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A Geoelectric Approach for Karst Groundwater Analysis

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

作者： Amallia Ferhat Taufik Seizarsyah Mohammad Prasanto Bimantio Nanda Satya Nugraha Dian Pratama Putra Teddy Suparyanto Alam Ahmad Hidayat Bens Pardamean Agribusiness Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Geophysical Engineering Department Universitas Pembangunan Nasional 'Veteran' Yogyakarta Indonesia Agricultural Crop Technology Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Forestry Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Agricultural Engineering Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Artesian well is one of the major efforts to obtain water source for fulfilling water demands in Eroniti Conservation park, Ponjong, Yogyakarta by drilling deep into several soil layers. Vertical Electrical Sounding (VES) method is the most common approach to determine the existence of groundwater. The method probes layers of rock below the ground surface based on their electrical properties, since the electrical resistivity of each layer is theoretically different. This study aims to utilize the VES approach for investigating the properties of the rock layers in the area to explore groundwater sources. We install six different VES points in the observation area using Schlumberger electrode configuration. The methodology of the work consists of three steps: the planning of the placement of the sounding points, the measurement step performed by a unit of IRIS SYSCAL Resistivity meter, and the data analysis and interpretation. Employing the resistivity analysis, we conclude that the observed region consists of Mediterranean soil as a result of weathering of limestone as well as lithology of the limestone. Furthermore, there are two types of aquifer found in the area: a perched aquifer found 27 meters below the ground surface of VES point 1 and a confined aquifer 166 meters below the ground surface of VES point 2 and 6.

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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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Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

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Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

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Democratising Knowledge Representation with BioCypher

arXiv

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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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Correction to: FLAGS, frequently mutated genes in public exomes

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BMC medical genomics 2017年第1期10卷 69页

作者： Casper Shyr Maja Tarailo-Graovac Michael Gottlieb Jessica Jy Lee Clara van Karnebeek Wyeth W Wasserman Centre for Molecular Medicine and Therapeutics Child and Family Research Institute Vancouver BC Canada. Treatable Intellectual Disability Endeavour in British Columbia Vancouver Canada. Bioinformatics Graduate Program University of British Columbia Vancouver BC Canada. Department of Medical Genetics University of British Columbia Vancouver BC Canada. Genome Science and Technology Graduate Program University of British Columbia Vancouver BC Canada. Division of Biochemical Diseases BC Children's Hospital Vancouver BC Canada. Department of Pediatrics University of British Columbia Vancouver BC Canada. Centre for Molecular Medicine and Therapeutics Child and Family Research Institute Vancouver BC Canada. wyeth@cmmt.ubc.ca. Department of Medical Genetics University of British Columbia Vancouver BC Canada. wyeth@cmmt.ubc.ca. Treatable Intellectual Disability Endeavour in British Columbia Vancouver Canada. wyeth@cmmt.ubc.ca.

Unfortunately, the original article [1] contained an error. The additional files were included incorrectly. The correct additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and 14 are published in this correction.

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Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil (vol 13, 1004, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-11页

作者： Naslavsky, Michel S. Scliar, Marilia O. Yamamoto, Guilherme L. Wang, Jaqueline Yu Ting Zverinova, Stepanka Karp, Tatiana Nunes, Kelly Ceroni, Jose Ricardo Magliocco de Carvalho, Diego Lima da Silva Simoes, Carlos Eduardo Bozoklian, Daniel Nonaka, Ricardo dos Santos Brito Silva, Nayane da Silva Souza, Andreia de Souza Andrade, Heloisa Passos, Marilia Rodrigues Silva Castro, Camila Ferreira Bannwart Mendes-Junior, Celso T. Mercuri, Rafael L. V. Miller, Thiago L. A. Buzzo, Jose Leonel Rego, Fernanda O. Araujo, Nathalia M. Magalhaes, Wagner C. S. Mingroni-Netto, Regina Celia Borda, Victor Guio, Heinner Rojas, Carlos P. Sanchez, Cesar Caceres, Omar Dean, Michael Barreto, Mauricio L. Lima-Costa, Maria Fernanda Horta, Bernardo L. Tarazona-Santos, Eduardo Meyer, Diogo Galante, Pedro A. F. Guryev, Victor Castelli, Erick C. Duarte, Yeda A. O. Passos-Bueno, Maria Rita Zatz, Mayana Human Genome and Stem Cell Research Center University of São Paulo São Paulo SP Brazil Department of Genetics and Evolutionary Biology Biosciences Institute University of São Paulo São Paulo SP Brazil Hospital Israelita Albert Einstein São Paulo SP Brazil Instituto da Criança Faculdade de Medicina da Universidade de São Paulo São Paulo SP Brazil Orthopedic Research Labs Boston Children’s Hospital and Department of Genetics Harvard Medical School Boston MA USA Laboratório DASA São Paulo Brazil Laboratory of Genome Structure and Ageing European Research Institute for the Biology of Ageing University Medical Center Groningen Groningen Netherlands São Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory School of Medicine Botucatu State of São Paulo Brazil São Paulo State University (UNESP) Department of Pathology School of Medicine Botucatu State of São Paulo Brazil Departamento de Química Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto São Paulo Brazil Centro de Oncologia Molecular Hospital Sirio-Libanes São Paulo Brazil Department of Biochemistry Institute of Chemistry University of São Paulo São Paulo São Paulo Brazil Bioinformatics Graduate program University of São Paulo São Paulo Brazil Departamento de Genética Ecologia e Evolução Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte MG Brazil Núcleo de Ensino e Pesquisa Instituto Mário Penna Belo Horizonte MG Brazil Laboratorio de Biotecnologia y Biologia Molecular Instituto Nacional de Salud Lima Peru Universidad de Huánuco Huánuco Peru Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA Instituto de Saúde Coletiva Universidade Federal da Bahia Salvador BA 40110-040 Brazil Center for Data and Knowledge Integration for Health Institute Gonçalo Muniz Fundação Oswaldo Cruz Salvador BA Brazil Instituto de Pesquisas René Rachou Fundação Os

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.

关键词： Data publication and archiving Haplotypes Mobile elements Rare variants Structural variation

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Effects of gamma irradiation dose-rate on sterile male Aedesaegypti

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AIP Conference Proceedings 2017年第1期1854卷

作者： Beni Ernawan Usman Sumo Friend Tambunan Irawan Sugoro Hadian Iman Sasmita 1Center for Isotopes and Radiation Application-National Nuclear Energy Agency. Jl. Lebak Bulus Raya No. 49 Jakarta 12440 Indonesia. Tel. +62-21-7690709 Fax. +62-21-7691607 2Graduate Program Department of Chemistry Faculty of Mathematics and Natural Science University of Indonesia. Kampus UI Depok West Java 16424 Indonesia 3Bioinformatics Research Group Department of Chemistry Faculty of Mathematics and Natural Science University of Indonesia. Kampus UI Depok West Java 16424 Indonesia

Aedesaegypti is the most important vector for dengue, yellow fever and Zika viruses. Considering its medical importance, vector population control program utilizing radiation-based sterile insect technique (SIT) is one of the potential methods for preventing and limiting the dispersal of these viruses. The present study was undertaken to evaluate the dose-rates effects of γ-sterilization on quality parameters of sterile males. Males *** at the pupal stage were sterilized by applying 70 Gyγ-rays in varies dose-rates, i.e. 0 (control), 300, 600, 900, 1200 and 1500Gy/h utilizing panoramic irradiator. Adult males that emerged from the pupal stage were assessed for their quality parameters, which are the percentage of emergence, longevity, sterility and mating competitiveness. The results herein indicate that there was no major effect of dose-rate on the percentage of emergence, the data showedthat there were no differences between irradiated males compared with control. Generally, the longevity of irradiated males was lower compared to control. The data also demonstrated that longevity was significantly increased at the dose-rate from 300 to 900Gy/h, then decreased at the dose-rate 900 to 1500 Gy/h. Sterility of irradiated maleswas significantly different compared to control, while there was no significantly different at dose rate 300 to 1500 Gy/h. Mating competitiveness of irradiated males was increased at the dose rate from 300 to 1200 Gy/h, then the value was decreased significantly at the dose rate 1500 Gy/h. The dose-rate effects of γ-sterilization were discussed in the context genetic vector control, in particular, the SIT. The results give information and contribute to better understanding towards γ-sterilization optimization and quality parameters of sterile male Ae. aegypti on SIT methods.

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Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV

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Antiviral research 2023年 216卷 105653页

作者： Yu-Jen Chang Uyen Nguyen Phuong Le Jia-Jun Liu Sin-Rong Li Shao-Ting Chao Hsueh-Chou Lai Yu-Feng Lin Kai-Cheng Hsu Chih-Hao Lu Cheng-Wen Lin The Ph.D. Program of Biotechnology and Biomedical Industry China Medical University Taichung Taiwan. Department of Medical Laboratory Science and Biotechnology China Medical University Taichung Taiwan Graduate Institute of Biological Sciences and Technology China Medical University Taichung Taiwan. Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan. Department of Laboratory Medicine China Medical University Hospital Taichung Taiwan. Department of Medical Laboratory Science and Biotechnology China Medical University Taichung Taiwan. Division of Hepato-Gastroenterology Department of Internal Medicine China Medical University Hospital Taichung Taiwan. Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan. Graduate Institute of Cancer Biology and Drug Discovery Taipei Medical University Taipei Taiwan. The Ph.D. Program of Biotechnology and Biomedical Industry China Medical University Taichung Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan. Electronic address: chlu@nycu.edu.tw. Graduate Institute of Biological Sciences and Technology China Medical University Taichung Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan. Electronic address: cwlin@mail.cmu.edu.tw.

The main protease (M) of SARS-CoV-2 is essential for viral replication, which suggests that the M is a critical target in the development of small molecules to treat COVID-19. This study used an in-silico prediction approach to investigate the complex structure of SARS-CoV-2 M in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 M in cis- and trans-cleavage proteolytic assays. Virtual screening of ∼280,000 compounds from the NCI database identified 10 compounds with highest site-moiety map scores. Compound NSC89640 (coded C1) showed marked inhibitory activity against the SARS-CoV-2 M in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 M enzymatic activity, with a half maximal inhibitory concentration (IC) of 2.69 μM and a selectivity index (SI) of >74.35. The C1 structure served as a template to identify structural analogs based on AtomPair fingerprints to refine and verify structure-function associations. M-mediated cis-/trans-cleavage assays conducted with the structural analogs revealed that compound NSC89641 (coded D2) exhibited the highest inhibitory potency against SARS-CoV-2 M enzymatic activity, with an IC of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC of <3.5 μM. Thus, C1 shows potential as an effective M inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 M and MERS-CoV M.

关键词： In-silico prediction MERS-CoV Main protease National cancer institute database SARS-CoV-2 cis-/trans-cleavage assay

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MutaScope: a high-sensitivity variant caller dedicated to high-throughput PCR amplicons sequencing

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BMC Proceedings 2012年第6期6卷 1-1页

作者： Shawn Yost Hakan Alakus Hiroko Matsui Kristen Jepsen Kelly Frazer Olivier Harismendy Richard Schwab Bioinformatics and Systems Biology Graduate program University of California San Diego La Jolla CA USA Division of Genome information Sciences Department of Pediatrics and Rady Children's Hospital University of California San Diego La Jolla CA USA Moores UCSD Cancer Center La Jolla CA USA Department of General Visceral and Cancer Surgery Center for Integrated Oncology University of Cologne Germany Clinical and Translational Research Institute University of California San Diego La Jolla CA USA Institute for Genomic Medicine University of California San Diego La Jolla CA USA

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LOW-FREQUENCY VARIANT IMPUTATION IDENTIFIES NOVEL DISEASE-ASSOCIATED LOCI IN A GENOME-WIDE ASSOCIATION STUDY OF LATE-ONSET ALZHEIMER'S DISEASE

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Alzheimer's & Dementia 2014年第4期10卷 P135-P135页

作者： Brian W. Kunkle Adam C. Naj Kara Hamilton-Nelson William R. Perry Amanda Partch Otto Valladares Jaeyoon Chung Gyungah Jun Mike Schmidt Gary Beecham Li-San Wang Eden Martin Richard Mayeux Jonathan Haines Lindsay A. Farrer Gerard D. Schellenberg Margaret Pericak-Vance University of Miami Hussman Institute for Human Genomics Miami Florida United States University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania United States University of Miami Miami Florida United States University of Pennsylvania Philadelphia Pennsylvania United States Boston University Bioinformatics Graduate Program Boston Massachusetts United States Boston University School of Medicine Boston Massachusetts United States University of Pennsylvania School of Medicine Philadelphia Pennsylvania United States Columbia University New York New York United States Case Western Reserve University Cleveland Ohio United States

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