Evidence on the impacts of chemicals arising from human activity on tropical reef-building corals; a systematic map

Background Tropical coral reefs cover ca. 0.1% of the Earth’s surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. They are currently threatened by local stressors (e.g. nutrient enrichment and chemical pollution arising from poor land management, sewage effluents, agriculture, industry) and global stressors (mainly seawater warming and acidification, i.e. climate change). Global and local stressors interact in different ways, but the presence of one stressor often reduces the tolerance to additional stress. While global stressors cannot be mitigated solely by local actions, local stressors can be reduced through ecosystem management, therefore minimizing the impact of climate change on coral reefs. We systematically mapped the evidence of impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems, to inform decision-makers on the available evidence on this topic. Methods We searched the relevant literature using English terms combined in a tested search string in two publication databases (Scopus and Web Of Science Core Collection). The search string combined terms describing the population (tropical reef-building corals) and the exposure (chemicals). We searched for additional literature through three search engines, three dissertations repositories, 11 specialist websites, and through a call to local stakeholders. Titles, abstracts, and full-texts were successively screened using pre-defined eligibility criteria. A database of all studies included in the map with coded metadata was produced. The evidence was described and knowledge clusters and gaps were identified through the distribution and frequency of studies into types of exposure and/or types of outcomes and/or types of study. Review findings The initial searches identified 23,403 articles which resulted in 15,177 articles after duplicate removal. Among them, 908 articles were retained after screening process, corresponding to 7937 studies (a study being the combination of a taxon, an exposure, and an outcome). Among these studies, 30.5% dealt with the impact of nutrient enrichment on corals while 25% concerned the impact of human activities without reference to a chemical. The most measured outcomes were those related to the chemical concentration in corals (bioaccumulation, 25.8%), to coral physiology (16.9%), cover (14%), and mortality (9%). Half of the studies (48.4%) were experimental—the exposure was controlled by the researchers—and were conducted in laboratory conditions (39.4%) and in situ (9%). The most studied taxa, exposure, and outcomes were different between experimental and observational studies. Conclusions We identified four well-represented subtopics that may be amenable to relevant full syntheses via systematic reviews: (1) evidence on bioaccumulation of chemicals by corals; (2) evidence on the effects of nutrient enrichment on corals; (3) evidence on the effects of human activities on corals; and (4) evidence on the ecotoxicological effects of chemicals on corals (except nutrient enrichment). The systematic map shows that corals in their natural environment can be exposed to many categories of chemicals, and that there is a complete gap in experimental research on the combined effects of more than two categories of chemicals. We therefore encourage research on this topic.

Digitally connected work and its consequences for strain – a systematic review

Background Evolving digitization has an impact not only on the organization of work, but also on the health of employees. Dealing with new technologies, integrating new processes and requirements into work, and restructuring tasks among others are demands that can be stressful and impair health. Objectives Our aim was to identify (clusters of) working conditions associated with digitally connected work and to analyze their relations with strain, that is, health and well-being outcomes. Methods Between May and October 2019, a search string was used to systematically search six databases (EMBASE, Medline, PSYNDEX, PsycInfo, SocIndex, WISO) for German and English texts according to the PEO scheme. The methodological quality was assessed using the Quality Assessment Tool for Studies with Diverse Design. Results 14 studies were identified. Despite the search string containing latest technologies, we identified mostly studies from the 1980s/90s. To aggregate findings, a categorization of work factors (cognitive demands, social factors, organizational factors, environmental factors) and health factors (motivation/satisfaction, reduced well-being/affective symptoms, physiological parameters/somatic complaints) is introduced. The most frequently identified work factors belong to the category of cognitive demands. For health factors, motivation/satisfaction was identified most often. 475 associations were found in total. Conclusions This systematic review provides an overview of work and health factors that have been studied between 1981 and 2019. Recent texts frequently study individualized health factors (e.g., life satisfaction) whereas objective physiological measurement data and objective survey methods such as workplace analysis are not used. This latter approach was predominantly found in the older studies. In order to obtain a comprehensive picture, however, it is worthwhile to use a combination of these subjective and objective approaches for future studies in this field.

O-165 Expert panel and evidence-based development of the Logbook for the Nurses and Midwives Certification programme of the European Society of Human Reproduction and Embryolog

Study question How was the Logbook for the Nurses and Midwives Certification programme of the European Society of Human Reproduction and Embryology (ESHRE) developed? Summary answer The Logbook for the ESHRE Nurses and Midwives Certification programme, which questions 56 roles, was developed based on an extensive literature review and expert opinion. What is known already The ESHRE Executive Committee established the Nurses and Midwives Certification Committee (NMCC) in 2012. Since inception (2015), the certification programme has been delivered annually, with the exception of 2020 because of SARS-CoV-2. One-hundred-fourteen nurses/midwives have obtained ESHRE certification (passing rate=72%) and the programme is now accessible to nurses/midwives globally. The Certification program aims (i) to recognise the extended role of nurses/midwives delivering fertility care and (ii) to expand their theoretical background. The pre-requisites for certification are (i) being educated to a bachelor level of education and (ii) completing a practice based Logbook to demonstrate supervision of professional experience. Study design, size, duration Between 2012 and 2014, the NMCC completed a systematic literature search for papers relating to clinical, non-clinical and extended roles of nurses and midwives in fertility settings. In addition, the NMCC invited a larger expert panel of European senior nurses and midwives to a meeting to discuss their needs and preferences regarding the certification programme and to survey the diverse roles performed by nurses and midwives in their country. Participants/materials, setting, methods The NMCC comprised four nurses/midwives, one clinical embryologist, and one medical doctor (both in advisory capacity). The Medline database was searched by entering a search string in PubMed combining (MeSH) terms related to reproductive medicine and nursing or midwifery. Opinion and empirical papers relating to roles of nurses/midwives in fertility settings were included. The surveyed expert panel included twelve nurses/midwives, representing Belgium, Denmark, Finland, France, Norway, Slovenia, Sweden, Turkey, Ukraine, and the United Kingdom. Main results and the role of chance A total of 49 papers, of which 24 empirical papers, were identified with the search string (n = 47) and snowball strategy (n = 2). The papers originated from 13 countries spread across Asia, Oceania, Europe, and North America. All twelve European senior nurses and midwives responded to the survey. Finally, 56 different roles were included in the Logbook. Forty-four roles were performed by nurses/midwives working in fertility settings according to the surveyed expert panel (n = 18), the literature (n = 8), or both the surveyed expert panel and literature (n = 18). An additional twelve observations of laboratory procedures were added by the NMCC. Substantial variation in roles and responsibilities existed across the countries from which the evidence originated. Whereas a considerate proportion of roles were performed in at least five countries (n = 16/56), a minority of roles were only performed by nurses/midwives in some countries (n = 7/56). Eight specialist roles (e.g. embryo transfer) were performed independently by nurses/midwives in some countries, whilst in other countries, nurses/midwives merely had an assisting role. In addition to completing the Logbook, participants were expected to write two ethical cases according to a guideline, testifying to their ability to reflect as a senior nurse/midwife. From 2015, the content of the Logbook was further developed. Limitations, reasons for caution This abstract relates to the development and content of the Logbook and not the curriculum/educational material required for the theoretical exam of the Nurses and Midwives Certification programme. The NMCC continuously improves the Logbook and elements have been added and removed since its creation. Wider implications of the findings The review and survey illustrated the variation in roles and responsibilities of nurses/midwives across the studied countries, further highlighting the opportunity for professional development within fertility care. Further research is required to elicit the experience of certified nurses/midwives with the programme and its impact on their professional and personal development. Trial registration number Not applicable

PEMETAAN RISET TENTANG DETEKSI TOPIK PADA TWITTER DENGAN TEKNIK SYSTEMATIC LITERATURE REVIEW

Sebuah dokumen atau tulisan pastinya mengandung suatu informasi penting di dalamnya. Peringkasan dokumen membuat penemuan informasi-informasi tersebut menjadi lebih mudah karena mempersingkat kalimat dengan cara menghilangkan kata atau kalimat yang tidak penting. Peringkasan dokumen saat ini sudah banyak dilakukan dengan cara yang otomatis menggunakan metode-metode yang dikembangkan dari model neural netowork. Penelitian ini bertujuan untuk mengetahui sejauh mana perkembangan metode neural network dalam meringkas dokumen dilakukan dengan cara menganalisis literatur atau penelitian menggunakan teknik systematic literature review. Pengumpulan literatur dilakukan dengan cara melakukan pencarian pada beberapa digital library dengan memasukkan search string yang telah dibuat berdasarkan research question dengan batas publikasi antara tahun 2014-2018. Hasil dari penelitian ini menunjukkan bahwa dari 1266 literatur yang diperoleh 39 diantaranya layak untuk dianalisa. Berdasarkan dari 39 literatur tersebut diketahui bahwa metode neural network yang digunakan untuk meringkas dokumen adalah sebanyak 28 metode. Metode yang paling sering digunakan adalah metode Recurrent Neural Network (RNN) dan metode terbaik yang ditemukan untuk melakukan peringkasan adalah Deep Neural Network (DNN) dengan persentase ketepatan mencapai 62%.

AB0408 SYSTEMIC SCLERODERMA AND ENVIRONMENTAL RISK FACTORS: IDENTIFYING ASSOCIATIONS MINING THE BIOMEDICAL LITERATURE

Background:A debate still exists concerning the role of occupational and environmental factors in the pathogenesis of systemic scleroderma (SSc).Objectives:Our aim was to explore associations between SSc and environmental factors utilizing an automatic semantic interpretation of PubMed results.Methods:The literature search string: (“systemic sclerosis” OR “scleroderma”) AND (“occupational exposure” OR “environmental” OR “risk factor”) was used to retrieve abstracts from the entire PubMed database, using Semantic MEDLINE 2, on 6/14/2020. This application represents a network of semantic predications (triples of the form subject-predicate (or relation) -object, e.g. Occupational Exposure causes Systemic Scleroderma) on a knowledge graph. Subject and object arguments of each predication are concepts from the Unified Medical Language System (UMLS) Metathesaurus and the relation is taken from the UMLS Semantic Network. The system allows for choosing the central topic (“Systemic Scleroderma”), the length of the network (3 nodes), and automatic summarization, eliminating the less informative predications.Results:The search string retrieved 864 citations and identified 6,397 predications by using 34 types of relations. Initially, we focused our attention on the ‘CAUSES’ type of relation (Figure 1), displaying a network with 59 nodes and 57 edges.The central concepts of this network, identified as having causal relationship with SSc are autoimmune diseases/autoimmunity, chemicals such as bleomycin, occupational and environmental exposure, especially silica, vinyl chloride and trichloroethylene, genes, including HLA and non-HLA genes, genetic polymorphisms, transcription factors (TFs) such as Fli1 and KLF5, and fibrosis. Eosinophilia-myalgia syndrome, toxic oil syndrome and infection were all causally linked to autoimmune diseases. Minerals were associated with occupational exposure and with autoimmune diseases. Concepts causally linked to fibrosis were rare diseases, HLA genes, other non-HLA genes, such as STAT4, IR4, IR5, TLR4, TLR7 and Rho-associated Kinase, and vinyl chloride monomer. Pathogenic factors associated with SSc were endothelial dysfunction and extracellular matrix proteins. Many of the papers in the network also suggested that hormonal factors are involved.Conclusion:Inspection on the knowledge graphs reveals concepts central to research on the etiopathogenesis of SSc. The relations in which these concepts participate, provide more specific information. The Semantic MEDLINE graph supports the kind of patterns that underpin literature-based discovery.Although the pathogenesis of SSc remains elusive, it is accepted that initial vascular damage driven by autoimmunity and environmental factors causes abnormalities in the vasculature resulting in the activation of fibroblasts in various organs. Silica and solvents such as trichloroethylene seem to be the most consistently suspected environmental agents in SSc.References:[1]Rindflesch TC,et al. Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use 2011;31:15-21.Figure 1.Semantic Network of Casual Relationships of Systemic Scleroderma.Disclosure of Interests:None declared

AB0386 CORONAVIRUS INFECTION AND VASCULITIS: IDENTIFYING ASSOCIATIONS MINING THE BIOMEDICAL LITERATURE

Background:Based on recent publications suggesting an association between COVID-19 and vascularInflammation.Objectives:Our aim was to explore new associations between coronavirus infections and vasculitis utilizing semantic mining of PubMed results.Methods:The following literature search string: “(vasculitis OR vascular inflammation OR vascular damage) AND (coronavirus OR SARS virus OR MERS-CoV OR Covid-19)” was used to retrieve abstracts from the whole PubMed database, using Semantic MEDLINE 2. on 6/7/2020. This application represents a network of semantic predications (triples of the form subject-predicate-object, e.g. COVID-19 causes Disease) on a knowledge graph. The system allows for choosing the maximum number of nodes represented, the central topic, and the length of the network. For our network we chose to display all relations, COVID-19 (31 edges) as the central term, 3 lengths, and selecting the most informative nodes. Automatic summarization eliminated the less informative predications.Results:The search string retrieved 152 citations from PubMed and identified 1,028 predications. Thenetwork (Figure 1), displayed using COVID-19 as the central term, consisted of 72 nodes and 140 edges. The 5 most connected nodes were ’Patients: 19 nodes’, COVID-19: 13’, ‘Inflammation: 13’, ’Lung: 11’, and ‘Disease: 11’. Multiple links have been found between coronavirus and vasculitis. Animal coronaviruses, including the one causing feline infectious peritonitis (FIP), the murine coronavirus mouse hepatitis virus (MHV), the SARS-CoV in transgenic mice and coronavirus in ferrets, are known to cause vasculitis in animals. It is known that coronaviruses that infect animals can evolve and become new human coronaviruses. SARS produces inflammation in blood vessels. In 2005, a link between the coronavirus HCoV-NL63 or New Haven Coronavirus (HCoV-NH) and KD was reported,although later studies concluded that HCoV-NH did not play a dominant role in the etiology orpathogenesis of KD. In 2014, serological testing suggested the possible involvement of CoV-229E in the development of KD. There has also been a report of KD patients being infected by coronavirus OC43/HKU1.COVID-19 may infect the vessels and trigger inflammatory reactions like those of vasculitis, including vasculitis-like cutaneous lesions. COVID-19 patients develop thrombosis, and increased risk of thrombosis is also present in primary vasculitic syndromes. Children, many of whom tested positive for COVID-19 antibodies, developed Multisystem Inflammatory Syndrome in Children (MIS-C), an inflammatory condition similar to Kawasaki Disease (KD).Conclusion:Knowledge integration and discovery methods are an efficient and powerful way of retrieving and analyzing relevan information from multiple papers. Their main advantages are finding relations among biomedical concepts, generating new hypotheses, and opening them to literature-based discovery.SARS-CoV-2 may cause vasculitis or vasculitis-like syndromes. The KD-like syndrome reported mainly in children with COVID-19 revives the previous suspicion of coronavirus as a possible triggering agent of KD and the decades-old hypothesis of infection involvement in the pathogenesis of vasculitis.References:[1]Rindflesch TC,et al. Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use 2011;31:15-21.Figure 1.Semantic Networks Resulting from Pubmed. All relations COVID-19 (edges:140) 3 lengths Max nodes: F (all nodes considered relevant).Disclosure of Interests:None declared

Medial Sigmoid Depression of the Mandibular Ramus as a Lesion-Mimicking Anatomical Variation: A Systematic Review

(1) Background: Medial sigmoid depression (MSD) of the mandibular ramus is an anatomical variation that resembles non-odontogenic cystic lesion. (2) Aim: The aim of this systematic review was to survey the literature to identify the relevant journal publications, reveal their scientific impact in terms of citations and compare the reported prevalence of MSD. (3) Materials and methods: PubMed, Google Scholar, Scopus and Web of Science were queried to identify relevant publications. The search string was: “medial depression of mandibular ramus” OR “medial depression of the mandibular ramus” OR “medial depression of the mandibular rami” OR “medial depression of mandibular rami” OR “medial sigmoid depression”. (4) Results: Eight studies were identified. Dry mandibles and patient dental panoramic radiographs were evaluated in four and seven of the eight studies, respectively. The prevalence of MSD varied from 20.2% to 82.0%. In male and female patients, the prevalence was 18.3–76.0% and 22.0–64.0%, respectively. MSD tended to occur bilaterally and most prevalent in patients with Angle’s Class II occlusion. The semilunar and triangular shapes were more common than teardrop and circular shapes. The most cited study had 12 citations. (5) Conclusions: MSD was a seldom investigated and cited anatomical variation that was not uncommon. Its recognition should be further promoted.

UniBioDicts: Unified access to Biological Dictionaries

Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms. Availability and implementation The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license. Supplementary information Supplementary data are available at Bioinformatics online.