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Weeds e-Catalog as a Tool for Identification of Weeds in Plantation

IOP Conference Series: Earth and Environmental science 2021年第1期794卷

作者： Hangger Gahara Mawandha Teddy Suparyanto Bens Pardamean Agrotechnology Department Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Agricultural Engineering Department Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Universitas Bina Nusantara Jakarta Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta

Weeds are one of the organisms that interfere with plant growth. Information about the identity of weeds becomes very important on plantations. Although weeds data digitization has been done a lot, currently there is still not much weeds data information system can be accessed online. Weeds management is often dealt with weeds herbarium or weeds photographs. In an effort to provide a good information system for farmers, this research aims to create a database of various types of weeds and an information system that can be accessed online. The methodology for developing a weed catalog information system uses the Software Development Life Cycle (SDLC). Weed samples in database were collected through systematic random sampling in the form of images and text. The result of this study is a Weeds Electronic Catalog or Weeds e-Catalog that can facilitate the information of weeds identity such as names, classifications, morphology, life cycles, and habitats of various types of weeds that grow on plantation land. Weeds e-Catalog can be used by plantation practitioners and farmers to make decisions in controlling weeds.

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From modular decomposition trees to rooted median graphs

arXiv

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arXiv 2021年

作者： Bruckmann, Carmen Stadler, Peter F. Hellmuth, Marc Helmholtz-Centre for Environmental Research Permoserstraße 15 LeipzigD-04318 Germany Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16–18 LeipzigD-04107 Germany Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine at Leipzig University Universität Leipzig Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Institute for Theoretical Chemistry University of Vienna Währingerstrasse 17 WienA-1090 Austria Facultad de Ciencias Universidad National de Colombia Sede Bogotá Colombia Santa Fe Insitute 1399 Hyde Park Rd. Santa FeNM87501 United States Department of Mathematics Faculty of Science Stockholm University StockholmSE-10691 Sweden

The modular decomposition of a symmetric map δ: X ×X → ϒ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features of δ in labeled trees. A map δ is explained by a vertex-labeled rooted tree (T,t) if the label δ(x,y) coincides with the label of the last common ancestor of x and y in T, i.e., if δ(x,y) = t(lca(x,y)). Only maps whose modular decomposition does not contain prime nodes, i.e., the symbolic ultrametrics, can be exaplained in this manner. Here we consider rooted median graphs as a generalization to (modular decomposition) trees to explain symmetric maps. We first show that every symmetric map can be explained by "extended" hypercubes and half-grids. We then derive a a linear-time algorithm that stepwisely resolves prime vertices in the modular decomposition tree to obtain a rooted and labeled median graph that explains a given symmetric map δ. We argue that the resulting "tree-like" median graphs may be of use in phylogenetics as a model of evolutionary relationships. © 2021, CC BY.

关键词： Undirected graphs

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Phylogeny, ancestral ranges and reclassification of sand dollars

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Scientific Reports 2023年第1期13卷 1-12页

作者： Lee, Hsin Lee, Kwen-Shen Hsu, Chia-Hsin Lee, Chen-Wei Li, Ching-En Wang, Jia-Kang Tseng, Chien-Chia Chen, Wei-Jen Horng, Ching-Chang Ford, Colby T. Kroh, Andreas Bronstein, Omri Tanaka, Hayate Oji, Tatsuo Lin, Jih-Pai Janies, Daniel National Museum of Marine Biology and Aquarium Pingtung 944401 Taiwan Department of Geosciences National Taiwan University Taipei 10617 Taiwan Institute of Oceanography National Taiwan University Taipei 10617 Taiwan Biology Department National Museum of Natural Science Taichung 40453 Taiwan Tuple LLC 2413 Commonwealth Ave Charlotte 28205 NC United States School of Data Science University of North Carolina at Charlotte 9201 University City Blvd Charlotte 28223 NC United States Department of Bioinformatics and Genomics University of North Carolina at Charlotte 9201 University City Blvd Charlotte 28223 NC United States Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER) University of North Carolina at Charlotte 9201 University City Blvd Charlotte 28223 NC United States Department of Geology and Palaeontology Natural History Museum Vienna Vienna 1010 Austria School of Zoology Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel Steinhardt Museum of Natural History Tel Aviv University Tel Aviv 6997801 Israel Department of Biological Sciences Graduate School of Science University of Tokyo Tokyo 113-0033 Japan University Museum Nagoya University Furo-cho Nagoya 464-8601 Japan

Classification of the Class Echinoidea is under significant revision in light of emerging molecular phylogenetic evidence. In particular, the sister-group relationships within the superorder Luminacea (Echinoidea: Irregularia) have been considerably updated. However, the placement of many families remains largely unresolved due to a series of incongruent evidence obtained from morphological, paleontological, and genetic data for the majority of extant representatives. In this study, we investigated the phylogenetic relationships of 25 taxa, belonging to eleven luminacean families. We proposed three new superfamilies: Astriclypeoidea, Mellitoidea, and Taiwanasteroidea (including Dendrasteridae, Taiwanasteridae, Scutellidae, and Echinarachniidae), instead of the currently recognized superfamily Scutelloidea Gray, 1825. In light of the new data obtained from ten additional species, the historical biogeography reconstructed shows that the tropical western Pacific and eastern Indian Oceans are the cradle for early sand dollar diversification. Hothouse conditions during the late Cretaceous and early Paleogene were coupled with diversification events of major clades of sand dollars. We also demonstrate that Taiwan fauna can play a key role in terms of understanding the major Cenozoic migration and dispersal events in the evolutionary history of Luminacea. © 2023, The Author(s).

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Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank 4

Analyzing the heterogeneity of rule-based EHR phenotyping al...

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4th International Workshop on Knowledge Discovery in Healthcare data, KDH 2019

作者： Denaxas, Spiros Parkinson, Helen Fitzpatrick, Natalie Sudlow, Cathie Hemingway, Harry Institute of Health Informatics University College London United Kingdom Health Data Research UK London Cambridge United Kingdom UCL Hospitals Biomedical Research Center London United Kingdom European Bioinformatics Institute Cambridge United Kingdom Centre for Medical Informatics Usher Institute of Population Health Science and Informatics University of Edinburgh Edinburgh United Kingdom

Electronic Health Records (EHR) are data generated during routine interactions across healthcare settings and contain rich, longitudinal information on diagnoses, symptoms, medications, investigations and tests. A primary use-case for EHR is the creation of phenotyping algorithms used to identify disease status, onset and progression or extraction of information on risk factors or biomarkers. Phenotyping however is challenging since EHR are collected for different purposes, have variable data quality and often require significant harmonization. While considerable effort goes into the phenotyping process, no consistent methodology for representing algorithms exists in the UK. Creating a national repository of curated algorithms can potentially enable algorithm dissemination and reuse by the wider community. A critical first step is the creation of a robust minimum information standard for phenotyping algorithm components (metadata, implementation logic, validation evidence) which involves identifying and reviewing the complexity and heterogeneity of current UK EHR algorithms. In this study, we analyzed all available EHR phenotyping algorithms (n=70) from two large-scale contemporary EHR resources in the UK (CALIBER and UK Biobank). We documented EHR sources, controlled clinical terminologies, evidence of algorithm validation, representation and implementation logic patterns. Understanding the heterogeneity of UK EHR algorithms and identifying common implementation patterns will facilitate the design of a minimum information standard for representing and curating algorithms nationally and internationally. © 2019 for this paper by its authors.

关键词： Diagnosis

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6Développement de nouveaux ”endpoints” cliniques à l'aide de biomarqueurs numériques basés sur la voix pour le suivi à distance, en vie réelle, de patients en recherche clinique: exemple de biomarqueurs vocaux pour le suivi du statut symptomatique de patients avec COVID-19

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Revue d'Épidémiologie et de Santé Publique 2022年 70卷 S260-S261页

作者： G. Fagherazzi L. Zhang A. Elbéji M. Pizzimenti P. Nazarov G. Aguayo A. Fischer Deep Digital Phenotyping Research Unit Department of Precision Health Luxembourg Institute of Health Strassen Luxembourg Bioinformatics Platform Luxembourg Institute of Health 1A-B rue Thomas Edison L-1445 Strassen Luxembourg Luxembourg Multiomics Data Science Department of Cancer Research Luxembourg Institute of Health 1A-B rueThomas Edison L-1445 Strassen Luxembourg

Introduction Les opportunités offertes par les nouvelles technologies en santé permettent de repenser la conduite d’études cliniques, afin d'alléger le fardeau de participation des patients, diminuer le nombre de visites sur site, ainsi que d'améliorer le suivi à distance inter-visites. Pour cela, parmi toutes les technologies numériques émergentes, le champ des biomarqueurs vocaux est particulièrement prometteur [1]. Nous proposons ici une méthodologie d'identification et de validation de biomarqueurs vocaux à l'aide de Méthodes d'analyse du signal et d'intelligence artificielle (Fig. 1), que nous illustrons avec des Résultats dans le cadre du suivi de patients avec COVID-19 ou un COVID long pour le suivi du statut symptomatique. Méthodes Nous avons régulièrement collecté des enregistrements audio standardisés pendant les deux premières semaines de suivi en vie réelle de N=272 participants de l’étude de cohorte Predi-COVID [2], tous ayant eu la maladie COVID-19, confirmée par test PCR positif. Des biomarqueurs vocaux ont été entrainés pour prédire le statut symptomatique, défini à partir d'une liste quotidienne des symptômes liés à COVID-19 les plus fréquents. Les audios (lecture d'un texte standardisé de 25 secondes) ont été nettoyés et harmonisés, puis 6473 caractéristiques audio en ont été extraites, afin d'entrainer des modèles de machine learning, dont les performances ont été évaluées à l'aide de métriques habituelles pour la discrimination (AUC, accuracy, precision, recall, F1-score) et le score de Brier pour la calibration. Résultats Au total, 1775 enregistrements ont été analysés (6,5 enregistrements/participant en moyenne). Le modèle de Support Vector Machine a fourni les meilleurs performances (AUC=0.91, accuracy=0,85) avec une bonne calibration (Brier Score=0,11) (Fig. 2). Le biomarqueur vocal dérivé de ces modèles, à partir de la probabilité prédite d’être symptomatique, permettait de discriminer les personnes asymptomatiques des personnes symptomatiqu

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WorkflowHub: a registry for computational workflows

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Scientific data 2025年第1期12卷 837页

作者： Ove Johan Ragnar Gustafsson Sean R Wilkinson Finn Bacall Stian Soiland-Reyes Simone Leo Luca Pireddu Stuart Owen Nick Juty José M Fernández Tom Brown Hervé Ménager Björn Grüning Salvador Capella-Gutierrez Frederik Coppens Carole Goble Australian BioCommons University of Melbourne Melbourne Victoria Australia. Oak Ridge Leadership Computing Facility Oak Ridge National Laboratory Oak Ridge Tennessee USA. Department of Computer Science The University of Manchester Manchester UK. Informatics Institute University of Amsterdam Amsterdam The Netherlands. Center for Advanced Studies Research and Development in Sardinia (CRS4) Pula Cagliari Italy. Barcelona Supercomputing Center (BSC) Barcelona Spain. Spanish National Bioinformatics Institute (INB) Barcelona Spain. Leibniz Institute for Zoo- and Wildlife Research Berlin Germany. Institut Pasteur Université Paris Cité Bioinformatics of Biostatistics Hub Paris 75015 France. CNRS UMS 3601 Institut Français de Bioinformatique Evry France. Albert-Ludwigs-Universität Freiburg Freiburg Germany. VIB Data Core VIB Technologies Ghent Belgium. Department of Computer Science The University of Manchester Manchester UK. carole.goble@manchester.ac.uk.

The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of analysis and descriptions of processing steps, workflows should be reproducible, reusable, adaptable, and available. Workflow sharing presents opportunities to reduce unnecessary reinvention, promote reuse, increase access to best practice analyses for non-experts, and increase productivity. In reality, workflows are scattered and difficult to find, in part due to the diversity of available workflow engines and ecosystems, and because workflow sharing is not yet part of research practice. WorkflowHub provides a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR). By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.

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Climate-influenced vector-borne diseases in Africa:a call to empower the next generation of African researchers for sustainable solutions

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Infectious Diseases of Poverty 2024年第2期13卷 83-92页

作者： Judicaël Obame-Nkoghe Adjoavi Esse Agossou Gerald Mboowa Basile Kamgang Cyril Caminade Dawn C.Duke Andrew Karanja Githeko Obed M.Ogega Nestor Engone Elloué Fatou Bintou Sarr DieudonnéNkoghe Pierre Kengne Nicaise T.Ndam Christophe Paupy Moses Bockarie Patricks Voua Otomo Molecular and Cellular Biology Laboratory(LabMC) Biology DepartmentUniversity of Science and Technology of MasukuBP 901FrancevilleGabon Ecology and Health Research Unit Interdisciplinary Center for Medical Research of FrancevilleBP 769FrancevilleGabon Department of Zoology and Entomology Faculty of Natural and Agricultural SciencesUniversity of the Free StatePrivate Bag x13Phuthaditjhaba 9866Republic of South Africa Laboratory of Pharmacology and Improved Traditional Medicines Department of Animal PhysiologyFaculty of Science and TechnologyUniversity of Abomey-CalaviBP 526CotonouBenin The African Center of Excellence in Bioinformatics and Data-Intensive Sciences Infectious Diseases InstituteCollege of Health SciencesMakerere UniversityP.O Box 22418KampalaUganda Africa Centers for Disease Control and Prevention African Union CommissionRoosevelt StreetP.O.Box 3243W21 K19 Addis AbabaEthiopia Centre for Research in Infectious Diseases P.O.Box 13591YaoundéCameroon Earth System Physics Department The Abdus Salam International Centre for Theoretical PhysicsTriesteItaly Africa Research Excellence Fund 99 Charterhouse StreetLondon EC1M 6HRUK Community Health Support Program P.O.Box 872Kisumu 40100Kenya The African Academy of Sciences NairobiKenya Center for Phylosophical Studies and Research(CERP) Omar Bongo University(UOB)BP 13131LibrevilleGabon UMRED Health Training and Research UnitUniversity of Iba Der Thiam of ThièsBP 967ThièsSenegal National Parasitic Diseases Control Program Ministry of HealthLibrevilleGabon MIVEGEC Univ.MontpellierCNRSIRDMontpellierFrance MERIT IRDParis CitéUniversity75006 ParisFrance Department of Parasitology Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLG 54AccraGhana School of Community Health Sciences Njala UniversityBoSierra Leone

We look at the link between climate change and vector-borne diseases in low-and middle-income countries in *** large endemicity and escalating threat of diseases such as malaria and arboviral diseases,intensified by climate change,disproportionately affects vulnerable communities *** highlight the urgency of prioritizing research and development,advocating for robust scientific inquiry to promote adaptation strategies,and the vital role that the next generation of African research leaders will play in addressing these *** significant challenges such as funding shortages within countries,various pan-African-oriented funding bodies such as the African Academy of sciences,the Africa Research Excellence Fund,the Wellcome Trust,the *** Institutes of Health,and the Bill and Melinda Gates Foundation as well as initiatives such as the African Research Initiative for Scientific Excellence and the Pan-African Mosquito Control Association,have empowered(or are empowering)these researchers by supporting capacity building activities,including continental and global networking,skill development,mentoring,and African-led *** article underscores the urgency of increased national investment in research,proposing the establishment of research government agencies to drive evidence-based *** between governments and scientific communities,sustained by pan-African funding bodies,is *** these efforts,African nations are likely to enhance the resilience and adaptive capacity of their systems and communities by navigating these challenges effectively,fostering scientific excellence and implementing transformative solutions against climate-sensitive vector-borne diseases.

关键词： Climate change Vector-borne diseases Africa Environmental justice Research and development Pan-African funding initiatives

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180P Recalling pre-existing microbiota-specific T cells to target tumors

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Immuno-Oncology and Technology 2022年 16卷 100292-100292页

作者： Carpier, J-M. Talpin, A. Kulakowski, G. Dos Santos Leite, A.M. Laviolette, K. Noguerol, J. Mersceman, T. Garnier, A. Gaal, C. Pereira Oliveira, C. Calderon, C. Boullerot, L. Malfroy, M. Strozzi, F. Gouttefangeas, C. Adotevi, O. Joffre, O. Gamelas Magalhaes, J. Chêne, L. Bonny, C. Immuno-Oncology Enterome Paris France Immunology Eberhard Karls University Tuebingen Germany Inserm U1291 Institut Toulousain des Maladies Infectieuses et Inflammatoires Toulouse France Bioinformatics and Data Science Enterome Paris France Inserm UMR1098 Université de Bourgogne Franche Comté Besancon France Drug Discovery Platform Enterome Paris France

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data-driven modeling reveals a universal dynamic underlying the COVID-19 pandemic under social distancing

arXiv

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arXiv 2020年

作者： Marsland, Robert Mehta, Pankaj Department of Physics Boston University BostonMA02215 United States Biological Design Center Boston University BostonMA02215 United States Microbiome Initiative Boston University BostonMA02215 United States Bioinformatics Program Boston University BostonMA02215 United States College of Data Science Boston University BostonMA02215 United States

We show that the COVID-19 pandemic under social distancing exhibits universal dynamics. The cumulative numbers of both infections and deaths quickly cross over from exponential growth at early times to a longer period of power law growth, before eventually slowing. In agreement with a recent statistical forecasting model by the IHME, we show that this dynamics is well described by the erf function. Using this functional form, we perform a data collapse across countries and US states with very different population characteristics and social distancing policies, confirming the universal behavior of the COVID-19 outbreak. We show that the predictive power of statistical models is limited until a few days before curves flatten, forecast deaths and infections assuming current policies continue and compare our predictions to the IHME models. We present simulations showing this universal dynamics is consistent with disease transmission on scale-free networks and random networks with non-Markovian transmission dynamics. Copyright © 2020, The Authors. All rights reserved.

关键词： Dynamics

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Planar median graphs and cubesquare-graphs

arXiv

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arXiv 2021年

作者： Seemann, Carsten R. Moulton, Vincent Stadler, Peter F. Hellmuth, Marc Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany School of Computing Sciences University of East Anglia NorwichNR4 7TJ United Kingdom Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Germany Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine Leipzig University Härtelstraße 16-18 LeipzigD-04107 Germany Institute for Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Facultad de Ciencias Universidad Nacional de Colombia Sede Bogotá Colombia The Santa Fe Institute 1399 Hyde Park Rd. Santa FeNM87501 United States Department of Mathematics Faculty of Science Stockholm University StockholmSE - 106 91 Sweden

Median graphs are connected graphs in which for all three vertices there is a unique vertex that belongs to shortest paths between each pair of these three vertices. In this paper we provide several novel characterizations of planar median graphs. More specifically, we characterize when a planar graph G is a median graph in terms of forbidden subgraphs and the structure of isometric cycles in G, and also in terms of subgraphs of G that are contained inside and outside of 4-cycles with respect to an arbitrary planar embedding of G. These results lead us to a new characterization of planar median graphs in terms of cubesquare-graphs that is, graphs that can be obtained by starting with cubes and square graphs, and iteratively replacing 4-cycle boundaries (relative to some embedding) by cubes or square-graphs. As a corollary we also show that a graph is planar median if and only if it can be obtained from cubes and square-graphs by a sequence of "square-boundary" amalgamations. These considerations also lead to an O(n log n)-time recognition algorithm to compute a decomposition of a planar median graph with n vertices into cubes and square-graphs. Copyright © 2021, The Authors. All rights reserved.

关键词： Graphic methods

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