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Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

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Nature communications 2023年第1期14卷 6540页

作者： Hitomi Takada Yohei Sasagawa Mika Yoshimura Kaori Tanaka Yoshimi Iwayama Tetsutaro Hayashi Ayako Isomura-Matoba Itoshi Nikaido Akira Kurisaki Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. itoshi.nikaido@riken.jp. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. itoshi.nikaido@riken.jp. Master's/Doctoral Program in Life Science Innovation (Bioinformatics) Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Ibaraki Japan. itoshi.nikaido@riken.jp. Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. akikuri@bs.naist.jp.

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Developing zebrafish models for the study of Wnt-related central nervous system pathologies

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Neuroscience 2025年

作者： Natalia Erofeeva Murilo S. de Abreu Jiahao Cui Lee Wei Lim Longen Yang Allan V. Kalueff Institute of Translational Biomedicine St. Petersburg State University St. Petersburg Russia Institute of Experimental Medicine Almazov National Medical Research Center Ministry of Health of Russian Federation St. Petersburg Russia Graduate Program in Health Sciences Federal University of Health Sciences of Porto Alegre Porto Alegre Brazil Department of Biosciences and Bioinformatics School of Science Xi’an Jiaotong-Liverpool University Suzhou China Suzhou Key Laboratory on Neurobiology and Cell Signaling School of Science Xi’an Jiaotong-Liverpool University Suzhou China

The wingless-related integration site (Wnt) signaling pathway plays a crucial role in the development and pathology of the central nervous system (CNS), modulating neurogenesis, synaptic plasticity and cell fate determination. Dysregulation of this pathway is strongly implicated in the pathogenesis of several CNS disorders. Recognizing the growing importance of the Wnt signaling in the brain, here we provide novel insights into experimental animal models studying this mechanism, with a particular emphasis on zebrafish ( Danio rerio ), including CNS development, and high-throughput drug screening of compounds that modulate Wnt signaling. Despite certain limitations, zebrafish provide a promising and powerful model system to increase our understanding of the role of Wnt signaling in CNS function, and to foster the development of novel therapies for brain disorders associated with this signaling pathway.

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The Suok ‘ropewalking’ test of rodent anxiety and sensorimotor disintegration: А 20-year summary of its application in neuroscience research

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Behavioural Brain Research 2025年 493卷

作者： Vyacheslav D. Riga Alisa E. Makhortykh David S. Galstyan Murilo S. de Abreu Allan V. Kalueff Neurobiology Program Scientific Center for Genetics and Life Sciences Sirius University of Science and Technology Federal Territory Sirius Sochi Russia Almazov National Medical Research Centre Petersburg Russia Institute of Translational Biomedicine St. Petersburg State University Petersburg Russia Graduate Program in Health Sciences Federal University of Health Sciences of Porto Alegre Porto Alegre Brazil Western Caspian University Baku Azerbaijan Department of Biosciences and Bioinformatics School of Science Xi’an Jiaotong-Liverpool University Suzhou China Suzhou Key Municipal Laboratory of Neurobiology and Cell Signaling School of Science Xi’an Jiaotong-Liverpool University Suzhou China

The Suok (ropewalking) test has been developed in 2004 to simultaneously assess rodent locomotor activity, anxiety-like behavior, sensorimotor disintegration, and their interplay. Over the last 20 years, this ‘hybrid’ test has been used in rat and mouse neurobehavioral research by various laboratories globally. Here, we provide a detailed overview of the Suok test, its past and present uses, methodological strengths, limitations, the existing problems, potential future modifications and practical applications. We also discuss the implications of results obtained in this test for improving our understanding of brain pathogenesis and the development of therapies for anxiety, vestibular disorders, sensorimotor disintegration and its stress-induced subtype. Finally, we suggest novel potential avenues for adapting this behavioral paradigm to the current needs and challenges of rodent preclinical neuroscience and drug discovery research.

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Detecting Hemileia vastatrix using Vision AI as Supporting to Food Security for Smallholder Coffee Commodities

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IOP Conference Series: Earth and Environmental Science 2022年第1期998卷

作者： Teddy Suparyanto Erick Firmansyah Tjeng Wawan Cenggoro Digdo Sudigyo Bens Pardamean Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

The loss of food crops during the COVID-19 pandemic threatens food security in Indonesia as one of the world's top coffee producers. This affects the insecurity of coffee commodities which is influenced by several factors other than the pandemic such as pests, plant diseases, and extreme weather. Plant diseases, such as leaf rust, are a significant factor in the insecurity problem in coffee commodities. The fungus Hemileia vastatrix B et Br causes leaf rust disease, which is a pest that frequently damages coffee plants. This disease not only interferes with plant growth but also causes a decrease in coffee quality and quantity. This initial research aims to carry out early prevention of these diseases as supporting to food security in smallholder coffee commodities. An AI-based visual detection application is the result of this research. We collected 100 images of coffee leaves from various coffee plants. The image is reshaped to 256 x 256 pixels and randomly trimmed to 224 x 224 pixels to fulfill the size requirements of a standard Deep Learning technique. Each image was classified into two classes by a plant pest and disease specialist. The dataset was divided into training, validation, and testing series with a ratio of 60:20:20 for training procedures. The Convolutional Neural Network (CNN) research method used a variation of the ResNet CNN model with 18 layers. The best model validation was 59%.

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Choroid plexus apocrine secretion shapes CSF proteome during mouse brain development

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Nature neuroscience 2025年 2025 May 28页

作者： Ya'el Courtney Joshua P Head Neil Dani Olga V Chechneva Frederick B Shipley Yong Zhang Michael J Holtzman Cameron Sadegh Towia A Libermann Maria K Lehtinen Department of Pathology Boston Children's Hospital and Harvard Medical School Boston MA USA. Graduate Program in Neuroscience Harvard Medical School Boston MA USA. Department of Cell and Developmental Biology Vanderbilt University Nashville TN USA. Department of Neurosurgery University of California Davis Sacramento CA USA. Graduate Program in Biophysics Harvard University Cambridge MA USA. Pulmonary and Critical Care Medicine Department of Medicine Washington University School of Medicine St. Louis MO USA. Proteomics Bioinformatics and Systems Biology Center Beth Israel Deaconess Medical Center and Harvard Medical School Boston MA USA. Department of Pathology Boston Children's Hospital and Harvard Medical School Boston MA USA. maria.lehtinen@childrens.harvard.edu. Graduate Program in Neuroscience Harvard Medical School Boston MA USA. maria.lehtinen@childrens.harvard.edu. Graduate Program in Biophysics Harvard University Cambridge MA USA. maria.lehtinen@childrens.harvard.edu.

The choroid plexus (ChP) regulates cerebrospinal fluid (CSF) composition, providing essential molecular cues for brain development; yet, embryonic ChP secretory mechanisms remain poorly defined. Here we identify apocrine secretion by embryonic ChP epithelial cells as a key regulator of the CSF proteome and neurodevelopment in male and female mice. We demonstrate that the activation of serotonergic 5-HT receptors (by WAY-161503) triggers sustained Ca signaling, driving high-volume apocrine secretion in mouse and human ChP. This secretion alters the CSF proteome, stimulating neural progenitors lining the brain's ventricles and shifting their developmental trajectory. Inducing ChP secretion in utero in mice disrupts neural progenitor dynamics, cerebral cortical architecture and offspring behavior. Additionally, illness or lysergic acid diethylamide exposure during pregnancy provokes coordinated ChP secretion in the mouse embryo. Our findings reveal a fundamental secretory pathway in the ChP that shapes brain development, highlighting how its disruption can have lasting consequences for brain health.

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Correction: Resistance QTLs controlling leaf and neck blast disease identified in a doubled haploid rice population

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Euphytica 2023年第7期219卷 1-1页

作者： Korinsak, Siripar Sriprakhon, Saengchai Sirithunya, Kanyanat Sriwongchai, Tanee Wongsaprom, Chanakarn Plabpla, Anucha Vanavichit, Apichart Toojinda, Theerayut National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA) Khlong Luang Thailand Faculty of Science and Agricultural Technology Rajamangala University of Technology Lanna Chiangmai Thailand Department of Agronomy Faculty of Agriculture Kasetsart University Bangkok Thailand Interdisciplinary Graduate Program in Genetic Engineering and Bioinformatics Kasetsart University Bangkok Thailand Department of Agronomy Faculty of Agriculture at Kamphaeng Saen Kasetsart University Nakhon Pathom Thailand Rice Science Center Kasetsart University Nakhon Pathom Thailand

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*** as digital platform for vegetation analysis and estimation of carbon stock in KEHATI aqua park

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AIP Conference Proceedings 2024年第1期3026卷

作者： Nanda Satya Nugraha Dian Pratama Putra Mohammad Prasanto Bimantio Amallia Ferhat Rama Zakaria Rudi Nirwantono Teddy Suparyanto Bens Pardamean Faculty of Forestry Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agriculture Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia 55282 PT. Tirta Investama Pabrik Klaten Klaten Central Java Indonesia 57474 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 1148 Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

KEHATI AQUA Park is one of the green areas managed by PT. Tirta Investama Klaten (Klaten Factory). This area is located in Wangen and Ponggok Villages, Polanharjo District, Klaten Regency, Central Java, and is an integral part of the company’s seriousness in carbon reduction movement. When maintenance of the area is important for the sustainability of the park, there is however no data on the trees inventory in the area. Therefore, this study aims to invent the trees at KEHATI AQUA Park and evaluate the potential of the area to become a carbon sink using *** application. This study was conducted at the KEHATI AQUA Park. The census method was performed to collect tree data, and the result was recorded in *** application. The carbon stock calculation was estimated using the application according to the tree data submitted in the application. The study included a total of 1048 plantation spots in 51 tree species. From those numbers, about 738 trees existed, and the remaining spots were blank spaces. Based on the condition of the trees, those were 660 good trees, 17 dry trees, and 61 under pest infection. The carbon stock estimation at KEHATI AQUA Park Klaten in the next five years (2026) is around 40 tons of carbon. Therefore, it can be concluded that the park is valuable as an area to preserve biodiversity and as a carbon sink.

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Avatar-Like Body Imaging of Dermal Exposure to Melamine in Factory Workers Analyzed by Ambient Mass Spectrometry

SSRN

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SSRN 2022年

作者： Wu, Ming-Tsang Hsu, Yu-Ming Wu, Chia-Fang Huang, Min-Zong Shiea, Jentaie Pan, Chih-Hung Liu, Chia-Chu Chen, Chu-Chih Wang, Yin-Han Cheng, Ching-Mei Research Center for Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Clinical Medicine Department of Chemistry National Sun Yat-Sen University Kaohsiung Taiwan Institute of Labor Occupational Safety and Health Ministry of Labor Executive Yuan Taipei Taiwan Department of Urology Kaohsiung Medical University Hospital Kaohsiung Medical University Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Department of Laboratory Medicine Kaohsiung Municipal Hsiao-Kang Hospital Kaohsiung Taiwan PhD Program of Environmental and Occupational Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Clinical Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Public Health Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan

Ambient mass spectrometry thermal desorption-electrospray ionization/mass spectrometry (TD-ESI/MS) can rapidly identify chemicals without pretreatment of biological samples. This study used a high-throughput and semi-quantitative TD-ESI/MS screening technique for probe skin sampling of melamine workers occupationally exposed to different ambient melamine concentrations to create avatar-like body images, which were then used to study temporal and dynamic changes in nephrotoxic melamine exposure. We enrolled four voluntary melamine workers, each from one of four factory worksites. Melamine exposure was highest in manufacturing and molding, followed by grinding and polishing, packing, and administration, the lowest. Skin samples were collected Friday (end-of-shift) and Monday (pre-shift). Early morning one-spot urine samples were also collected right after skin sampling. In total, 2198 probe skin samples were collected and subjected to semi-quantitative TD-ESI/MS analyses of melamine chemical within 40 hours. Converted standardized body image scores revealed exposure to be highest in the manufacturing worker on Friday and lowest in the administrative worker on Monday. The absolute differences (Friday − Monday) of standardized body image scores were all significantly positive in each individual worker and across all four workers (permutation test, all p-values © 2022, The Authors. All rights reserved.

关键词： Chemical analysis

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GestaltMML: Enhancing Rare Genetic Disease Diagnosis through Multimodal Machine Learning Combining Facial Images and Clinical Texts

arXiv

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arXiv 2023年

作者： Wu, Da Yang, Jingye Liu, Cong Hsieh, Tzung-Chien Marchi, Elaine Blair, Justin Krawitz, Peter Weng, Chunhua Chung, Wendy Lyon, Gholson J. Krantz, Ian D. Kalish, Jennifer M. Wang, Kai Raymond G. Perelman Center for Cellular and Molecular Therapeutics Children's Hospital of Philadelphia PhiladelphiaPA19104 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Institute for Genomic Statistics and Bioinformatics University Hospital Bonn Rheinische Friedrich-Wilhelms-Universität Bonn Bonn Germany Department of Human Genetics New York State Institute for Basic Research in Developmental Disabilities Staten IslandNY United States Division of Human Genetics Children's Hospital of Philadelphia PhiladelphiaPA19104 United States Department of Pediatrics Boston Children’s Hospital Harvard Medical School BostonMA United States Biology PhD Program The Graduate Center The City University of New York New York United States Department of Genetics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pediatrics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA19104 United States

Individuals with suspected rare genetic disorders often undergo multiple clinical evaluations, imaging studies, laboratory tests and genetic tests, to find a possible answer over a prolonged period of time. Addressing this "diagnostic odyssey" thus has substantial clinical, psychosocial, and economic benefits. Many rare genetic diseases have distinctive facial features, which can be used by artificial intelligence algorithms to facilitate clinical diagnosis, in prioritizing candidate diseases to be further examined by lab tests or genetic assays, or in helping the phenotype-driven reinterpretation of genome/exome sequencing data. Existing methods using frontal facial photos were built on conventional Convolutional Neural Networks (CNNs), rely exclusively on facial images, and cannot capture non-facial phenotypic traits and demographic information essential for guiding accurate diagnoses. Here we introduce GestaltMML, a multimodal machine learning (MML) approach solely based on the Transformer architecture. It integrates facial images, demographic information (age, sex, ethnicity), and clinical notes (optionally, a list of Human Phenotype Ontology terms) to improve prediction accuracy. Furthermore, we also evaluated GestaltMML on a diverse range of datasets, including 528 diseases from the GestaltMatcher Database, several in-house datasets of Beckwith-Wiedemann syndrome (BWS, over-growth syndrome with distinct facial features), Sotos syndrome (overgrowth syndrome with overlapping features with BWS), NAA10-related neurodevelopmental syndrome, Cornelia de Lange syndrome (multiple malformation syndrome), and KBG syndrome (multiple malformation syndrome). Our results suggest that GestaltMML effectively incorporates multiple modalities of data, greatly narrowing candidate genetic diagnoses of rare diseases and may facilitate the reinterpretation of genome/exome sequencing data. © 2023, CC BY.

关键词： Diseases

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Assessing Family Medicine Residency programs’ Training on Human Trafficking: A National Survey of program Directors

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Journal of Human Trafficking 2020年第4期7卷 1-13页

作者： Mishori, Ranit Stolarz, Katherine Ravi, Anita Korostyshevskiy, Valeriy R. Chambers, Ronald Cronholm, Peter Global Health Initiatives Georgetown University School of Medicine Washington DC United States Global Health Dept. of Family Medicine MedStar Franklin Square Medical Center Baltimore MD United States The Institute for Family Health Department of Family Medicine Community Health Icahn School of Medicine at Mount Sinai New York NY United States Graduate Studies Department of Biostatistics Bioinformatics and Biomathematics Georgetown University Washington DC United States DIO Family Medicine Residency Program Chair Family Medicine Department Medical Director Mercy Family Health Center and Mercy Human Trafficking Clinic Sacramento CA United States Family Medicine and Community Health Perelman School of Medicine University of Pennsylvania Philadelphia PA United States

Background: Human trafficking (HT) affects millions globally, and is linked to significant health effects. Studies suggest victims interact with the healthcare system while exploited, yet go unrecognized. We sought to determine the content and extent of HT training in family medicine residency programs and to identify barriers to providing formal training. Methodology: Participation in the Council of Academic Family Medicine Educational Research Alliance (CERA) program Director (PD) survey in 2018. Results: Almost half of program directors stated their program had no HT training (45.8%), 35.4% had required training and 18.8% offer electives. HT was primarily taught via lectures (77.1%) vs. experiential learning (21.5%);the majority of programs dedicated 1–3 hours total during residency (79.5%) to HT. Nearly 2/3 of residents have reported “basic” competency (60.9%) but only 6% had advanced competency. Required training was associated with higher odds of residents graduating with an advanced level. programs with institutional protocols were 10 times more likely to have residents with advanced competency. Conclusion: Gaps remain in U.S. Family Medicine Residency programs' HT education, though it is unclear how that compares to other specialties. HT knowledge and practice should be linked to Accreditation Council graduate Medical Education competencies and integrated into residency curricula. © 2020, © 2020 Taylor & Francis.

关键词： family medicine graduate medical education Human trafficking primary care

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