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Ten Simples Rules on How to Organise a Bioinformatics Hackathon 关于如何组织生物信息学黑客马拉松的十条简单规则

EMBnet.journal Pub Date : 2021-10-19 DOI: 10.14806/ej.26.0.983

Susanne Hollmann, B. Regierer, T. Attwood, A. Gisel, J. van Helden, G. Rossier, P. Kersey, E. Korpelainen, G. Vriend, E. Bongcam-Rudloff

{"title":"Ten Simples Rules on How to Organise a Bioinformatics Hackathon","authors":"Susanne Hollmann, B. Regierer, T. Attwood, A. Gisel, J. van Helden, G. Rossier, P. Kersey, E. Korpelainen, G. Vriend, E. Bongcam-Rudloff","doi":"10.14806/ej.26.0.983","DOIUrl":"https://doi.org/10.14806/ej.26.0.983","url":null,"abstract":"The completion of the human genome sequence triggered worldwide efforts to unravel the secrets hidden in its deceptively simple code. Numerous bioinformatics projects were undertaken to hunt for genes, predict their protein products, function and post-translational modifications, analyse protein-protein interactions, etc. Many novel analytic and predictive computer programmes fully optimised for manipulating human genome sequence data have been developed, whereas considerably less effort has been invested in exploring the many thousands of other available genomes, from unicellular organisms to plants and non-human animals. Nevertheless, a detailed understanding of these organisms can have a significant impact on human health and well-being.New advances in genome sequencing technologies, bioinformatics, automation, artificial intelligence, etc., enable us to extend the reach of genomic research to all organisms. To this aim gather, develop and implement new bioinformatics solutions (usually in the form of software) is pivotal. A helpful model, often used by the bioinformatics community, is the so-called hackathon. These are events when all stakeholders beyond their disciplines work together creatively to solve a problem. During its runtime, the consortium of the EU-funded project AllBio - Broadening the Bioinformatics Infrastructure to cellular, animal and plant science - conducted many successful hackathons with researchers from different Life Science areas. Based on this experience, in the following, the authors present a step-by-step and standardised workflow explaining how to organise a bioinformatics hackathon to develop software solutions to biological problems.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75259422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The impact of COVID-19 during pregnancy on maternal and neonatal outcomes: a systematic review. 妊娠期COVID-19对孕产妇和新生儿结局的影响:系统综述

EMBnet.journal Pub Date : 2021-10-01 Epub Date: 2021-10-22 DOI: 10.14806/ej.26.1.969

Despoina Michailidou, Androniki Stavridou, Eleni D Panagouli, Theodoros N Sergentanis, Theodora Psaltopoulou, Flora Bacopoulou, Valentina Baltag, Donald E Greydanus, George Mastorakos, George P Chrousos, Maria N Tsolia, Artemis K Tsitsika, Nikolaos Vlahos

{"title":"The impact of COVID-19 during pregnancy on maternal and neonatal outcomes: a systematic review.","authors":"Despoina Michailidou, Androniki Stavridou, Eleni D Panagouli, Theodoros N Sergentanis, Theodora Psaltopoulou, Flora Bacopoulou, Valentina Baltag, Donald E Greydanus, George Mastorakos, George P Chrousos, Maria N Tsolia, Artemis K Tsitsika, Nikolaos Vlahos","doi":"10.14806/ej.26.1.969","DOIUrl":"10.14806/ej.26.1.969","url":null,"abstract":"<p><p>Several months after the onset of the epidemic, COVID-19 remains a global health issue. Scientific data on pregnancy, perinatal outcomes and vertical transmission of SARS-CoV-2 are constantly emerging but are still limited and unclear. The purpose of this systematic review was to summarize current evidence on vertical transmission rates, maternal, perinatal and neonatal outcomes and mode of delivery in pregnancies affected by COVID-19. An extensive search was conducted in PubMed, Google Scholar, Embase, and Scopus databases up to June 20, 2020. A total of 133 articles (51 case reports, 31 case series, 40 cohort studies and 2 case-control studies) reporting data from 8,092 subjects (6,046 pregnant women and 2,046 neonates) were considered eligible for inclusion in the systematic review. A substantial proportion of pregnant women with COVID-19 underwent caesarean section (case reports 82.2%, case series 74.2% and cohort studies 66.0%). Regarding vertical transmission, most neonates were tested negative (case reports 92.7%, case series studies 84.2%, cohort studies 97.1% and case control studies 100%). Maternal mortality rates ranged from 1% in cohort studies to 5.7% in case reports; neonatal mortality ranged from 2% in case reports to 3.3% in case series. Vertical transmission of SARS-CoV-2 from mother to child is rare. Careful screening of pregnant women seems important and specific guidelines with evidence-based decision algorithms for the mode of delivery in the context of a pregnancy affected by COVID-19 should be established.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"26 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9119021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10516901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Validation of the Copenhagen Psychosocial Questionnaire-Long Version II (COPSOQ II) in Greek employees 哥本哈根社会心理问卷-长版II (COPSOQ II)在希腊雇员中的验证

EMBnet.journal Pub Date : 2021-10-01 DOI: 10.14806/ej.26.1.977

Eleni Zigkiri, Maria Charalampopoulou, Anastasia Kokka, F. Bacopoulou, C. Darviri, G. Chrousos

{"title":"Validation of the Copenhagen Psychosocial Questionnaire-Long Version II (COPSOQ II) in Greek employees","authors":"Eleni Zigkiri, Maria Charalampopoulou, Anastasia Kokka, F. Bacopoulou, C. Darviri, G. Chrousos","doi":"10.14806/ej.26.1.977","DOIUrl":"https://doi.org/10.14806/ej.26.1.977","url":null,"abstract":"The aim of this study was to validate the long second version of the Copenhagen Psychosocial Questionnaire (COPSOQ II) in the Greek language. The study was carried out in two phases following a mixed-method design. Six hundred and fifty-two Greek employees (response rate 93.3%) responded in the second phase of the study, either online or in writing. Both types of participation to the study were confidential for the participants and the companies as well. Most participants were females (68.1%), married (47.4%), aged 30-49 years (60.9%), with high educational level (60.4%). The majority were occupied in the health and the social care services (37.4%) and employed by the private sector (63.2%). Internal consistency of the GR-COPSOQ II was assessed with the Cronbach alpha criterion (Cronbach’s a) and it was acceptable (0.8>α>0.7) for most of the scales. Mean scores were high in many scales that describe exposure to psychosocial risk factors at the workplace. Construct validity was established by exploratory factor analysis (EFA) for the entire study sample and scales. In conclusion, the Greek version of the COPSOQ-II (GR-COPSOQ II) has good psychometric properties and can be recommended as a valid tool for the assessment of psychosocial risk in Greek employees.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84803737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Environmental impacts of war’s social consequences. Case Study: Aleppo Governorate Syria 战争的社会后果对环境的影响。案例研究:叙利亚阿勒颇省

EMBnet.journal Pub Date : 2021-09-30 DOI: 10.14806/ej.26.1.965

Kyriaki Papadimitriou, Dimitrios Koumoulidis, Lida Papalamprou, C. Kasimatis, Panagiotis Sparangis, Nikolaos Katsenios, D. Vlachakis, Dimitris Triantakonstantis, Aspasia Efthimiadou

{"title":"Environmental impacts of war’s social consequences. Case Study: Aleppo Governorate Syria","authors":"Kyriaki Papadimitriou, Dimitrios Koumoulidis, Lida Papalamprou, C. Kasimatis, Panagiotis Sparangis, Nikolaos Katsenios, D. Vlachakis, Dimitris Triantakonstantis, Aspasia Efthimiadou","doi":"10.14806/ej.26.1.965","DOIUrl":"https://doi.org/10.14806/ej.26.1.965","url":null,"abstract":"War is an anthropogenic phenomenon with devastating effects, which cause loss of human life, alongside the disastrous effects on the natural environment. The environmental impacts of armed conflicts can be either direct, arising from the act of war itself, or indirect due to the massive population displacement, infrastructure breakdown, and militarised zones. Impacts may be irreversible, affecting areas even far away from the territory of the conflict where they manifest. The environmental impacts of war create social and economic consequences that lead to greater environmental degradation by showing the interdependent relationship between the environment, society, and economy. It is imperative to address the subject in a multidisciplinary approach and implement stricter international legislation on environmental disasters during wars. This study aims to identify environmental impacts by using satellite-derived images at Aleppo Governorate, analyse them via statistics supplemented with the available information for the research region, and demonstrate the subsequent social and economic consequences by creating indices, such as the Normalised Difference Vegetation Index (NDVI), digital image composites and classified images, which record the extent of reduction of healthy vegetation and the extent of destruction at the city of Aleppo. Data from international organisations corroborated the findings, and hereinafter societal and economic effects were analysed. Using remote sensing alongside with geographic information systems can be a useful tool as it offers access to war zones where physical observations are usually impossible.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"201 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75995875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SOILomics; where Microbiome Genetics meets Precision Agriculture SOILomics;微生物组遗传学与精准农业的结合

EMBnet.journal Pub Date : 2021-07-09 DOI: 10.14806/EJ.26.0.940

D. Vlachakis, Aspasia Efthimiadou

引用次数: 0

Mechanisms of epigenetic inheritance in children following exposure to abuse 儿童受虐后的表观遗传机制

EMBnet.journal Pub Date : 2021-07-08 DOI: 10.14806/EJ.26.A.995

Elissavet Damaskopoulou, G. Chrousos, E. Eliopoulos, D. Vlachakis

引用次数: 0

Benefits of a grape-rich diet on human health: a nutrigenomics study underlining the potential role of non-coding RNAs 富含葡萄的饮食对人体健康的益处:一项强调非编码rna潜在作用的营养基因组学研究

EMBnet.journal Pub Date : 2021-07-08 DOI: 10.14806/EJ.26.A.989

Rosa Anna Milella, M. Gasparro, F. Alagna, M. Cardone, S. Rotunno, C. Ammollo, F. Semeraro, Apollonia Tullo, F. Marzano, D. Catalano, Mario Colucci, D. D’Elia

引用次数: 0

Plant micro RNAs can control cancer genes expression through a sequence-specific targeting mechanism: the case of MALAT1 and NEAT1 植物微rna可以通过序列特异性靶向机制控制癌基因的表达:MALAT1和NEAT1的例子

EMBnet.journal Pub Date : 2021-07-08 DOI: 10.14806/EJ.26.A.984

F. Marzano, M. F. Caratozzolo, A. Consiglio, F. Licciulli, S. Liuni, E. Sbisà, D. D’Elia, Apollonia Tullo, D. Catalano

引用次数: 0

An ERASMUS student exchange involving nodes from Belgium, Sweden, Colombia, Slovakia and Greece was organized during 2020 2020年，组织了来自比利时、瑞典、哥伦比亚、斯洛伐克和希腊的ERASMUS学生交流活动

EMBnet.journal Pub Date : 2021-07-08 DOI: 10.14806/EJ.26.A.1003

David R.A. Coornaert, Cyril Radermecker, Ahmed Kanfoud

引用次数: 0

Precision dairy farming – A Phenomenal opportunity 精准的奶牛养殖-一个非凡的机会

EMBnet.journal Pub Date : 2021-07-08 DOI: 10.14806/EJ.26.A.966

T. Klingström, K. Petersson, N. von der Lehr, H. Persson, D. de Koning

引用次数: 0