70 research outputs found

    The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

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    A global genome database of all of Earth‚Äôs species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ‚ąľ1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects

    Computer Vision-Aided Intelligent Monitoring of Coffee: Towards Sustainable Coffee Production

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    Coffee which is prepared from the grinded roasted seeds of harvested coffee cherries, is one of the most consumed beverage and traded commodity, globally. To manually monitor the coffee field regularly, and inform about plant and soil health, as well as estimate yield and harvesting time, is labor-intensive, time-consuming and error-prone. Some recent studies have developed sensors for estimating coffee yield at the time of harvest, however a more inclusive and applicable technology to remotely monitor multiple parameters of the field and estimate coffee yield and quality even at pre-harvest stage, was missing. Following precision agriculture approach, we employed machine learning algorithm YOLO, for image processing of coffee plant. In this study, the latest version of the state-of-the-art algorithm YOLOv7 was trained with 324 annotated images followed by its evaluation with 82 unannotated images as test data. Next, as an innovative approach for annotating the training data, we trained K-means models which led to machine-generated color classes of coffee fruit and could thus characterize the informed objects in the image. Finally, we attempted to develop an AI-based handy mobile application which would not only efficiently predict harvest time, estimate coffee yield and quality, but also inform about plant health. Resultantly, the developed model efficiently analyzed the test data with a mean average precision of 0.89. Strikingly, our innovative semi-supervised method with an mean average precision of 0.77 for multi-class mode surpassed the supervised method with mean average precision of only 0.60, leading to faster and more accurate annotation. The mobile application we designed based on the developed code, was named CoffeApp, which possesses multiple features of analyzing fruit from the image taken by phone camera with in field and can thus track fruit ripening in real time

    Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

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    Background Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)

    An√°lise de teses e disserta√ß√Ķes sobre higieniza√ß√£o das m√£os no Brasil: estudo bibliom√©trico

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    Background and Objectives: in relation to hand hygiene, it is important to highlight the absence of documented investigations in the scientific literature that address the analysis of theses and dissertations related to this practice. This gap justifies the carrying out of this study, which aims to strengthen and expand the knowledge base related to this topic, highlighting its relevance in the areas of teaching, research, extension and innovation. The objective was to analyze theses and dissertations published in stricto sensu graduate programs on hand hygiene practices in Brazil. Methods: this is a bibliometric study conducted in the Coordination for the Improvement of Higher Education Personnel Theesis and Dissertation Catalog, considering the period from 2013 to 2022. Results: thirty-one (100%) studies were included, 21 (67.7%) dissertations and six (19.3%) theses. Nursing was the main area of assessment (65.6%), which mainly analyzed adherence to hand hygiene practices (29.0%), health education (12.9%), and carried out microbiological analysis of hands (12.9%). Only three publications used theoretical bases as the central core of the research. Conclusion: this study allowed us to identify the need to study the topic at doctoral level, using theoretical bases that will provide the conceptual and philosophical foundation for clinical practice.Justificaci√≥n y Objetivos: en relaci√≥n a la higiene de manos, es importante resaltar la ausencia de investigaciones documentadas en la literatura cient√≠fica que aborden el an√°lisis de tesis y disertaciones relacionadas con esta pr√°ctica. Este vac√≠o justifica la realizaci√≥n de este estudio, que tiene como objetivo fortalecer y ampliar la base de conocimientos relacionados con este tema, destacando su relevancia en las √°reas de docencia, investigaci√≥n, extensi√≥n e innovaci√≥n. El objetivo fue analizar tesis y disertaciones publicadas en programas de posgrado estricto sensu sobre pr√°cticas de higiene de manos en Brasil. M√©todos: estudio bibliom√©trico realizado en el Cat√°logo de Tesis y Disertaciones de la Coordinaci√≥n de Perfeccionamiento del Personal de Educaci√≥n Superior, considerando el per√≠odo de 2013 a 2022. Resultados: se incluyeron 31 (100%) estudios, 21 (67,7%) disertaciones y seis (19,3%) tesis. Enfermer√≠a fue la principal √°rea de evaluaci√≥n (65,6%), que analiz√≥ principalmente la adherencia a las pr√°cticas de higiene de manos (29,0%), educaci√≥n para la salud (12,9%) y realiz√≥ an√°lisis microbiol√≥gicos de las manos (12,9%). S√≥lo tres publicaciones utilizaron bases te√≥ricas como n√ļcleo central de la investigaci√≥n. Conclusi√≥n: este estudio identific√≥ la necesidad de estudiar el tema a nivel de doctorado, utilizando marcos te√≥ricos que proporcionar√°n la base conceptual y filos√≥fica para la pr√°ctica cl√≠nica.Justificativa e Objetivos: em rela√ß√£o √† higieniza√ß√£o das m√£os, √© importante ressaltar a aus√™ncia de investiga√ß√Ķes documentadas na literatura cient√≠fica que abordem a an√°lise de teses e disserta√ß√Ķes relacionadas a essa pr√°tica. Tal lacuna justifica a realiza√ß√£o deste estudo, que visa fortalecer e expandir a base de conhecimento relativa a essa tem√°tica, destacando sua relev√Ęncia nos dom√≠nios do ensino, da pesquisa, extens√£o e inova√ß√£o. Objetivou-se analisar teses e disserta√ß√Ķes publicadas em programas de p√≥s-gradua√ß√£o stricto sensu sobre as pr√°ticas de higieniza√ß√£o das m√£os no Brasil. M√©todos: estudo bibliom√©trico, realizado no Cat√°logo de Teses e Disserta√ß√Ķes da Coordena√ß√£o de Aperfei√ßoamento de Pessoal de N√≠vel Superior, considerando o per√≠odo de 2013 a 2022. Resultados: foram inclu√≠dos 31 (100%) estudos, sendo 21 (67,7%) disserta√ß√Ķes e seis (19,3%) teses. A enfermagem foi a principal √°rea de avalia√ß√£o (65,6%) que analisou, principalmente, a ades√£o √†s pr√°ticas de higiene das m√£os (29,0%), a educa√ß√£o em sa√ļde (12,9%), e realizou an√°lise microbiol√≥gica das m√£os (12,9%). Apenas tr√™s publica√ß√Ķes utilizaram bases te√≥ricas como n√ļcleo central da pesquisa. Conclus√£o: este estudo permitiu identificar a necessidade de estudar a tem√°tica em n√≠vel de doutorado, utilizando bases te√≥ricas que fornecer√£o o alicerce conceitual e filos√≥fico para a pr√°tica cl√≠nica

    Search for Spatial Correlations of Neutrinos with Ultra-high-energy Cosmic Rays

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    For several decades, the origin of ultra-high-energy cosmic rays (UHECRs) has been an unsolved question of high-energy astrophysics. One approach for solving this puzzle is to correlate UHECRs with high-energy neutrinos, since neutrinos are a direct probe of hadronic interactions of cosmic rays and are not deflected by magnetic fields. In this paper, we present three different approaches for correlating the arrival directions of neutrinos with the arrival directions of UHECRs. The neutrino data are provided by the IceCube Neutrino Observatory and ANTARES, while the UHECR data with energies above ‚ąľ50 EeV are provided by the Pierre Auger Observatory and the Telescope Array. All experiments provide increased statistics and improved reconstructions with respect to our previous results reported in 2015. The first analysis uses a high-statistics neutrino sample optimized for point-source searches to search for excesses of neutrino clustering in the vicinity of UHECR directions. The second analysis searches for an excess of UHECRs in the direction of the highest-energy neutrinos. The third analysis searches for an excess of pairs of UHECRs and highest-energy neutrinos on different angular scales. None of the analyses have found a significant excess, and previously reported overfluctuations are reduced in significance. Based on these results, we further constrain the neutrino flux spatially correlated with UHECRs

    Síndrome de fraser : Fraser syndrome

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    Introdu√ß√£o: a S√≠ndrome de Fraser √© caracterizada por presen√ßa de criptoftalmo, sindactilia, anormalidades da genit√°lia e outras malforma√ß√Ķes cong√™nitas do nariz, ouvido ou laringe, defeitos esquel√©ticos, h√©rnia umbilical, agenesia renal e retardo mental. √Č uma express√£o fenot√≠pica que depende da consanguinidade dos pais. Apresenta√ß√£o do caso: paciente do sexo feminino, tr√™s meses de idade, em acompanhamento no centro de refer√™ncia oftalmol√≥gica da Faculdade de Medicina da Universidade S√£o Paulo. Na ultrassonografia de abdome total, foi apenas evidenciada presen√ßa de h√©rnia umbilical simples. Discuss√£o: a preval√™ncia √© igual entre os sexos e a doen√ßa pode ser diagnosticada √† ultrassonografia pr√©-natal e fetoscopia ou no momento do nascimento frente √†s altera√ß√Ķes apresentadas pelo paciente, por crit√©rios maiores e menores. O tratamento √© multidisciplinar e dependente das malforma√ß√Ķes presentes, assim como o progn√≥stico, que √© pior em casos de malforma√ß√Ķes urogenitais e lar√≠ngeas graves. Conclus√£o: os m√©dicos devem estar atentos, para as manifesta√ß√Ķes cl√≠nicas e o diagn√≥stico preciso, oferecendo tratamento adequado e aconselhamento gen√©tico aos casais

    Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study