Article
Biochemistry & Molecular Biology
Ziyuan Wang, Junjie Tan, Yanling Long, Yijia Liu, Wenyan Lei, Jing Cai, Yi Yang, Zhibin Liu
Summary: Multiple DNA/RNA sequence alignment is a crucial tool in bioinformatics for phylogenetic tree construction. By optimizing a dynamic programming algorithm using the longest common substring method, we developed an efficient alignment tool that outperforms existing tools for large datasets and long sequences.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Gokhan Ozsari, Ahmet Sureyya Rifaioglu, Ahmet Atakan, Tunca Dogan, Maria Jesus Martin, Rengul Cetin Atalay, Volkan Atalay
Summary: In this study, the researchers propose SLPred, an ensemble-based multi-view and multi-label protein subcellular localization prediction tool, which provides predictions for nine main subcellular locations using independent machine-learning models. The results show that SLPred outperforms other tools in most cases.
Article
Chemistry, Analytical
Ying Sun, Jun Hu, Juntong Yun, Ying Liu, Dongxu Bai, Xin Liu, Guojun Zhao, Guozhang Jiang, Jianyi Kong, Baojia Chen
Summary: SLAM technology is used for locating and mapping in unknown environments, but the constructed maps often lack readability and interactivity, making it difficult to grasp the information accurately. To enable intelligent robots to interact meaningfully with their environment, it is necessary to understand both the geometric and semantic properties of the scene. The proposed method reduces absolute positional errors, constructs dense semantic point cloud maps, and segments point cloud models of objects in the environment with high accuracy.
Article
Automation & Control Systems
Hyungmo Koo, Jongseok Bae, Woojin Choi, Hansik Oh, Hongjun Lim, Jongmin Lee, Chanmi Song, Kangyoon Lee, Keumcheol Hwang, Youngoo Yang
Summary: The retrodirective or retroreflective method is used as a radio-frequency beamforming method for massive antenna arrays, with a specific calibration technique for optimal operation. The proposed calibration method was verified for a 5.2 GHz MPT system, achieving optimal retroreflective beamforming for charging mobile handsets at short- and mid-range distances.
IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS
(2021)
Article
Computer Science, Artificial Intelligence
Yael Balbastre, Mikael Brudfors, Michela Azzarito, Christian Lambert, Martina F. Callaghan, John Ashburner
Summary: Quantitative MR imaging is gaining popularity, but noise in parameter maps is a common issue. This study proposes a probabilistic generative model to jointly recover parameter maps, achieving rapid and stable convergence with a second order optimization method. Implemented with PyTorch, the framework can further decrease noise in maps.
MEDICAL IMAGE ANALYSIS
(2021)
Article
Biochemical Research Methods
Zhiwen Lu, Lu Guo, Jianhua Chen, Rongshu Wang
Summary: A large number of researchers have focused on improving the speed and reducing the cost of genome sequencing, which has made it easier for researchers to study and analyze genome data. However, storing and transmitting the vast amount of genome data generated by high-throughput sequencing technologies efficiently is a challenge for data compression researchers. This paper proposes an algorithm based on reference genome sequences to compress genome data in FASTA format. The algorithm utilizes the characteristics of suffix array (SA) and longest common prefix (LCP) array to select appropriate substrings and compress the target genome sequence.
BMC BIOINFORMATICS
(2023)
Article
Environmental Sciences
Jesper H. Andersen, Miguel Caetano, Anne Grouhel-Pellouin, Eva Therese Harvey, Johnny Reker, Ciaran J. Murray
Summary: We have conducted a comprehensive assessment of contamination in Europe's seas and coastal areas, using various data sources and assessment tools. This study is of great significance in terms of supporting decision-making.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Green & Sustainable Science & Technology
Bingchao Zhao, Han Wang, Zhihao Huang, Qianqian Sun
Summary: This research provides an automated Multi-Criteria Decision Making (MCDM) technique with geographical information system (GIS) to solve the intricate nature of location identification and prioritization difficulty caused by the availability of numerous indicators, such as economic and environmental technical, social, and risk criteria. The F-TOPSIS outperforms the other methods with the highest performance ratio of 98.78% when compared to others.
SUSTAINABLE ENERGY TECHNOLOGIES AND ASSESSMENTS
(2022)
Article
Chemistry, Physical
Wei Bin Seh, Ran Xu, Shuo Deng, Zeqing Sun, Zhixun Wang, Zheng Fan, Lei Wei, Qing Zhang
Summary: This work demonstrates the conversion of ultrasonic vibration power to DC output using semiconducting wire-based electric generators, enabling the capability of a self-driven powered ultrasonic sensor.
Article
Computer Science, Information Systems
Jiacheng Shang, Si Chen, Jie Wu, Shu Yin
Summary: This paper explores a user location tracking system in augmented reality applications and demonstrates its effectiveness and accuracy through experiments. It also highlights the security threats in current location-based multi-player AR applications and proposes mitigation methods.
IEEE TRANSACTIONS ON MOBILE COMPUTING
(2022)
Article
Chemistry, Analytical
Yuting Jia, Honghong Wang, Hui Wang, Fangfang Wang, Kejian Gao, Zhengping Li
Summary: In this study, a new method that combines DNA probes, capillary electrophoresis, and universal PCR amplification was developed for the specific and sensitive detection of disease-related mRNA splice variants. This method improves the specificity and quantitative accuracy of mRNA splice variant assays and has been successfully applied to cell samples, providing a new strategy for mRNA splice variant-based clinical diagnosis and research.
Article
Engineering, Marine
Chuntong Li, Pengyu Wei, Xiaomeng Luo, Ze Jiang, Deyu Wang
Summary: Computer-aided design (CAD), computer-aided engineering (CAE), and virtual reality (VR) are integrated into a unified tool for ship structure design/analysis/virtual evaluation based on Multi-Domain Feature Mapping (MDFM). This tool utilizes Extensible Markup Language (XML) to establish a multi-layer transmission and matching mechanism between data, information and knowledge, allowing CAD, CAE, and VR to be interconnected. Additionally, a visual expression strategy of CAD model and FEA data based on Unified Mesh Model (UMM) is proposed for virtual visualization and model reconstruction and evaluation. The effectiveness of this tool is demonstrated through engineering examples.
Review
Urban Studies
Laryssa Tarachucky, Jamile Sabatini-Marques, Tan Yigitcanlar, Maria Jose Baldessar, Surabhi Pancholi
Summary: This paper investigates the applicability of emerging location-based and mapping technologies in urban environments, aiming to develop a clearer understanding by identifying and categorizing key drivers. The study findings reveal three types of mapping approaches linked to two modes of use.
Article
Environmental Sciences
Iyke Maduako, Zhuangfang Yi, Naroa Zurutuza, Shilpa Arora, Christopher Fabian, Do-Hyung Kim
Summary: Computer vision for large scale building detection is challenging, especially when detecting specific buildings globally. However, using deep learning techniques and high-resolution satellite imagery, a Deep Convolutional Neural Network (CNN) can be trained to successfully map school locations. Regional models perform better due to exposure to diverse school structures and features, while the global model struggles with generalizing across different regions and countries.
Article
Engineering, Electrical & Electronic
Zhuyin Li, Andrea Giorgetti, Sithamparanathan Kandeepan
Summary: This paper proposes a method for multiple PU localization based on UAV-mounted antenna array's measurement of received power, with two algorithms applied to estimate the number and positions of PUs from the score map. Despite being a blind method, it exhibits excellent localization accuracy in large outdoor scenarios.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Chak Kwong Cheng, Xiao Lin, Yujie Pu, Joyce Ka Yu Tse, Yu Wang, Cheng-Lin Zhang, Xiaoyun Cao, Chi Wai Lau, Juan Huang, Lei He, Jiang-Yun Luo, Yu-Tsung Shih, Song Wan, Chi Fai Ng, Li Wang, Ronald Ching Wan, Jeng-Jiann Chiu, Ting Fung Chan, Xiao Yu Tian, Yu Huang
Summary: This study utilized single-cell RNA sequencing to explore the transcriptional landscape and heterogeneity of dysfunctional endothelial cells in atherosclerotic aortae. SOX4 was identified as a novel marker for atherosclerosis and was shown to promote atherogenesis and endothelial-to-mesenchymal transition. Hyperlipidemia-associated cytokines and oscillatory blood flow were found to upregulate SOX4 expression, while the anti-diabetic drug metformin suppressed SOX4 levels in endothelial cells.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Jizhou Zhang, Xiao Lin, Yuelong Chen, Tsz-Ho Li, Alan Chun-Kit Lee, Eugene Yui-Ching Chow, William Chi-Shing Cho, Ting-Fung Chan
Summary: Characterization of subcellular RNA distribution was conducted using subcellular nanopore direct RNA-sequencing (DRS) and a computational pipeline called LAFITE. The study showed that LAFITE outperforms current methods in detecting full-length transcripts, especially low-abundance isoforms. Experimental validation confirmed the reliability of LAFITE in identifying novel isoforms. Applying LAFITE to subcellular DRS data revealed the complexity of the nuclear transcriptome at the isoform level.
Review
Biochemistry & Molecular Biology
Ki-Kei Chan, Ting-Fung Chan, William Bendena, Jerome H. L. Hui
Summary: The importance of RNAs is traditionally associated with protein-coding RNAs, while non-coding RNAs (ncRNAs) were believed to be useless. However, in the past decade, ncRNAs have been found to play significant roles in various biological activities, including hormonal and metabolic regulation. Among ncRNAs, microRNA (miRNA) is a small RNA transcript of approximately 20 nucleotides, long non-coding RNA (lncRNA) is an RNA transcript with more than 200 nucleotides, and circular RNA (circRNA) is derived from back-splicing of pre-mRNA. These ncRNAs can regulate gene expression levels at epigenetic, transcriptional, and post-transcriptional levels through various mechanisms in insects. Understanding these key regulators is crucial for both basic and applied entomology. This review aims to summarize and discuss the current knowledge of miRNA, lncRNA, and circRNA in the well-studied insect model, the fruit fly Drosophila.
Article
Endocrinology & Metabolism
Claudia H. T. Tam, Cadmon K. P. Lim, Andrea O. Y. Luk, Mai Shi, Hoi Man Cheung, Alex C. W. Ng, Heung-man Lee, Eric S. H. Lau, Baoqi Fan, Guozhi Jiang, Alice P. S. Kong, Risa Ozaki, Elaine Y. K. Chow, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny Y. Y. Leung, Elaine Y. N. Cheung, Man Wo Tsang, Grace Kam, Ip Tim Lau, June K. Y. Li, Vincent T. F. Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, Xiaodan Fan, Ting Fung Chan, Kevin Y. L. Yip, Si Lok, Weichuan Yu, Stephen K. W. Tsui, Hui-Yao Lan, Cheuk Chun Szeto, Nelson L. S. Tang, Brian Tomlinson, Yu Huang, Alicia J. Jenkins, Anthony Keech, Wing-Yee So, Juliana C. N. Chan, Ronald C. W. Ma
Summary: The objective of this study was to uncover genetic determinants of coronary heart disease (CHD) in type 2 diabetes (T2D) and explore their applications. The study identified a novel variant associated with CHD and blood pressure (BP) in Chinese T2D patients, and found that this variant interacts with BP goal attainment to have divergent effects on CHD risk.
Article
Biochemistry & Molecular Biology
Chi Tung Choy, Un Kei Chan, Pui Ling Kella Siu, Junwei Zhou, Chi Ho Wong, Yuk Wai Lee, Ho Wang Chan, Joseph Chi Ching Tsui, Steven King Fan Loo, Stephen Kwok Wing Tsui
Summary: Psoriasis is a common chronic immune-mediated inflammatory skin disease with various comorbidities. Gut microbiome dysbiosis can exacerbate inflammation and affect the immune system in psoriasis patients, and the gut microbiome can be modulated by probiotics. In this study, psoriasis patients in Southern China were compared to healthy subjects, and the influence of gut microbiome dysbiosis on psoriasis was investigated. It was found that certain bacteria were enriched in psoriasis patients and healthy subjects, and metabolic functional pathways differed between the two groups. Additionally, the use of probiotics improved symptoms and restored gut dysbiosis in psoriasis patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Qiao Du, Fang Peng, Qing Xiong, Kejin Xu, Kevin Yi Yang, Mingqiang Wang, Zhitian Wu, Shanying Li, Xiaorui Cheng, Xinjie Rao, Yuyouye Wang, Stephen Kwok-Wing Tsui, Xi Zeng
Summary: In the genome of Beihai amphioxus, 347 viral homologous fragments (HFs) were found, mostly located on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, especially in their CDS regions and promoters. A variety of amphioxus genes with a high frequency of HFs, including histone-related genes, were identified. This comprehensive analysis of viral HFs sheds light on the often overlooked role of viral integration in amphioxus evolution.
Article
Engineering, Environmental
Tsz Chun Ho, Hin Ting Wan, Wang Ka Lee, Thomas Ka Yam Lam, Xiao Lin, Ting Fung Chan, Keng Po Lai, Chris Kong Chu Wong
Summary: Prenatal exposure to PFOS increases the metabolic risk of fetuses and alters lipid and glucose metabolism in fetal livers. PFOS activates AMPK signaling and modulates the expression of PPARα and PPARγ downstream target genes, promoting fatty acid oxidation and lipogenesis, thus affecting the postnatal susceptibility of fetuses to metabolic challenges.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yiwei Wang, Jinpao Hou, Joseph Chi-Ching Tsui, Lin Wang, Junwei Zhou, Un Kei Chan, Claudia Jun Yi Lo, Pui Ling Kella Siu, Steven King Fan Loo, Stephen Kwok Wing Tsui
Summary: The study found that there are differences in the gut microbiome structure and metabolic functions between adult atopic dermatitis (AD) patients and healthy individuals. AD patients are more prone to allergies, especially non-food allergies. Additionally, the gut microbiome composition differs significantly between the AD and normal groups. The study also suggests potential therapeutic strategies targeting the gut microbiome for AD and provides evidence for the involvement of the gut-skin axis in AD patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Vanika Garg, Aamir W. Khan, Kevin Fengler, Victor Llaca, Yuxuan Yuan, Tri D. Vuong, Charlotte Harris, Ting-Fung Chan, Hon Ming Lam, Rajeev K. Varshney, Henry T. Nguyen
Summary: Highly contiguous genome assemblies were generated for two economically important soybean cultivars, Williams 82 and Lee, using complementary genomics technologies and assembly algorithms. Centromeric and telomeric repeats were clearly annotated on all chromosomes of both cultivars. The complete reconstructions of several chromosomes without any gaps and the identification of protein-coding genes will greatly contribute to soybean research and improvement.
Article
Cell Biology
Huanhuan Zhou, Lu Yang, Xiao Lin, Ting Fung Chan, Nikki Pui-Yue Lee, William Ka Fai Tse, Xing Zhang, Rong Li, Keng Po Lai
Summary: Hepatocellular carcinoma (HCC) is a common and deadly cancer. The study found that USP44 expression is suppressed in HCC tissue, and low USP44 expression is associated with poor survival and advanced tumor stage in HCC patients. Functional analysis showed that USP44 plays an important role in HCC cell growth and cell cycle regulation. Transcriptomic analysis and pathway analysis revealed that USP44 regulates gene networks involved in cell proliferation, metastasis, and apoptosis in HCC.
Correction
Biochemistry & Molecular Biology
Qu Zhe, Wing Chung Yiu, Ho Yin Yip, Wenyan Nong, Clare W. C. Yu, Ivy H. T. Lee, Annette Y. P. Wong, Nicola W. Y. Wong, Fiona K. M. C. Cheung, Ting Fung Chan, Kwok Fai Lau, Silin Zhong, Ka Hou Chu, Stephen S. Tobe, David E. K. Ferrier, William G. Bendena, Jerome H. L. Hui
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Letter
Plant Sciences
Wai-Shing Yung, Ting-Fung Chan, Fanjiang Kong, Hon-Ming Lam
Article
Plant Sciences
Tri D. Vuong, Liliana Florez-Palacios, Leandro Mozzoni, Michael Clubb, Chuck Quigley, Qijian Song, Shaila Kadam, Yuxuan Yuan, Ting Fung Chan, Mohamed Abdur Rouf Mian, Henry T. Nguyen
Summary: This study identified a new major QTL for seed protein and oil on chromosome 20 using Infinium BARCSoySNP6K BeadChips, which explained high phenotypic variation for these traits across multiple field environments.
Article
Biochemical Research Methods
Chen Li, Ting-Fung Chan, Can Yang, Zhixiang Lin
Summary: The study introduces a method called stVAE, based on the variational autoencoder framework, to deconvolve the cell-type composition of cellular resolution spatial transcriptomic datasets. It accurately identifies spatial patterns of cell types and their relative proportions across spots.
Article
Environmental Sciences
Zulvikar Syambani Ulhaq, Delbert Almerick T. Boncan, Ting Fung Chan, William Ka Fai Tse
Summary: This study investigated the toxicity of PFHxS using a zebrafish model. One experiment demonstrated that PFHxS might affect glucose and fatty acid metabolism, leading to oxidative stress, developmental defects, and cell cycle arrest. Another experiment showed that exposure to PFHxS changed the concentrations of various metabolites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
