Modeling local repeats on genomic sequences

This paper deals with the specification and search of repeats of biological interest, i.e. repeats that may have a role in genomic structures or functions. Although some particular repeats such as tandem repeats have been well formalized, models developed so far remain of limited expressivity with respect to known forms of repeats in biological sequences. This paper introduces new general and realistic concepts characterizing potentially useful repeats in a sequence: Locality and several refinements around the Maximality concept. Locality is related to the distribution of occurrences of repeated elements and characterizes the way occurrences are clustered in this distribution. The associated notion of neighborhood allows to indirectly exhibit words with a distribution of occurrences that is correlated to a given distribution. Maximality is related to the contextual delimitation of the repeated units. We have extended the usual notion of maximality, working on the inclusion relation between repeats and taking into account larger contexts. Mainly, we introduced a new repeat concept, largest maximal repeats, looking for the existence of a subset of maximal occurrences of a repeated word instead of a global maximization. We propose algorithms checking for local and refined maximal repeats using at the conceptual level a suffix tree data structure. Experiments on natural and artificial data further illustrate various aspects of this new setting. All programs are available on the genouest platform, at http://genouest.org/modulome

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Effektivisering av universitetene - er Lean svaret? En studie av Lean-arbeidet ved UiT Norges arktiske universitet

Vi er interessert i fenomenet som vi her kaller jaget etter effektivisering av offentlig sektor og de verktøy som tas i bruk for å oppfylle samfunnets og politikernes krav om bedre effektivitet og mindre byråkrati. Vi vil spesielt fokusere på organisasjonsideen – eller oppskriften - Lean, som de siste tiårene har blitt et populært og utbredt fenomen, også i offentlig sektor, med ideen om at tjenesteproduksjonen kan effektiviseres gjennom forbedring av produksjonsprosessene. I hvilken grad kan endring ved bruk av slike oppskrifter bidra til å nå målet om avbyråkratisering og effektivisering i offentlig sektor? Vi ønsker spesielt å se på implementering av konseptet i profesjonelle byråkrati som universitets- og høyskolesektoren defineres å være, og har valgt å fokusere på forbedringsarbeidet ved Det helsevitenskapelige fakultet, UiT Norges arktiske universitet

Explaining variation in reverse diffusion of HR practices: Evidence from the German and British subsidiaries of American multinationals

This paper examines the phenomenon of 'reverse diffusion' of HR practices in multinational companies, defined as the diffusion of practices from the foreign operations of MNCs to the home country. Drawing on research incorporating fieldwork in the British and German subsidiaries of US-based multinationals, we identify sources of variation in the incidence of reverse diffusion both between firms and between subsidiaries of the same firm.Multinational companies HR practices Reverse diffusion

Good Practice in Health Reporting – guidelines and recommendations

Health reporting provides descriptions of the health of a population, analyses problems and demonstrates areas in which action needs to be taken in health care, health promotion and disease prevention. As such, it provides a rational basis for participatory processes and a foundation for health policy decision-making. Good Practice in Health Reporting was developed by a working group that includes representatives from all levels of health reporting with the aim of strengthening the field at the local, federal-state and national level. The document sets out guidelines and recommendations that are intended to provide professional guidance for the creation of health reports. It makes 11 recommendations that address the ethical principles behind health reporting, the necessary framework, the selection of topics (the report’s focus), the foundation of the work undertaken (data quality), data preparation, analysis, interpretation and protection, as well as communications and quality assurance. The pilot version of the document was presented at the conferences of the German Society for Epidemiology (DGEpi), the German Society for Social Medicine and Prevention (DGSMP) and the Federal Association of Physicians of German Public Health Departments (BVÖGD) where it was discussed and subsequently revised. After further review, the guidelines were adopted by all of these institutions. Finally, Good Practice in Health Reporting is to be strengthened and developed further as part of a comprehensive review

Climate change curricula in physician associate and physician associate-comparable professional clinical programs

Purpose: Climate change has several known impacts on health, from increasing the spread of communicable disease, exacerbating the impacts of health disparities, disrupting food supplies, and detrimentally impacting mental health.  Both the Lancet and the Global Consortium on Climate and Health Education (GCCHE) argue for the inclusion of climate and health competencies in health professional training programs. While these impacts on health are increasingly well documented, little is known about whether, and to what extent, physician associate/physician associate-comparable (PA/PA-comparable) professions around the world are trained on the health impacts of climate change.  With this study, we aimed to assess whether a global sample of international PA/PA-comparable programs incorporated information about climate change and its impacts on health into their curricula. Methods: A survey developed by PA faculty members and an environmental epidemiologist was distributed to over 350 educational programs over a six-month period. Of these programs, 67 completed the survey, and these responses were analyzed using descriptive statistics. Results: 53.7% of programs do not currently incorporate climate change and health topics into their overall education plan. Main barriers include time constraints and coverage of a large amount of material. While most respondents felt only slightly knowledgeable in teaching related content, most felt a pre-made climate change curriculum would help facilitate inclusion of this content in their programs. Conclusion: While climate change has well-documented and widespread health impacts, these were not addressed in the majority of curricula of a global convenience sample of PA/PA comparable programs

Good Practice in Health reporting – guidelines and recommendations

Health reporting provides a description of the health of the population, analyses problems and demonstrates areas in which action needs to be taken in health care provision, health promotion and disease prevention. Accordingly, it offers a rational basis for participatory processes and health policy decision-making. This edition of Good Practice in Health Reporting resulted from a revision of the first edition, which was first published in March 2017. It incorporates contributions from experts, and various institutions and associations from the German federal-state and national levels. This revised edition rose out of the need for continual development in health reporting. In some cases, a number of changes were made so that certain aspects could be defined more clearly; in other cases, changes were made to methodology, for example, in order to accommodate participatory and qualitative approaches. This publication is aimed at providing people working in health reporting with professional direction and guidance. We welcome your feedback.Peer Reviewe