryotic mRNAs, regulating various biological processes. The computational framework MASS, based on multi-task curriculum learning, outperforms existing methods in capturing m(6)A features across multiple species. MASS also helps elucidate m(6)A similarities and differences among species and their relationships with gene regulation properties.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Agustina De Francesco, Amelia H. Lovelace, Dipan Shaw, Min Qiu, Yuanchao Wang, Fatta Gurung, Veronica Ancona, Chunxia Wang, Amit Levy, Tao Jiang, Wenbo Ma
Summary: This study determined the expression profiles of 'Candidatus Liberibacter asiaticus' (Las) genes using a bacterial cell enrichment procedure. The results revealed highly expressed genes in citrus and differentially expressed genes between citrus and Asian citrus psyllids. The study provides insights into the biology of Huanglongbing and the interactions between Las, its plant host, and insect vector.
Article
Biochemistry & Molecular Biology
Da-Cheng Hao, Hao Chen, Pei-Gen Xiao, Tao Jiang
Summary: In this study, the first global analysis of AS events in Dichocarpum was conducted using full-length transcriptome datasets of five Chinese endemic species. The research identified numerous AS events and successfully predicted the functions of AS isoforms.
Article
Genetics & Heredity
Hao Chen, Dipan Shaw, Dongbo Bu, Tao Jiang
Summary: Annotating the functions of gene products is crucial in biology, with various databases established for recording functional knowledge at the gene level. There is a growing demand for functional annotations at the isoform resolution in many biological applications. Prediction of isoform functions and isoform-isoform interactions have been treated as separate computational problems, but they are actually intertwined and could benefit from each other.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Proceedings Paper
Computer Science, Artificial Intelligence
Zhiwei Hong, Xiaocheng Fan, Tao Jiang, Jianxing Feng
THIRTY-FOURTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, THE THIRTY-SECOND INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE AND THE TENTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE
(2020)
Article
Mathematical & Computational Biology
Jianyu Zhou, Pan Li, Wanwen Zeng, Wenxiu Ma, Zhipeng Lu, Rui Jiang, Qiangfeng Cliff Zhang, Tao Jiang
QUANTITATIVE BIOLOGY
(2020)
Article
Mathematical & Computational Biology
Jie Shi, Xiangrui Zeng, Rui Jiang, Tao Jiang, Min Xu
QUANTITATIVE BIOLOGY
(2020)
Article
Endocrinology & Metabolism
Poonamjot Deol, Elena Kozlova, Matthew Valdez, Catherine Ho, Ei-Wen Yang, Holly Richardson, Gwendolyn Gonzalez, Edward Truong, Jack Reid, Joseph Valdez, Jonathan R. Deans, Jose Martinez-Lomeli, Jane R. Evans, Tao Jiang, Frances M. Sladek, Margarita C. Curras-Collazo
Article
Biochemical Research Methods
Weihua Pan, Tao Jiang, Stefano Lonardi
JOURNAL OF COMPUTATIONAL BIOLOGY
(2020)