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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Elina Tjioe Michael Berry Ramin Homayouni Genome Science and Technology Graduate School University of Tennessee Knoxville TN USA Department of Electrical Engineering and Computer Science University of Tennessee Knoxville TN USA Bioinformatics Program Department of Biology University of Memphis Memphis TN USA

The rapid growth of the biomedical literature and genomic information presents a major challenge for determining the functional relationships among genes. In this study, we develop a Web-based bioinformatics software environment called FAUN or feature annotation using nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity and parameterization of NMF for processing gene sets are discussed. We tested FAUN on three manually constructed gene document collections, and then used it to analyze several microarray-derived gene sets obtained from studies of the developing cerebellum in normal and mutant mice. FAUN provides utilities for collaborative knowledge discovery and identification of new gene relationships from text streams and repositories (e.g., MEDLINE). It is particularly useful for the validation and analysis of gene associations suggested by microarray experimentation.

关键词： Bioinformatics Genomics Data mining Matrix decomposition Large scale integration Feature extraction Iterative methods Biological system modeling Computer science Computational biology

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Molecular characterization of an anther-preferential gene from rice

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Journal of Plant Biology 2000年第4期43卷 232-237页

作者： Young -Ju Choi Ayahiko Shomura Takuji Sasaki Gynheung An Yong -Yoon Chung Department of Biology Korea University Seoul Korea Rice Genome Research Program National Institute of Agrobiological Resources Tsukuba Japan National Research Laboratory of Plant Functional Genomics Division of Molecular Life Sciences Pohang University of Science and Technology (POSTECH) Pohang Korea

Expression levels of anther-expressed genes in rice were estimated by plaque hybridization. A total of 33 cDNAs, isolated randomly from an anther-enriched cDNA library, were used as probes to hybridize both anther and leaf cDNAs. The expression level of individual cDNA clones was then estimated by counting the number of plaques hybridized to each probe. Based on abundance patterns that appeared in both anther and leaf cDNA libraries, the clones were classified into three groups. This classification showed that the majority of the clones (one group) exhibited expression in both cDNA libraries at almost equal frequency. The other two groups showed either low or no expression in the leaf cDNA library. Among the cDNA clones,RA1003 (detected only in the anther cDNA library) was selected and further characterized at the molecular level. Consistent with the results of the plaque hybridization experiment, northern blot analysis also revealed no gene expression in vegetative organs, leaves, or roots. However, expression was high in the flowers, especially in the anthers. Detailed molecular studies of the gene are also described and discussed here.

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Lin28a maintains a subset of adult muscle stem cells in an embryonic-like state

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细胞研究（英文版） 2023年第9期33卷 712-726页

作者： Peng Wang Xupeng Liu Ziyue Yao Yu Chen Lanfang Luo Kun Liang Jun-Hao Elwin Tan Min-Wen Jason Chua Yan-Jiang Benjamin Chua Shilin Ma Liping Zhang Wenwu Ma Shuqing Liu Wenhua Cao Luyao Guo Lu Guang Yuefan Wang He Zhao Na Ai Yun Li Chunwei Li Ruiqi Rachel Wang Bin Tean Teh Lan Jiang Kang Yu Ng Shyh Chang Institute of Zoology Chinese Academy of SciencesBeijingChina Beijing.Institute for Stem Cell and Regenerative Medicine Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina NUS Graduate School for Integrative Sciences and Engineering National University of SingaporeSingaporeSIngapore institute of Molecular and Cell Biology Genome Institute of SingaporeAgency for Science Technology and ResearchSingaporeSingapore Laboratory of Cancer Therapeutics Program in Cancer and Stem Cell BiologyDuke-National University of Singapore Medical SchoolSingaporeSingapore Laboratory of Cancer Epigenome Division of Medical ScienceNational Cancer Centre SingaporeSingaporeSingapore University of Chinese Academy of Sciences BeijingChina CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina Department of Clinical Nutrition Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina Institute of Zoology Chinese Academy of SciencesBeijingChina Beijing.Institute for Stem Cell and Regenerative Medicine Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina Laboratory of Cancer Therapeutics Program in Cancer and Stem Cell BiologyDuke-National University of Singapore Medical SchoolSingaporeSingapore Laboratory of Cancer Epigenome Division of Medical ScienceNational Cancer Centre SingaporeSingaporeSingapore CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina

During homeostasis and after injury,adult muscle stem cells(MuSCs)activate to mediate muscle ***,much remains unclear regarding the heterogeneous capacity of MuSCs for self-renewal and ***,we show that Lin28a is expressed in embryonic limb bud muscle progenitors,and that a rare reserve subset of Lin28a+Pax7-skeletal MuSCs can respond to injury at adult stage by replenishing the Pax7+MuSC pool to drive muscle *** with adult Pax7+MuSCs,Lin28a+MuSCs displayed enhanced myogenic potency in vitro and in vivo upon *** epigenome of adult Lin28a+MuSCs showed resemblance to embryonic muscle *** addition,RNA-sequencing revealed that Lin28a+MuSCs co-expressed higher levels of certain embryonic limb bud transcription factors,telomerase components and the p53 inhibitor Mdm4,and lower levels of myogenic differentiation markers compared to adult Pax7+MuSCs,resulting in enhanced self-renewal and stress-response ***,conditional ablation and induction of Lin28a+MuSCs in adult mice revealed that these cells are necessary and sufficient for efficient muscle ***,our findings connect the embryonic factor Lin28a to adult stem cell self-renewal and juvenile regeneration.

关键词： Muscle stem cells Regeneration

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Designing a Novel Low-Density, High-Strength Ti27.5zr26.5nb25.5ta8.5al12 Refractory High-Entropy Alloy for High-Temperature Applications

SSRN

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SSRN 2024年

作者： Naseer, Hashim Wang, Yangwei Bao, Jiawei Khan, Muhammad Abubaker Afifi, Mohamed A. School of Materials Science and Engineering Beijing Institute of Technology Beijing100081 China Tangshan Research Institute Beijing Institute of Technology Tangshan063000 China Beijing Advanced Innovation Center for Materials Genome Engineering School of Materials Science and Engineering University of Science and Technology Beijing Beijing100083 China Mechanical Engineering Program School of Engineering and Applied Sciences Nile University Giza12677 Egypt

This study introduces a novel Refractory High-Entropy Alloy (RHEA) with the composition Ti27.5Zr26.5Nb25.5Ta8.5Al12, designed for high-temperature structural applications while addressing the limitations of traditional nickel-based superalloys. The alloy was synthesized using vacuum arc melting and characterized through comprehensive experimental methods including X-ray diffraction (XRD), scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS), and transmission electron microscopy (TEM). This RHEA demonstrated exceptional mechanical properties, achieving a yield strength of 1356 MPa and a specific yield strength of 197.3 MPa·g⁻¹·cm³ at room temperature, with notable ductility (compressive strain >50%) across a wide temperature range up to 1000°C. The microstructural analysis revealed a two-phase BCC/B2 nanodomain structure that contributes significantly to its strength and ductility. This structure was further refined through controlled thermomechanical treatments, eliminating the need for additional heat treatment. The findings suggest that the Ti27.5Zr26.5Nb25.5Ta8.5Al12 RHEA holds great potential as a low-density, high-performance material for demanding environments, offering a viable alternative to heavier superalloys. © 2024, The Authors. All rights reserved.

关键词： Scanning electron microscopy

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Report of two cases of snRNA gene RNU4-2 related syndromic intellectual disability from Southeast Asia

Rare. Open Research in Rare Diseases

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Rare. Open Research in Rare Diseases 2025年 3卷 100054-100054页

作者： Goh, Jeannette Lim, Jiin Ying Simons, Annet Ewans, Lisa Kam, Sylvia Goh, Jasmine Teo, Jing Xian Chan, Sock Hoai Chan, Shermaine Ling, Simon Thomas, Terrence Tan, Gavin Lim, Weng Khong Lai, Angeline Jamuar, Saumya Shekhar Genetics service Department of Paediatrics KK Women’s and Children’s Hospital Singapore SingHealth Duke-NUS Genomic Medicine Centre Singapore Radboud University Nijmegen the Netherlands Centre for Clinical Genetics Sydney Children’s Hospitals Network Randwick NSW Australia Genomics and Inherited Disease Program Garvan Institute of Medical Research University of New South Wales Sydney Sydney NSW Australia School of Clinical Medicine Medicine & Health University of New South Wales Sydney NSW Australia SingHealth Duke-NUS Institute of Precision Medicine Singapore KK Research Centre KK Women’s and Children’s Hospital Singapore Neurology service Department of Paediatrics KK Women’s and Children’s Hospital Singapore Ocular Diagnostic Department Singapore National Eye Centre Singapore Cancer & Stem Cell Biology Program Duke-NUS Medical School Singapore Genome Institute of Singapore Agency for Science Technology and Research Singapore

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Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats

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Frontiers of Environmental science & Engineering 2019年第3期13卷 173-184页

作者： Gaston Azziz Matias Gimenez Hector Romero Patricia M. Valdespino-Castillo Luisa I. Falcon Lucas A. M. Ruberto Walter P. Mac Cormack Silvia Batista Molecular Microbiology Unit Clemente Estable Biological Research Insitute Montevideo 11600 Uruguay Microbiology Laboratory Faculty of Agronomy UdelaR Montevideo 12900 Uruguay Genome Organization and Evolution Laboratory Ecology and Evolution Department Faculty of Sciences UdelaR Montevideo 11400 Uruguay Molecular Biophysics and Integrated Bioimaging BSISB Imaging Program Lawrence Berkeley National Laboratory Berkeley CA 94720 USA Bacteial Ecology Laboratory Ecology Institute National Autonomous University of Mexico CDMX 04510 Mexico UN AM Yucatan Technology and Science Park Merida 97302 Mexico Argentine Antarctic Institute Buenos Aires 1650 Argentina Biotechnology Unit Faculty of Pharmacy and Biochemistry Nanobiotec Institute UBA-CONICET Buenos Aires 1113 Argentina

Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification, using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes. Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences. While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.

关键词： Beta-lactamases Antibiotic resistance coding genes Metagenomes Antarctic microbial mats

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Synthesis and Characterization of Solid-State Thermochromic Materials for Smart Windows

SSRN

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SSRN 2023年

作者： Zeng, Kai Yang, Siyu Xue, Chang Wu, Jinbo Wen, Weijia Materials Genome Institute Shanghai University China20444 China Faculty of Materials Science Shenzhen MSU-BIT University China Division of Emerging Interdisciplinary Areas Interdisciplinary Program Office The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Department of Physics The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong

This paper describes the synthesis and characterization of a novel material with reversible thermotropic transmittance, prepared via emulsion polymerization. The material consists of 75% Oc-tadecylamine (ODA) and 1% allyl methacrylate (ALMA), which displays a discoloration phe-nomenon at 35°C with a visible light transmittance greater than 90%. The synthesized powder was characterized using differential scanning calorimetry-thermogravimetric analysis (DSC-TG) and scanning electron microscopy (SEM), which revealed good thermal processing performance, uni-form particle size, and anchoring properties. Additionally, thermochromic polyvinyl butyral (PVB) film and laminated glass were fabricated, using co-extrusion, and compared with different types of glass. The laminated glass with thermochromic PVB film showed a reduction in solar irradiance of 20-30% compared to double silver Low-E glass, demonstrating its effective shading and heat in-sulation properties. Overall, this study offers a promising approach for the development of smart materials with thermotropic transmittance for energy-efficient applications. © 2023, The Authors. All rights reserved.

关键词： Polyvinyl butyral

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Research Highlights: Shear-activated nanotherapeutics

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Nanomedicine 2012年第11期7卷 1653-1655页

作者： Sukanya Iyer Mitchel J Doktycz Graduate Program in Genome Science & Technology University of Tennessee Knoxville TN 37996 USA Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak Ridge TN 37831 USA.

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Mechano-active cartilage tissue engineering: The effect of dynamic compressive stimulation

Mechano-active cartilage tissue engineering: The effect of d...

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作者： Jung, Youngmee Kim, Soo Hyun Kim, Sang-Heon Kim, Young Ha Xie, Jun Matsuda, Takehisa Min, Byoung Goo Biomaterials Research Center Korea Institute of Science and Technology P.O.Box 131 Cheongryang Seoul 130-650 Korea Republic of Interdisciplinary Program Medical and Biological Engineering Major Seoul National University 28 Yeongeon Chongro Seoul 110-790 Korea Republic of Department of Materials Science and Engineering Gwangju Institute of Science and Technology 1 Oryang Buk Gwangju 500-712 Korea Republic of Department of Orthopaedic Surgery School of Medicine Fukuoka University 8-19-1 Nanakuma Jonan Fukuoka 814-0180 Japan Genome and Biomedical Engineering Laboratory Kanazawa Institute of Technology 7-1 Ohgigaoka Nonoichi Ishikawa 921 - 8501 Japan Department of Biomedical Engineering Seoul National University 28 Yeongeon Chongro Seoul 110-790 Korea Republic of

Mechano-active scaffolds were fabricated from very elastic poly(lactide-co-carprolactone) by a gel-pressing method. The scaffolds were seeded with bone marrow stromal cells and the continuous compressive deformation was applied to cell-polymer constructs in the chondrogenic media. Then, they were implanted in nude mice subcutaneously to evaluate for the effect of dynamic compression for regeneration of cartilage. From the biochemical analyses, chondrogenic differentiation was sustained and enhanced significantly and chondral extracellular matrix was increased through mechanical stimulation. Histological analyses showed that implants stimulated mechanically formed mature and well-developed cartilaginous tissue, as evidenced by bone marrow derived chondrocytes within lacunae. Consequently, the periodic application of dynamic compression can encourage bone marrow stromal cells to differentiation to chondrogenic lineage and to maintain their phenotypes.

关键词： Cartilage

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Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone

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Scientific Data 2017年第1期4卷 170158页

作者： Hallam, Steven J. Torres-Beltrán, Mónica Hawley, Alyse K. Department of Microbiology and Immunology University of British Columbia Vancouver V6T 1Z3 BC Canada Peter Wall Institute for Advanced Studies University of British Columbia Vancouver V6T 1Z2 BC Canada Genome Science and Technology Program University of British Columbia Vancouver V6T 1Z4 BC Canada Graduate Program in Bioinformatics University of British Columbia Vancouver V6T 1Z4 BC Canada ECOSCOPE Training Program University of British Columbia Vancouver V6T 1Z4 BC Canada

Today in Scientific Data, two compendia of geochemical and multi-omic sequence information (DNA, RNA, protein) generated over almost a decade of time series monitoring in a seasonally anoxic coastal marine setting are presented to the scientific community. These data descriptors introduce a model ecosystem for the study of microbial responses to ocean deoxygenation, a phenotype that is currently expanding due to climate change. Public access to this time series information is intended to promote scientific collaborations and the generation of new hypotheses relevant to microbial ecology, biogeochemistry and global change issues. © The Author(s) 2017.

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