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Erratum To: Respiratory viral pathogens among Singapore military servicemen 2009 – 2012: epidemiology and clinical characteristics

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BMC Infectious Diseases 2014年第1期14卷 1-2页

作者： Xin Quan Tan Vernon J Lee Xiahong Zhao Mark I-Cheng Chen Alex Richard Cook Jin Phang Loh Boon Huan Tan Wee Hong Victor Koh Sock Hoon Ng Biodefence Centre Ministry of Defence Singapore Singapore Preventive Medicine Residency Programme National University Health System Singapore Singapore Saw Swee Hock School of Public Health National University of Singapore Singapore Singapore Department of Clinical Epidemiology Tan Tock Seng Hospital Singapore Singapore Yale-NUS College National University of Singapore Singapore Singapore Program in Health Services and Systems Research Duke-NUS Graduate Medical School Singapore Singapore Department of Statistics and Applied Probability National University of Singapore Singapore Singapore Defence Medical and Environmental Research Institute Singapore Singapore

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A Novel Coated Suture Displays Antimicrobial Activity Without Compromising Structural Properties

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Journal of Oral and Maxillofacial Surgery 2024年第9期82卷 1147-1162页

作者： Daood, Umer Ilyas, Muhammad Sharjeel Ashraf, Mariam Akbar, Munazza Asif, Amina Khan, Abdul Samad Sidhu, Preena Sheikh, Zeeshan Davamani, Fabian Matinlinna, Jukka Peters, Ove A. Yiu, Cynthia Associate Professor Head of Restorative Division Division of Restorative Dentistry School of Dentistry International Medical University Kuala Lumpur Kuala Lumpur Malaysia Assistant Professor Department of Oral Biology Post Graduate Medical Institute Lahore Pakistan Associate Professor Postgraduate Medical Institute Lahore Pakistan Professor Postgraduate Medical Institute Lahore Pakistan Assistant Professor Postgraduate Medical Institute Lahore Pakistan Professor Department of Restorative Dental Sciences College of Dentistry Imam Abdulrahman Bin Faisal University Dammam Saudi Arabia Senior Lecturer Head of Restorative Division Division of Restorative Dentistry School of Dentistry International Medical University Kuala Lumpur Kuala Lumpur Malaysia Assistant Professor Department of Periodontology Applied Oral Sciences & Dental Clinical Sciences Faculty of Dentistry Dalhousie University Halifax NS Canada Associate Professor Division of Human Biology Faculty of Biomedical Science School of Health Sciences International Medical University Kuala Lumpur Malaysia Professor Applied Dental Sciences Division of Human Biology Dental Materials Science Applied Oral Sciences & Community Dental Care Faculty of Dentistry The University of Hong Kong Hong Kong China Professor Applied Dental Sciences University of Manchester School of Dentistry Manchester United Kingdom Professor Program Convenor Department of Endodontics Arthur A Dugoni School of Dentistry University of the Pacific San Francisco Professor Program Convenor Department of Endodontics The University of Queensland Brisbane QLD Australia Professor Head of Paediatric Dentistry Pediatric Dentistry Division Paediatric Dentistry and Orthodontics Faculty of Dentistry The University of Hong Kong Hong Kong China

Background: Treated or coated sutures promise to prevent contamination of wounds. Purpose: The purpose of the study was to coat surgical sutures with a new quaternary ammonium silane (QAS) antimicrobial compound at two different application temperatures and then to evaluate the resulting structural, physical, mechanical, and biological properties. Study Design, Setting, Sample: In vitro and in vivo studies were conducted using male albino Wistar rats approved by the Joint Ethical Committee of IMU and Postgraduate Medical Institute, Lahore. Only suture samples, coated uniformly with verified presence of the compound and of adequate length were used. Samples which were not coated uniformly and with inadequate length or damaged were excluded. Predictor Variable: Predictor variables were sutures with and without QAS coatings and different temperatures. Sutures were coated with QAS at 0.5 and 1.0% wt/vol using the dip coating technique and sutures with and without QAS coating were tested at 25 and 40 °C temperatures. Main Outcome Variable(s): Outcome variables of structural and physico-mechanical properties of QAS-coated and non-coated sutures were measured using Fourier transform infrared spectroscopy (for structural changes), confocal laser and scanning electron (for diameter changes), and tensile strength/modulus (for mechanical testing). Biologic outcome variables were tested (bacterial viability);macrophage cultures from Wistar rats were tested (M1/M2 polarization detecting IL-6 and IL-10). Macrophage cells were analyzed with CD80+ (M1) and CD163+ (M2). Chemotaxis index was calculated as a ratio of quantitative fluorescence of cells. Covariates: Not applicable. Analyses: Ordinal data among groups were compared using the Wilcoxon Mann-Whitney U test along with the comparison of histological analysis using the Wilcoxon Sign-rank test (P < .05). Results: Fourier transform infrared spectroscopy peak at 1490 cm⁻¹ confirmed the presence of QAS on suture's surfa

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Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in hepatocellular carcinoma:the PLANET study

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National Science Review 2022年第3期9卷 96-109页

作者： Weiwei Zhai Hannah Lai Neslihan Arife Kaya Jianbin Chen Hechuan Yang Bingxin Lu Jia Qi Lim Siming Ma Sin Chi Chew Khi Pin Chua Jacob Josiah Santiago Alvarez Pauline Jieqi Chen Mei Mei Chang Lingyan Wu Brian K.P.Goh Alexander Yaw-Fui Chung Chung Yip Chan Peng Chung Cheow Ser Yee Lee Juinn Huar Kam Alfred Wei-Chieh Kow Iyer Shridhar Ganpathi Rawisak Chanwat Jidapa Thammasiri Boon Koon Yoong Diana Bee-Lan Ong Vanessa H.de Villa Rouchelle D.Dela Cruz Tracy Jiezhen Loh Wei Keat Wan Zeng Zeng Anders Jacobsen Skanderup Yin Huei Pang Krishnakumar Madhavan Tony Kiat-Hon Lim Glenn Bonney Wei Qiang Leow Valerie Chew Yock Young Dan Wai Leong Tam Han Chong Toh Roger Sik-Yin Foo Pierce Kah-Hoe Chow Genome Institute of Singapore Agency for Science Technology and Research Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences School of Biological Sciences Nanyang Technological University Division of Biosciences Faculty of Life Sciences Division of Surgery and Surgical Oncology National Cancer Centre Department of Hepato-Pancreato-Biliary and Transplant Surgery Singapore General Hospital Division of Hepatobiliary and Pancreatic Surgery Department of Surgery University Surgical Cluster National University Health System Hepato-Pancreato-Biliary Surgery Unit Department of Surgery National Cancer Institute Division of Pathology National Cancer Institute Department of Surgery Faculty of Medicine University of Malaya Department of Surgery and Center for Liver Disease Management and Transplantation The Medical City Department of Laboratories The Medical City Department of Pathology Singapore General Hospital Institute for Infocomm Research ASTAR Department of Pathology National University Health System Translational Immunology Institute (TII) Sing Health Duke-NUS Academic Medical Centre Division of Gastroenterology and Hepatology University Medicine Cluster National University Hospital Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore Cancer Science Institute of Singapore National University of Singapore Division of Medical Oncology National Cancer Center Singapore Cardiovascular Research Institute National University of Singapore National University Healthcare System Singhealth-Duke-NUS Academic Surgery Program Duke-NUS Graduate Medical School Institute of Molecular and Cell Biology Agency for Science Technology and Research

Intra-tumor heterogeneity(ITH) is a key challenge in cancer treatment, but previous studies have focused mainly on the genomic alterations without exploring phenotypic(transcriptomic and immune)heterogeneity. Using one of the largest prospective surgical cohorts for hepatocellular carcinoma(HCC)with multi-region sampling, we sequenced whole genomes and paired transcriptomes from 67 HCC patients(331 samples). We found that while genomic ITH was rather constant across stages, phenotypic ITH had a very different trajectory and quickly diversified in stage Ⅱ patients. Most strikingly, 30% of patients were found to contain more than one transcriptomic subtype within a single tumor. Such phenotypic ITH was found to be much more informative in predicting patient survival than genomic ITH and explains the poor efficacy of single-target systemic therapies in HCC. Taken together, we not only revealed an unprecedentedly dynamic landscape of phenotypic heterogeneity in HCC, but also highlighted the importance of studying phenotypic evolution across cancer types.

关键词： hepatocellular carcinoma intra-tumor heterogeneity phenotypic evolution tumor evolution

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Low Energy Nanoemulsification of Origanum Vulgare Essential Oil: Factors of Influence

SSRN

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SSRN 2024年

作者： da Silva, Kaisa J. Machado, Francisco P. de Oliveira, Raquel N. Fernandes, Caio P. Mourão, Samanta C. Post-Graduate Program in Applied Sciences to Health Products Fluminense Federal University RJ NiteróiCEP 24241-000 Brazil Laboratory of Pharmaceutical Technology Fluminense Federal University Niterói RJ Rio de JaneiroCEP 24241-000 Brazil Laboratory of Technology in Natural Products Fluminense Federal University Niterói RJ Rio de JaneiroCEP 24241-000 Brazil

Origanum vulgare essential oil (EO) is widely used as a preservative in food but its low water solubility limits application in aqueous systems. This study investigated the influence of some factors in the nanoemulsification of this food additive, using a low-energy method. The impact of different surfactants, essential oil-to-surfactant ratios (EOSR), and the use of linseed mucilage in the aqueous phase were evaluated. Carvacrol (70.14%) and o-cymene (7.84%) were the major EO compounds. Linseed mucilage, obtained after lyophilization of the fluid extract, had 63.5% total fiber content and showed characteristic infra-red absorption bands related to polysaccharide. Polysorbate 80 produced smaller droplets compared to Polysorbate 20 at higher EOSR, likely due to better solubilization. Sorbitan monooleate stabilized emulsions at HLB 12.0 and EOSR 1:9, with droplet sizes of 170-180 nm and a polydispersity index below 0.250. Linseed mucilage further reduced droplet size to 140-150 nm at EOSR 1:9 and HLB 13.2. © 2024, The Authors. All rights reserved.

关键词： Oilseeds

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Integrated application of grafted ZnO and fungicide to control the fungicide-resistant Colletotrichum spp

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Journal of the Taiwan Institute of Chemical Engineers 2024年 155卷

作者： Chang, Tao-Ho Chen, Yi-Chi Lai, Yu-Fang Wu, Tzu-Chien Lai, Chian-Hui Hsueh, Han-Yu Chang, Pi-Fang Linda Program in Plant Health Care Academy of Circular Economy National Chung Hsing University Nantou540216 Taiwan Innovation and Development Center of Sustainable Agriculture National Chung Hsing University Taichung402202 Taiwan Master Program for Plant Medicine and Good Agricultural Practice National Chung Hsing University Taichung402202 Taiwan Department of Material Science & Engineering National Chung Hsing University Taichung402202 Taiwan Graduate Institute of Biomedical Engineering National Chung Hsing University Taichung402202 Taiwan Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung807378 Taiwan Department of Plant Pathology National Chung Hsing University 402202 Taiwan

Background: The Food and Agriculture Organization has reported approximately 40 % of food loss due to damage from plant pests and diseases, including fungal infections. Continuous application of agrichemicals for controlling fungal infection cause the occurrence of fungicide resistance. Colletotrichum spp., major causal agents for strawberry anthracnose, have gained concern for fungicide resistance issues. Methods: We developed novel antifungal strategies in the present study by integrating multibranched flower-like ZnO (fZnO) and agrochemicals (trifloxystrobin). fZnO compounds were synthesised using an eco-friendly and efficient hydrothermal method. Charged polymers with steric structures, such as hydrophilic polyacrylic acid (PAA) and polyethyleneimine (PEI), were grafted onto fZnO surfaces to improve the suspension ability of the compounds. We used the grafted fZnO compounds in combination with the fungicide trifloxystrobin to evaluate the in vitro and in vivo activities. Significant findings: Grafted fZnO (80 ppm) and trifloxystrobin (100 ppm) effectively inhibited the growth of fungicide-resistant Colletotrichum spp. and limited strawberry anthracnose on leaves. PEI-grafted fZnO shows promise as an eco-friendly additive in sustainable agriculture due to its photocatalytic activity and ability to withstand environmental factors. © 2023

关键词： Zinc oxide

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Mechanistic Insights into CLNS1A-Mediated Chemoresistance and Tumor Progression in Non-small Cell Lung Cancer

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Cancer letters 2025年 626卷 217783页

作者： Tong-You Wade Wei Jiun-Yi Hsia Tsung-Ying Yang Yu-Xu Huang Guo-Zhi Wang Yi-Chung Liu Yi-Wun Wang Fangzhou He Jo-Mei Maureen Chen Guo-Jun Zhao Ping-Chiang Lyu Li-Jen Su Shao-Chih Chiu Chang-Tze Ricky Yu Department of Applied Chemistry National Chi Nan University Nantou Taiwan Division of Cardiology Department of Medicine University of California San Diego La Jolla California USA. Electronic address: t1wei@health.ucsd.edu. Division of Thoracic Surgery Chung Shan Medical University Hospital Taichung Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan. Department of Chest Medicine Taichung Veterans General Hospital Taichung Taiwan Doctoral Program in Translational Medicine National Chung Hsing University Taichung Taiwan. Department of Medicine JingGangShan University Ji'an China. Division of Thoracic Surgery Chung Shan Medical University Hospital Taichung Taiwan. Department of Life Sciences National Tsing Hua University Hsinchu Taiwan. Cardiovascular Research Center School of Basic Medical Sciences Xi'an Jiaotong University Health Science Center Xi'an China. Department of Applied Chemistry National Chi Nan University Nantou Taiwan. Department of Cardiology The First Affiliated Hospital of Zhengzhou University Zhengzhou China. Institute of Bioinformatics and Structural Biology Department of Life Science National Tsing Hua University Hsinchu Taiwan. Department of Biomedical Sciences and Engineering Education and Research Center for Technology Assisted Substance Abuse Prevention and Management and Core Facilities for High Throughput Experimental Analysis National Central University Taoyuan Taiwan. Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Translational Cell Therapy Center Department of Medical Research China Medical University Hospital Taichung Taiwan. Electronic address: scchiu@mail.cmu.edu.tw. Department of Applied Chemistry National Chi Nan University Nantou Taiwan. Electronic address: ctyu@ncnu.edu.tw.

CLNS1A is a chloride channel protein and an essential component of the methylosome complex, which additionally comprises PRMT5 and MEP50. In this study, we investigated its contribution to lung cancer and its potential as a therapeutic target. Analysis of transcriptomic datasets and western blotting revealed that CLNS1A, PRMT5, and MEP50 were overexpressed in lung cancer tissues, with elevated CLNS1A expression correlating with poor patient survival. CLNS1A overexpression enhanced platinum clearance from cells, increased the IC values for chemotherapy, and improved cell survival. Conversely, the knockdown of CLNS1A increased drug accumulation, reduced survival, and increased sensitivity to chemotherapy. The 3W mutant, a chloride channel-defective variant with steric hindrance at key bottleneck residues, impaired chloride ion transport, thereby reducing drug resistance, migration, and anchorage-independent growth. Mechanistically, CLNS1A promotes drug efflux through its chloride channel activity and activates the FAK-SRC-RAC1 pathway to enhance motility and clonogenicity. It also facilitates PRMT5-mediated RUVBL1 methylation to support anti-apoptotic DNA damage response signaling. In vivo, CLNS1A overexpression accelerated tumor growth and reduced survival, whereas CLNS1A knockdown sensitized tumors to cisplatin, enhancing therapeutic efficacy. These findings suggest that CLNS1A is a potential biomarker and therapeutic target, and its inhibition offers a strategy to overcome drug resistance and limit the metastatic progression of lung cancer.

关键词： Chemoresistance Chloride channel DNA damage response Lung cancer Metastasis

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vailá: VERSATILE ANARCHO INTEGRATED LIBERATION ÁNALYSIS IN MULTIMODAL TOOLBOX

arXiv

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arXiv 2024年

作者： Santiago, Paulo Roberto Pereira Chinaglia, Abel Gonçalves Flanagan, Kira Bedo, Bruno L.S. Mochida, Ligia Yumi Aceros, Juan Bononi, Aline Cesar, Guilherme Manna Biomechanics and Motor Control Laboratory School of Physical Education and Sport USP Brazil Graduate Program in Rehabilitation and Functional Performance Medical School USP Brazil Technology and Sports Performance Analysis Laboratory School of Physical Education USP Brazil Laboratory of Applied Biomechanics and Engineering Brooks College of Health UNF United States Department of Physical Therapy Brooks College of Health UNF United States College of Computing Engineering and Construction UNF United States Municipal Pharmacy Ribeirão Preto Brazil

Human movement analysis is crucial in health and sports biomechanics for understanding physical performance, guiding rehabilitation, and preventing injuries. However, existing tools are often proprietary, expensive, and function as "black boxes", limiting user control and customization. This paper introduces vailá—Versatile Anarcho Integrated Liberation Ánalysis in Multimodal Toolbox—an open-source, Python-based platform designed to enhance human movement analysis by integrating data from multiple biomechanical systems. vailá supports data from diverse sources, including retroreflective motion capture systems, inertial measurement units (IMUs), markerless video capture technology, electromyography (EMG), force plates, and GPS/GNSS systems, enabling comprehensive analysis of movement patterns. Developed entirely in Python 3.11.9, which offers improved efficiency and long-term support, and featuring a straightforward installation process, vailá is accessible to users without extensive programming experience. In this paper, we also present several workflow examples that demonstrate how vailá allows the rapid processing of large batches of data, independent of the type of collection method. This flexibility is especially valuable in research scenarios where unexpected data collection challenges arise, ensuring no valuable data point is lost. We demonstrate the application of vailá in analyzing sit-to-stand movements in pediatric disability, showcasing its capability to provide deeper insights even with unexpected movement patterns. By fostering a collaborative and open environment, vailá encourages users to innovate, customize, and freely explore their analysis needs, potentially contributing to the advancement of rehabilitation strategies and performance optimization. For more details in GitHub repository: https://***/vaila-multimodaltoolbox/vaila and the online documentation: https://*** Codes 92C10, 68U10, 65D18, 65K10 © 2024, CC BY-SA.

关键词： Electromyography

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I see sick people: Beliefs about sensory detection of infectious disease are largely consistent across cultures

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Brain, Behavior, and Immunity 2025年 128卷 737-750页

作者： Ackerman, Joshua M. Samore, Theodore Fessler, Daniel M.T. Kupfer, Tom R. Choi, Soyeon Merrell, Wilson N. Aarøe, Lene Aavik, Toivo Acabado, Stephen Akello, Grace Alfian, Ilham N. Al-Shawaf, Laith Alvarez, Marinés M. Ammann, Jeanine Arikan, Gizem Asha, Saiyeda A. Astobiza, Anibal M. Baeza-Ugarte, Carmen G. Barclay, Pat Barlow, Fiona Kate Bizarro, Lisiane Bressan, Paola Castellanos-Chacón, Andres Choy, Bryan K.C. Chusairi, Achmad Contreras-Garduño, Jorge Chávez Cosamalón, Brenda L. Costa-Neves, Bernardo De, Mallika de Lima, Tiago J.S. de Zoysa, Piyanjali Dryžaitė, Ieva Elbæk, Christian T. Fedor, Peter Fernández, Ana M. Fernandez-Morales, Regina Fülöp, Márta Gamsakhurdia, Vladimer Lado Garcia-Gómez, Leonor Garcia-Marques, Leonel Garduño-Franco, Jimena Pilar Grazioso, María del Habacht, Fanny Hasan, Youssef Haugestad, Camila P. Haugestad, Christian A.P. Havlíček, Jan Hernandez, Earl J. Hoang, Vu M. Hong, Minsung Hromatko, Ivana Iliško, Dzintra Imada, Hirotaka Jakšić, Ivana Jarmakowski, Tomasz Hjördísar Jónsdóttir, Harpa L. Kajokaite, Kotrina Kaňková, Šárka Kervyn, Nicolas Kim, Jinseok P. Kunst, Jonas R. Laakasuo, Michael Leongómez, Juan David Li, Norman P. Lu, Junsong Lynch, Nathan Maegli, María A. Manley, Harry Marcu, Gabriela McAfee, Thea Mitkidis, Panagiotis Molnár, Nándor B. Morvinski, Coby Muhamad, Haslina Nejat, Pegah Huy, Hoang Nguyen Oliveira, Angelica N. Olsson, Mats J. Onyishi, Charity N. Onyishi, Ike E. Orozco, Reegan Otterbring, Tobias Ottersen, Ida S. Pacheco-López, Gustavo Panagiotopoulou, Penny Paniagua, Walter Parvin, Roksana Pavlović, Zoran Prokop, Pavol Raffman, Emma Rizwan, Muhammad Rojas, Sheila Różycka-Tran, Joanna Sánchez, Oscar R. Selim, Heyla Sevi, Barış Shani, Yaniv Shastry, Madhulika S. Stieger, Stefan Suh, Eunkook M. Sumari, Melati Takemura, Kosuke Tognetti, Arnaud Trombetta, Roberta Z.R. Tybur, Joshua M. Ucak, Eylul B. Uchida, Yukiko Valentova, Jaroslava V. Viciana, Hugo Visine, Amandine Wang, Jin Wang, XT Yahiiaiev, Illia I. Zein, Rizqy A. Žeželj, Iris Department of Psychology University of Michigan Ann Arbor MI United States Religion Programme University of Otago Dunedin New Zealand Department of Anthropology University of California Los Angeles Los Angeles CA United States Center for Behavior Evolution & Culture University of California Los Angeles Los Angeles CA United States Bedari Kindness Institute University of California Los Angeles Los Angeles CA United States Department of Psychology Nottingham Trent University England Nottingham United Kingdom Department of Psychology University of Wisconsin-Madison Madison WI United States Center for the Experimental-Philosophical Study of Discrimination Aarhus University Aarhus Denmark Department of Political Science Aarhus University Aarhus Denmark Institute of Psychology University of Tartu Tartu Estonia Department of Mental Health Faculty of Medicine Gulu University Gulu Uganda Department of Psychology Universitas Airlangga East Java Indonesia Department of Psychology University of Colorado Colorado Springs Colorado Springs CO United States Department of Psychology Universidad del Valle Guatemala Guatemala City Guatemala Agroscope Research group Economic Modelling and Policy Analysis Ettenhausen Switzerland Department of Political Science Trinity College Dublin Dublin Ireland Department of Psychology International University of Business Agriculture and Technology Dhaka Bangladesh Department of Philosophy University of Granada Granada Spain Department of Psychology University of Guelph Guelph ON Canada School of Psychology University of Queensland Brisbane QLD Australia Graduate Program in Psychology Universidade Federal do Rio Grande Do Sul RS Porto Alegre Brazil Department of General Psychology University of Padova Padova Italy Faculty of Psychology Universidad El Bosque Bogotá Colombia Ministry of Defence Singapore Sustainability and Education Policy Network Saskatoon SK Canada Escuela Nacional de Estudios Superiores unid

Identifying cues to contagious disease is critical for effectively tracking and defending against interpersonal infection threats. People hold lay beliefs about the types of sensory information most relevant for identifying whether others are sick with transmissible illnesses. Are these beliefs universal, or do they vary along cultural and ecological dimensions? Participants in 58 countries (N = 19,217) judged how effective, and how likely they were to use, cues involving each of the five major sensory modalities in an imagined social interaction during a flu outbreak. Belief patterns were strongly consistent across countries (sight > audition > touch > smell > taste), suggesting a largely universal conceptualization of the role of sensory information for interpersonal respiratory disease detection. Results also support a safe senses hypothesis, with perceivers reporting that they would use senses that function at a distance—and thus reduce pathogen transmission risk—more than would be expected given participants’ beliefs as to the efficacy of these senses for disease detection. Where societal variation did emerge, it was captured by a cohesive set of socio-ecological factors, including human development, latitude, pathogen prevalence, and population density. Together, these findings reveal a shared lens through which contagious respiratory disease is assessed, one that prioritizes minimizing risk to perceivers, and may offer leverage for designing interventions to improve public health. © 2025 Elsevier Inc.

关键词： Behavioral immune system Culture Iterpersonal perception Pathogen threat Sensation Threat detection

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Histological Biomarkers and Microbiological Parameters of an Estuarine Fish from the Brazilian Amazon Coast as Potential Indicators of Risk to Human health

SSRN

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SSRN 2024年

作者： de Macedo, Gustavo Henrique Rodrigues Vale Castro, Jonatas da Silva de Jesus, Wanda Batista Costa, Ana Laíssa Pereira Ribeiro, Rafael do Carmo Silva Pires, Samanda de Jesus Roland de Miranda, Rita de Cássia Mendonça Firmo, Wellyson da Cunha Araújo Nascimento da Silva, Luís Cláudio Filho, Raimundo Nonato Diniz Costa Neta, Raimunda Nonata Fortes Carvalho Pinheiro Sousa, Débora Batista Federal University of Maranhão Maranhão São Luís65085-580 Brazil Coordination of Environmental Engineering Federal University of Maranhão Maranhão Balsas65800-000 Brazil Graduate Program in Biomedicine Faculty Florence Maranhão São Luís65020-470 Brazil Maranhão São Luís65075-441 Brazil Postgraduate Program in Biosciences Applied to Health Ceuma University Maranhão São Luís65075–120 Brazil Coordination of Electrical Engineering Federal University of Maranhão Maranhão Balsas65800-000 Brazil Department of Biology Maranhão State University Campus Paulo VI Maranhão São Luís65055-970 Brazil

This study aimed to isolate and identify pathogenic bacteria in the intestinal tract, skin and muscles of Sciades herzbergii, detect histopathological changes in the gill and liver, and use these biomarkers for the assessment of potential risks to human health. Fish were sampled during the rainy and dry seasons at two points: Ilha dos Caranguejos (IC) and Porto Grande (PG). Isolation and quantification were carried out using COLItest®. Colonies were subjected to identification and phenotypic investigation of antimicrobial resistance using Vitek®. Gill and liver samples were subjected to routine histological examination. The results indicated the presence of Klebsiella pneumoniae and Escherichia coli, the latter of which showed phenotypic resistance to norfloxacin and gentamicin. Fish caught at PG exhibited more extensive gill and liver damage than fish caught at IC. The findings suggest that histological changes in target organs of S. herzbergii may be influenced by infection with pathogenic bacteria. © 2024, The Authors. All rights reserved.

关键词： Biomarkers

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Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

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Nucleic acids research 2023年第13期51卷 6578-6592页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Bo-Jia Chen Yu-Te Lin Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Program in Integrative & Complex Diseases Department of Nutrition Texas A&M University College Station TX 77843 USA. Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

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