Open educational resources and widening participation in higher education: innovations and lessons from open universities

This paper, which references a European Lifelong Learning project under the Erasmus Virtual Campus programme, briefly reviews the role of open educational resources, open and distance learning and widening participation within European higher education. It also examines and analyses policies and practices from various European open universities, practices undertaken to widen the audience for higher education knowledge, increase engagement with higher education materials and improve participation in formal access higher education courses and programmes. It presents a framework for understanding the role of open educational resources and open and distance learning in widening participation based on their availability, accessibility, and acceptability. The paper concludes that open educational resources are beginning to influence educational opportunities in Europe, but that new policies and practices are required at all levels in the higher education system to address issues of openness and open educational resources in higher education study and the role that they can play in increasing and widening engagement and participation. There needs to be better collaboration between the various stakeholders if OER are not to be seen as a way of simply widening the audience for higher education knowledge rather than widening participation in formal studies

Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis

Background: Bedaquiline and clofazimine are important drugs in the treatment of drug-resistant tuberculosis and are commonly used across southern Africa, although drug susceptibility testing is not routinely performed. In this study, we did a genotypic and phenotypic analysis of drug-resistant Mycobacterium tuberculosis isolates from cohort studies in hospitals in KwaZulu-Natal, South Africa, to identify resistance-associated variants (RAVs) and assess the extent of clofazimine and bedaquiline cross-resistance. We also used a comprehensive dataset of whole-genome sequences to investigate the phylogenetic and geographical distribution of bedaquiline and clofazimine RAVs in southern Africa. Methods: In this study, we included M tuberculosis isolates reported from the PRAXIS study of patients with drug-resistant tuberculosis treated with bedaquiline (King Dinuzulu Hospital, Durban) and three other cohort studies of drug-resistant tuberculosis in other KwaZulu-Natal hospitals, and sequential isolates from six persistently culture-positive patients with extensively drug-resistant tuberculosis at the KwaZulu-Natal provincial referral laboratory. Samples were collected between 2013 and 2019. Microbiological cultures were done as part of all parent studies. We sequenced whole genomes of included isolates and measured bedaquiline and clofazimine minimum inhibitory concentrations (MICs) for isolates identified as carrying any Rv0678 variant or previously published atpE, pepQ, and Rv1979c RAVs, which were the subject of the phenotypic study. We combined all whole-genome sequences of M tuberculosis obtained in this study with publicly available sequence data from other tuberculosis studies in southern Africa (defined as the countries of the Southern African Development Community), including isolates with Rv0678 variants identified by screening public genomic databases. We used this extended dataset to reconstruct phylogenetic relationships across lineage 2 and 4 M tuberculosis isolates. Findings: We sequenced the whole genome of 648 isolates from 385 patients with drug-resistant tuberculosis recruited into cohort studies in KwaZulu-Natal, and 28 isolates from six patients from the KwaZulu-Natal referral laboratory. We identified 30 isolates with Rv0678 RAVs from 16 (4%) of 391 patients. We did not identify any atpE, pepQ, or Rv1979c RAVs. MICs were measured for 21 isolates with Rv0678 RAVs. MICs were above the critical concentration for bedaquiline resistance in nine (43%) of 21 isolates, in the intermediate category in nine (43%) isolates, and within the wild-type range in three (14%) isolates. Clofazimine MICs in genetically wild-type isolates ranged from 0·12-0·5 μg/mL, and in isolates with RAVs from 0·25-4·0 μg/mL. Phylogenetic analysis of the extended dataset including M tuberculosis isolates from southern Africa resolved multiple emergences of Rv0678 variants in lineages 2 and 4, documented two likely nosocomial transmission events, and identified the spread of a possibly bedaquiline and clofazimine cross-resistant clone in eSwatini. We also identified four patients with pepQ frameshift mutations that may confer resistance. Interpretation: Bedaquiline and clofazimine cross-resistance in southern Africa is emerging repeatedly, with evidence of onward transmission largely due to Rv0678 mutations in M tuberculosis. Roll-out of bedaquiline and clofazimine treatment in the setting of limited drug susceptibility testing could allow further spread of resistance. Designing strong regimens would help reduce the emergence of resistance. Drug susceptibility testing is required to identify where resistance does emerge. Funding: Wellcome Trust, National Institute of Allergy and Infectious Diseases and National Center for Advancing Translational Sciences of the National Institutes of Health

Clinical and self-reported markers of reproductive function in female survivors of childhood Hodgkin lymphoma

Purpose: To evaluate the impact of treatment for Hodgkin lymphoma (HL) on clinical reproductive markers and pregnancy outcomes.Methods: This study was embedded within the DCOG LATER-VEVO study; a Dutch, multicenter, retrospective cohort study between 2004 and 2014. Serum anti-Müllerian hormone (AMH), follicle stimulating hormone (FSH), inhibin B, antral follicle count (AFC), and self-reported (first) pregnancy outcomes were evaluated in female childhood HL survivors and controls.Results: 84 HL survivors and 798 controls were included, aged 29.6 and 32.7 years old at time of assessment. Median age at HL diagnosis was 13.4 years. Cyclophosphamide equivalent dose (CED-score) exceeded 6000 mg/m2 in 56 women and 14 survivors received pelvic irradiation.All clinical markers were significantly deteriorated in survivors (odds-ratio for low AMH (&lt; p10) 10.1 [95% CI 4.9; 20.6]; low AFC (&lt; p10) 4.6 [95% CI 2.1; 9.9]; elevated FSH (&gt; 10 IU/l) 15.3 [95% CI 5.7; 41.1], low Inhibin B (&lt; 20 ng/l) 3.6 [95% CI 1.7; 7.7], p &lt; 0.001). Pregnancy outcomes were comparable between survivors and controls (± 80% live birth, ± 20% miscarriage). However, survivors were significantly younger at first pregnancy (27.0 years vs 29.0 years, P = 0.04). Adjusted odds-ratio for time to pregnancy &gt; 12 months was 2.5 [95% CI 1.1; 5.6] in survivors, p = 0.031. Adverse outcomes were specifically present after treatment with procarbazine and higher CED-score.Conclusion: HL survivors appear to have an impaired ovarian reserve. However, chance to achieve pregnancy seems reassuring at a young age. Additional follow-up studies are needed to assess fertile life span and reproductive potential of HL survivors, in particular for current HL treatments that are hypothesized to be less gonadotoxic.</p

Cirsium species show disparity in patterns of genetic variation at their range-edge, despite similar patterns of reproduction and isolation

Genetic variation was assessed across the UK geographical range of Cirsium acaule and Cirsium heterophyllum. A decline in genetic diversity and increase in population divergence approaching the range edge of these species was predicted based on parallel declines in population density and seed production reported seperately. Patterns were compared with UK populations of the widespread Cirsium arvense.Populations were sampled along a latitudinal transect in the UK and genetic variation assessed using microsatellite markers. Cirsium acaule shows strong isolation by distance, a significant decline in diversity and an increase in divergence among range-edge populations. Geographical structure is also evident in C. arvense, whereas no such patterns are seen in C.heterophyllum. There is a major disparity between patterns of genetic variation in C. acaule and C. heterophyllum despite very similar patterns in seed production and population isolation in these species. This suggests it may be misleading to make assumptions about the geographical structure of genetic variation within species based solely on the present-day reproduction and distribution of populations

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotype

a pilot study, 2013

Introduction After recognition of European outbreaks of Clostridium difficile infections (CDIs) associated with the emergence of PCR ribotype 027/NAP1 in 2005, CDI surveillance at country level was encouraged by the European Centre for Disease Prevention and Control (ECDC) [1]. In 2008, an ECDC-supported European CDI survey (ECDIS) identified large intercountry variations in incidence rates and distribution of prevalent PCR ribotypes, with the outbreak-related PCR ribotype 027 being detected in 5% (range: 0–26) of the characterised isolates [2]. The surveillance period was limited to one month and the representation of European hospitals was incomplete; however, this has been the only European (comprising European Union (EU)/European Economic Area (EEA) and EU candidate countries) CDI surveillance study. The authors highlighted the need for national and European surveillance to control CDI. Yet, European countries were found to have limited capacity for diagnostic testing, particularly in terms of standard use of optimal methods and absence of surveillance protocols and a fully validated, standardised and exchangeable typing system for surveillance and/or outbreak investigation. As of 2011, 14 European countries had implemented national CDI surveillance, with various methodologies [3]. National surveillance systems have since reported a decrease in CDI incidence rate and/or prevalence of PCR ribotype 027 in some European countries [4-8]. However, CDI generally remains poorly controlled in Europe [9], and PCR ribotype 027 continues to spread in eastern Europe [10-12] and globally [13]. In 2010, ECDC launched a new project, the European C. difficile Infection Surveillance Network (ECDIS-Net), to enhance surveillance of CDI and laboratory capacity to test for CDI in Europe. The goal of ECDIS- Net was to establish a standardised CDI surveillance protocol suitable for application all over Europe in order to: (i) estimate the incidence rate and total infection rate of CDI (including recurrent CDI cases) in European acute care hospitals; (ii) provide participating hospitals with a standardised tool to measure and compare their own incidence rates with those observed in other participating hospitals; (iii) assess adverse outcomes of CDI such as complications and death; and (iv) describe the epidemiology of CDI concerning antibiotic susceptibility, PCR ribotypes, presence of tcdA, tcdB and binary toxins and detect new emerging types at local, national and European level. The primary objectives of the present study were to: (i) test the pilot protocol for the surveillance of CDI in European acute care hospitals developed by ECDIS-Net (methodology, variables and indicators); (ii) assess the feasibility and workload of collecting the required hospital data, case- based epidemiological and microbiological data; and (iii) evaluate the quality of data collected, whether in the presence or absence of existing national CDI surveillance activities. A secondary aim was to assess the relationship between patient and microbiological characteristics and in-hospital outcome of CDI to confirm the added value of collecting detailed epidemiological and microbiological data on CDI at European level

Standardised surveillance of Clostridium Difficile Infection in European acute care hospitals: A pilot study, 2013

Clostridium difficile infection (CDI) remains poorly controlled in many European countries, of which several have not yet implemented national CDI surveillance. In 2013, experts from the European CDI Surveillance Network project and from the European Centre for Disease Prevention and Control developed a protocol with three options of CDI surveillance for acute care hospitals: a ‘minimal’ option (aggregated hospital data), a ‘light’ option (including patient data for CDI cases) and an ‘enhanced’ option (including microbiological data on the first 10 CDI episodes per hospital). A total of 37 hospitals in 14 European countries tested these options for a three-month period (between 13 May and 1 November 2013). All 37 hospitals successfully completed the minimal surveillance option (for 1,152 patients). Clinical data were submitted for 94% (1,078/1,152) of the patients in the light option; information on CDI origin and outcome was complete for 94% (1,016/1,078) and 98% (294/300) of the patients in the light and enhanced options, respectively. The workload of the options was 1.1, 2.0 and 3.0 person-days per 10,000 hospital discharges, respectively. Enhanced surveillance was tested and was successful in 32 of the hospitals, showing that C. difficile PCR ribotype 027 was predominant (30% (79/267)). This study showed that standardised multicountry surveillance, with the option of integrating clinical and molecular data, is a feasible strategy for monitoring CDI in Europe

A nationwide study on reproductive function, ovarian reserve, and risk of premature menopause in female survivors of childhood cancer: design and methodological challenges

<p>Abstract</p> <p>Background</p> <p>Advances in childhood cancer treatment over the past decades have significantly improved survival, resulting in a rapidly growing group of survivors. However, both chemo- and radiotherapy may adversely affect reproductive function. This paper describes the design and encountered methodological challenges of a nationwide study in the Netherlands investigating the effects of treatment on reproductive function, ovarian reserve, premature menopause and pregnancy outcomes in female childhood cancer survivors (CCS), the DCOG LATER-VEVO study.</p> <p>Methods</p> <p>The study is a retrospective cohort study consisting of two parts: a questionnaire assessing medical, menstrual, and obstetric history, and a clinical assessment evaluating ovarian and uterine function by hormonal analyses and transvaginal ultrasound measurements. The eligible study population consists of adult female 5-year survivors of childhood cancer treated in the Netherlands, whereas the control group consists of age-matched sisters of the participating CCS. To date, study invitations have been sent to 1611 CCS and 429 sister controls, of which 1215 (75%) and 333 (78%) have responded so far. Of these responders, the majority consented to participate in both parts of the study (53% vs. 65% for CCS and sister controls respectively). Several challenges were encountered involving the study population: dealing with bias due to the differences in characteristics of several types of (non-) participants and finding an adequately sized and well-matched control group. Moreover, the challenges related to the data collection process included: differences in response rates between web-based and paper-based questionnaires, validity of self-reported outcomes, interpretation of clinical measurements of women using hormonal contraceptives, and inter- and intra-observer variation of the ultrasound measurements.</p> <p>Discussion</p> <p>The DCOG LATER-VEVO study will provide valuable information about the reproductive potential of paediatric cancer patients as well as long-term survivors of childhood cancer. Other investigators planning to conduct large cohort studies on late effects may encounter similar challenges as those encountered during this study. The solutions to these challenges described in this paper may be useful to these investigators.</p> <p>Trial registration</p> <p>NTR2922; <url>http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2922</url></p

Electroosmotic flow reversal outside glass nanopores.

We report observations of a striking reversal in the direction of electroosmotic flow (EOF) outside a conical glass nanopore as a function of salt concentration. At high ionic strengths (>100 mM), we observe EOF in the expected direction as predicted by classical electrokinetic theory, while at low salt concentrations (<1 mM) the direction of the flow is reversed. The critical crossover salt concentration depends on the pore diameter. Finite-element simulations indicate a competition between the EOF generated from the inner and outer walls of the pore, which drives flows in opposite directions. We have developed a simple analytical model which reveals that, as the salt concentration is reduced, the flow rates inside the pore are geometrically constrained, whereas there is no such limit for flows outside the pore. This model captures all of the essential physics of the system and explains the observed data, highlighting the key role the external environment plays in determining the overall electroosmotic behavior