Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Transition from Secondary school CLIL to EMI at University: Initial evidence from research in Italy

Through vocabulary tests, interviews with students and recordings of classes/lectures, we measured students' English vocabulary knowledge against the vocabulary in the teachers' talk, the nature of classroom interaction in the two settings and the students' approaches to their learning in general and their in-class listening strategies in particular. In this way we aimed to identify the challenges students faced in English-medium education in the secondary and tertiary educational phases

Learning beyond the classroom: students’ attitudes towards the integration of CLIL and museum-based pedagogies

In the last two decades, several studies have reported on the benefits of Content and Language Integrated Learning (CLIL) on students’ affective and cognitive gains. These studies, however, have mainly concentrated on the implementation of CLIL within the formal (school) context, with very little research on its impact in non-formal (out-of-school) contexts. Thus, the present article addresses this gap by describing an action research project aimed at understanding secondary school students’ attitudes towards the integration of CLIL and museum-based pedagogies. The project involved 284 students (14–16 years old) in northern Italy, who participated in a CLIL museum visit on Animal Classification through English at the Natural History Museum in Venice. A mixed-method research design was implemented and data was collected through students’ questionnaires and focus groups. Results reveal that students showed very positive attitudes towards taking part in a CLIL museum visit based on the interaction among the following dimensions: engagement with museum objects, use of English beyond the classroom, methodology and students’ interests, self-concept and career plans

Does the Order of Invasive Species Removal Matter? The Case of the Eagle and the Pig

Invasive species are recognized as a primary driver of native species endangerment and their removal is often a key component of a conservation strategy. Removing invasive species is not always a straightforward task, however, especially when they interact with other species in complex ways to negatively influence native species. Because unintended consequences may arise if all invasive species cannot be removed simultaneously, the order of their removal is of paramount importance to ecological restoration. In the mid-1990s, three subspecies of the island fox Urocyon littoralis were driven to near extinction on the northern California Channel Islands owing to heightened predation by golden eagles Aquila chrysaetos. Eagles were lured to the islands by an abundant supply of feral pigs Sus scrofa and through the process of apparent competition pigs indirectly facilitated the decline in foxes. As a consequence, both pigs and eagles had to be removed to recover the critically endangered fox. Complete removal of pigs was problematic: removing pigs first could force eagles to concentrate on the remaining foxes, increasing their probability of extinction. Removing eagles first was difficult: eagles are not easily captured and lethal removal was politically distasteful.Using prey remains collected from eagle nests both before and after the eradication of pigs, we show that one pair of eagles that eluded capture did indeed focus more on foxes. These results support the premise that if the threat of eagle predation had not been mitigated prior to pig removal, fox extinction would have been a more likely outcome.If complete eradication of all interacting invasive species is not possible, the order in which they are removed requires careful consideration. If overlooked, unexpected consequences may result that could impede restoration

Baseline parameters for rotational thromboelastometry (ROTEM®) in healthy women undergoing elective caesarean delivery: A prospective observational study in Australia

Formal reference ranges for rotational thromboelastometry (ROTEM®) in pregnancy have not been obtained in the recommended minimum sample size of 120. This prospective observational study aimed to establish baseline parameters in an Australian population of women undergoing elective caesarean delivery. The secondary aim was to compare these reference ranges with those from prior studies and the manufacturer.Women undergoing elective caesarean delivery at term were included if they were at term, with normal body mass index and had no conditions affecting coagulation. ROTEM® reference ranges were derived by calculating the 2.5 and 97.5 percentiles for INTEM/EXTEM/FIBTEM amplitude at 5 minutes (A5), amplitude at 15 minutes (A15), coagulation time (CT), maximum clot firmness (MCF), and clot formation time (CFT).Of 202 women screened, 132 met the inclusion criteria, having a mean age of 32.7 ± 5.0 years and median body mass index of 23.8 kg/m (interquartile range 21.5-26.4). The reference ranges for selected ROTEM® parameters were as follows: FIBTEM A5 (13-28 mm), FIBTEM CT (40-74 s), FIBTEM MCF (16-34 mm), EXTEM A5 (39-66 mm), EXTEM CT (43-69 s), INTEM A5 (38-63 mm).ROTEM® reference ranges for women with uncomplicated term pregnancies were reported as per the International Federation of Clinical Chemistry. The FIBTEM MCF and FIBTEM/EXTEM/INTEM amplitudes were higher in comparison to the manufacturer's reference ranges for the non-obstetric population. The EXTEM CT was shorter than the non-obstetric reference ranges. These ranges show an increase in coagulability during normal pregnancy compared to the non-pregnant reference ranges

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (\u3ci\u3eUrocyon littoralis\u3c/i\u3e)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are pre- dicted to be strong on islands and both could drive population divergence and specia- tion. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Chan- nel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mech- anism driving population divergence among island fox populations. In particular, pop- ulations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential

Ebola Virus–Specific Neutralizing Antibody Persists at High Levels in Survivors 2 Years After Resolution of Disease in a Sierra Leonean Cohort

Ebola virus (EBOV) infection results in Ebola virus disease (EVD), an often severe disease with a nonspecific presentation. Since its recognition, periodic outbreaks of EVD continue to occur in sub-Saharan Africa. The 2013-2016 West African EVD outbreak was the largest recorded, resulting in a substantial cohort of EVD survivors with persistent health complaints and variable immune responses. In this study, we characterize humoral immune responses in EVD survivors and their contacts in Eastern Sierra Leone. We found high levels of EBOV IgG in EVD survivors and lower yet substantial antibody levels in household contacts, suggesting subclinical transmission. Neutralizing antibody function was prevalent but variable in EVD survivors, raising questions about the durability of immune responses from natural infection with EBOV. Additionally, we found that certain discrete symptoms-ophthalmologic and auditory-are associated with EBOV IgG seropositivity, while an array of symptoms are associated with the presence of neutralizing antibody