56 research outputs found

    Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.

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    Funder: Queensland GovernmentSyphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides

    The β-oxidation pathway is downregulated during diapause termination in Calanus copepods

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    Calanus copepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist of C. finmarchicus. However, the identification of C. glacialis in some samples underlines the need for performing molecular analyses to reliably identify Calanus species. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.publishedVersio

    B!SON: A Tool for Open Access Journal Recommendation

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    Finding a suitable open access journal to publish scientific work is a complex task: Researchers have to navigate a constantly growing number of journals, institutional agreements with publishers, funders’ conditions and the risk of Predatory Publishers. To help with these challenges, we introduce a web-based journal recommendation system called B!SON. It is developed based on a systematic requirements analysis, built on open data, gives publisher-independent recommendations and works across domains. It suggests open access journals based on title, abstract and references provided by the user. The recommendation quality has been evaluated using a large test set of 10,000 articles. Development by two German scientific libraries ensures the longevity of the project

    Archives, Access and Artificial Intelligence: Working with Born-Digital and Digitized Archival Collections

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    Digital archives are transforming the Humanities and the Sciences. Digitized collections of newspapers and books have pushed scholars to develop new, data-rich methods. Born-digital archives are now better preserved and managed thanks to the development of open-access and commercial software. Digital Humanities have moved from the fringe to the center of academia. Yet, the path from the appraisal of records to their analysis is far from smooth. This book explores crossovers between various disciplines to improve the discoverability, accessibility, and use of born-digital archives and other cultural assets

    Archives, Access and Artificial Intelligence

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    Digital archives are transforming the Humanities and the Sciences. Digitized collections of newspapers and books have pushed scholars to develop new, data-rich methods. Born-digital archives are now better preserved and managed thanks to the development of open-access and commercial software. Digital Humanities have moved from the fringe to the center of academia. Yet, the path from the appraisal of records to their analysis is far from smooth. This book explores crossovers between various disciplines to improve the discoverability, accessibility, and use of born-digital archives and other cultural assets

    Ciencia de Datos versus Ciencia de la Información: informetría y análisis textual

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    The aim of this paper is identifying the characteristics of the scientific literature located in the superposition of Data Science (DC) and Information Science (IS). For this, a descriptive study with informetric applications, and, as a first approximation, textual analysis was carried out. 58 and 49 records were recovered in Scopus and WoS, respectively, for the period 1900-november, 2020. Scopus documents were the most cited and with a greater typological variety. Conceptually, data is the element that connects both domains. Both are conceived as transversal areas of knowledge, that is, they are intra, multi and transdisciplinary. DS and IS are recent disciplines, in their process of definition, reconceptualization and conformation of their methods and categories of analysis of large amounts of data and information. The sum of studies that appears in WoS and Scopus show us that DS and IS complement themselves and intersect with other areas of scientific knowledge. They are also communicated in other languages than English: Italian, French, Portuguese and JapaneseSe pretenden identificar las características de la literatura científica ubicadas en la superposición de la Ciencia de Datos (CD) y la Ciencia de la Información (CI). Para ello, se realiza un descriptivo con aplicaciones informétricas, y como primera aproximación el análisis textual. Para el periodo 1900-noviembre de 2020 se recuperaron 58 y 49 registros en Scopus y WoS, respectivamente, siendo los documentos de Scopus aquellos con mayor cantidad de citas y variedad tipológica. Conceptualmente, los datos, son el elemento que conectan a la CD y la CI. Ambas son concebidas como áreas del conocimiento transversales, es decir, son intra, multi y transdisciplinarias. La CD y la CI son disciplinas, recientes, en proceso de definiciones, reconceptualizaciones y conformación de métodos y categorías de análisis de grandes cantidades de datos e información. En tanto que la suma de estudios en CD y CI aparecen en WoS como en Scopus, se complementan e intersectan con otras áreas del saber científico, y se comunican, también en idiomas distintos del inglés: italiano, francés, portugués y japonés

    Archives, Access and Artificial Intelligence

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    Digital archives are transforming the Humanities and the Sciences. Digitized collections of newspapers and books have pushed scholars to develop new, data-rich methods. Born-digital archives are now better preserved and managed thanks to the development of open-access and commercial software. Digital Humanities have moved from the fringe to the center of academia. Yet, the path from the appraisal of records to their analysis is far from smooth. This book explores crossovers between various disciplines to improve the discoverability, accessibility, and use of born-digital archives and other cultural assets

    Scholarly Communication Librarianship and Open Knowledge

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    The intersection of scholarly communication librarianship and open education offers a unique opportunity to expand knowledge of scholarly communication topics in both education and practice. Open resources can address the gap in teaching timely and critical scholarly communication topics—copyright in teaching and research environments, academic publishing, emerging modes of scholarship, impact measurement—while increasing access to resources and equitable participation in education and scholarly communication. Scholarly Communication Librarianship and Open Knowledge is an open textbook and practitioner’s guide that collects theory, practice, and case studies from nearly 80 experts in scholarly communication and open education. Divided into three parts: *What is Scholarly Communication? *Scholarly Communication and Open Culture *Voices from the Field: Perspectives, Intersections, and Case Studies The book delves into the economic, social, policy, and legal aspects of scholarly communication as well as open access, open data, open education, and open science and infrastructure. Practitioners provide insight into the relationship between university presses and academic libraries, defining collection development as operational scholarly communication, and promotion and tenure and the challenge for open access. Scholarly Communication Librarianship and Open Knowledge is a thorough guide meant to increase instruction on scholarly communication and open education issues and practices so library workers can continue to meet the changing needs of students and faculty. It is also a political statement about the future to which we aspire and a challenge to the industrial, commercial, capitalistic tendencies encroaching on higher education. Students, readers, educators, and adaptors of this resource can find and embrace these themes throughout the text and embody them in their work

    A novel framework for user-centered research data management

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    Recent Open Data policies have led to a large-scale demand for research data repositories. Research data repositories are expected to function as an important instrument for research data preservation as well as for research collaboration and dissemination, helping to realize the advantages that motivated those policies. Existing research data management (RDM) systems and infrastructure, of which research data repositories form an important component, are currently inadequate to support and further this vision. Research data are complex compound objects, and their use, and also the mode of interacting with them, differs considerably from those of manuscript documents (e.g. research publications). This research proposes a holistic framework for RDM system design that expressly takes into account the needs of system users as well as the peculiar requirements of research data, to develop well-functioning systems. It demonstrates the development process of a simple prototype of a user-centered, data-conscious RDM system, called DataFinder, from the earliest stages of requirements gathering to requirements analyses, design, development, and evaluation. Importance is given as much to the final deliverable (i.e. DataFinder) as to the process of attaining it, since a substantial part of the research preceded the former, and the findings garnered along the way will likely prove useful for purposes of which system design forms only one

    Research data management in selected universities in South Africa

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    Includes summaries in Zulu and TswanaResearch Data Management (RDM) is an innovative trend that is growing exponentially, and globally influences the research arena, as well as academic institutions. However, the recipient of this ground-breaking research data management did not receive the same popularity as its predecessor, Open Access (OA). However, through the mandate of the National Research Foundation (NRF), slowly but surely, it is taking its position in the society of the research arena. Many academic institutions are flocking to deploy innovation time. The ultimate aim of this study was to explore how research data management in selected Universities in South Africa, is organised. It also aimed to establish the impact that the marketing of RDM services has on academic institutions in sustaining the visibility of research data management in an academic institution. The investigation adopted a predominantly quantitative motive approach. The targeted population was 20 and the focus was more on the personnel such as research data managers, research data supporting staff, ICTL and the marketing team of the library who are the RDM service providers of the designated institutions. The researcher used self-developed structured questionnaires that consist of both closed and open-end questions using Google Forms. The link and backup Ms-Word questionnaire were distributed to the identified population. The researcher reviewed the study's findings considering the study's aims. The findings were reviewed considering the pertinent literature review and the work of other researchers. The findings in this study evidently demonstrate the significance of establishing proper RDM services in selected Universities and marketing in various institutions. There are different strategies that are used by the institutions in marketing the RDM to the targeted users. Furthermore, different policies that support the functionality of the RDM are in place as one of the driving factors in the implementation of the RDM. The findings of the study further correlate with the literature on the role played by the ICT support service in enhancing the functionality and sustainability of the RDM services in academic institutions in selected universities in South AfricaUlawulo lweeNkcukacha zoPhando (RDM) yindlela entsha ekhula ngokukhawuleza, kwaye kwihlabathi jikelele inefuthe kwibala lophando, kunye namaziko emfundo. Nangona kunjalo, umamkeli wolu lawulo lwedatha yophando oluqhekezayo akazange afumane ukuthandwa okufanayo njengokwandulelayo, i-Open Access (OA). Nangona kunjalo, ngomyalelo weNational Research Foundation (NRF), ngokucothayo kodwa ngokuqinisekileyo, ithatha indawo yayo kuluntu lwebala lophando. Amaziko emfundo amaninzi athontelana ukuza kuhambisa ixesha lokuqamba izinto ezintsha. Eyona njongo yolu phononongo yayikukuphonononga indlela ulawulo lwedatha yophando kwiiYunivesithi ezikhethiweyo eMzantsi Afrika, olucwangciswa ngayo. Ikwajolise ekusekeni impembelelo yokuthengiswa kweenkonzo ze-RDM kumaziko emfundo ekuzinziseni ukubonakala kolawulo lwedatha yophando kwiziko lemfundo. Uphando lwamkele indlela yenjongo yobungakanani. Abemi ekujoliswe kubo yayingama-20 kwaye ingqwalasela yayingakumbi kubasebenzi abafana nabaphathi bedatha yophando, idatha yophando lwabasebenzi abaxhasayo, i-ICTL kunye neqela lentengiso yethala leencwadi elingababoneleli ngeenkonzo ze-RDM kumaziko atyunjiweyo. Umphandi usebenzise iikhweshine eziziphuhlisileyo ezakhiweyo ezibandakanya zombini ezivaliweyo kunye nemibuzo evulekileyo esebenzisa iiFom zikaGoogle. Ikhonkco kunye nekhweshine ye-Ms-Word egciniweyo yasasazwa kubantu abachongiweyo. Umphandi uphonononge iziphumo zophononongo ethathela ingqalelo iinjongo zophononongo. Iziphumo zaphononongwa ngokuqwalasela uphononongo loncwadi olufanelekileyo kunye nomsebenzi wabanye abaphandi. Iziphumo zolu phando zibonisa ngokucacileyo ukubaluleka kokuseka iinkonzo ezifanelekileyo ze-RDM kwiiYunivesithi ezikhethiweyo kunye nentengiso kumaziko ohlukeneyo. Kukho izicwangciso ezahlukeneyo ezisetyenziswa ngamaziko ekuthengiseni i-RDM kubasebenzisi ekujoliswe kubo. Ngaphaya koko, imigaqo-nkqubo eyahlukeneyo exhasa ukusebenza kwe-RDM ikhona njengenye yezinto eziqhubayo ekuphunyezweni kwe-RDM. Iziphumo zophando zihambelana ngakumbi noncwadi olungendima edlalwa yinkonzo yenkxaso ye-ICT ekwandiseni ukusebenza nozinzo lweenkonzo ze-RDM kumaziko emfundo kwiiyunivesithi ezikhethiweyo eMzantsi Afrika.Research Data Management (RDM) ke mokhoa oa boiqapelo o ntseng o hola ka sekhahla, 'me lefatšeng ka bophara o susumetsa lebala la lipatlisiso, hammoho le litsi tsa thuto. Leha ho le joalo, moamoheli oa taolo ena ea data ea bohlokoahali ea lipatlisiso ha a ka a fumana botumo bo tšoanang le ba pele ho eona, Open Access (OA). Leha ho le joalo, ka taelo ea Motheo oa Naha oa Lipatlisiso (NRF), butle-butle, e ntse e nka boemo ba eona sechabeng sa lebala la lipatlisiso. Litsi tse ngata tsa thuto li khobokana ho sebelisa nako ea boqapi. Maikaelelo a magolo a thutopatlisiso e e ne e le go sekaseka ka fa tsamaiso ya tshedimosetso ya patlisiso mo Diyunibesithing tse di tlhophilweng mo Aforika Borwa, e rulagantsweng ka teng. E ne e boetse e rerile ho theha phello eo ho bapatsa ha litšebeletso tsa RDM ho nang le eona ho litsi tsa thuto bakeng sa ho boloka ponahalo ea taolo ea data ea lipatlisiso setsing sa thuto. Patlisiso e ile ea amohela mokhoa oa sepheo sa bongata. Palo e neng e reretsoe batho e ne e le 20 'me ho ne ho tsepamisitsoe maikutlo haholo ho basebetsi ba kang baokameli ba lintlha tsa lipatlisiso, basebetsi ba tšehetsang lintlha tsa lipatlisiso, ICTL le sehlopha sa papatso sa laeborari bao e leng bafani ba litšebeletso tsa RDM ba litsi tse khethiloeng. Mofuputsi o sebelisitse lipotso tse iketselitseng tse hlophisitsoeng tse nang le lipotso tse koetsoeng le tse bulehileng li sebelisa Google Forms. Lihokelo le lethathamo la lipotso tsa bekapo tsa Ms-Word li ile tsa abeloa batho ba khethiloeng. Mofuputsi o hlahlobile liphuputso tsa phuputso a shebile merero ea thuto. Liphuputso li ile tsa hlahlojoa ho shebiloe tlhahlobo ea lingoliloeng tse amehang le mosebetsi oa bafuputsi ba bang. Liphuputso thutong ena li bonts'a bohlokoa ba ho theha litšebeletso tse nepahetseng tsa RDM Liunivesithing tse khethiloeng le ho bapatsa litsing tse fapaneng. Ho na le maano a fapaneng a sebelisoang ke litsi ho bapatsa RDM ho basebelisi ba shebiloeng. Ho feta moo, maano a fapaneng a ts'ehetsang ts'ebetso ea RDM a teng e le e 'ngoe ea lintlha tse susumetsang ts'ebetsong ea RDM. Dikutollo vii tsa phuputso di tswela pele ho tsamaellana le dingolwa tse mabapi le karolo e kgathilweng ke tshebeletso ya tshehetso ya ICT ho ntlafatseng tshebetso le botsitso ba ditshebeletso tsa RDM ditheong tsa thuto diyunibesithing tse kgethilweng tsa Aforika Borwa.Information ScienceM.A. (Information Science
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