An atypical carbohydrate deficient glycoprotein (CDG) syndrome patient in South Africa

No Abstrac

Quality of Computationally Inferred Gene Ontology Annotations

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

BACKGROUND: Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy. METHODS: RESTART was a prospective, randomised, open-label, blinded-endpoint, parallel-group trial at 122 hospitals in the UK that assessed whether starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. For this prespecified subgroup analysis, consultant neuroradiologists masked to treatment allocation reviewed brain CT or MRI scans performed before randomisation to confirm participant eligibility and rate features of the intracerebral haemorrhage and surrounding brain. We followed participants for primary (recurrent symptomatic intracerebral haemorrhage) and secondary (ischaemic stroke) outcomes for up to 5 years (reported elsewhere). For this report, we analysed eligible participants with intracerebral haemorrhage according to their treatment allocation in primary subgroup analyses of cerebral microbleeds on MRI and in exploratory subgroup analyses of other features on CT or MRI. The trial is registered with the ISRCTN registry, number ISRCTN71907627. FINDINGS: Between May 22, 2013, and May 31, 2018, 537 participants were enrolled, of whom 525 (98%) had intracerebral haemorrhage: 507 (97%) were diagnosed on CT (252 assigned to start antiplatelet therapy and 255 assigned to avoid antiplatelet therapy, of whom one withdrew and was not analysed) and 254 (48%) underwent the required brain MRI protocol (122 in the start antiplatelet therapy group and 132 in the avoid antiplatelet therapy group). There were no clinically or statistically significant hazards of antiplatelet therapy on recurrent intracerebral haemorrhage in primary subgroup analyses of cerebral microbleed presence (2 or more) versus absence (0 or 1) (adjusted hazard ratio [HR] 0·30 [95% CI 0·08-1·13] vs 0·77 [0·13-4·61]; pinteraction=0·41), cerebral microbleed number 0-1 versus 2-4 versus 5 or more (HR 0·77 [0·13-4·62] vs 0·32 [0·03-3·66] vs 0·33 [0·07-1·60]; pinteraction=0·75), or cerebral microbleed strictly lobar versus other location (HR 0·52 [0·004-6·79] vs 0·37 [0·09-1·28]; pinteraction=0·85). There was no evidence of heterogeneity in the effects of antiplatelet therapy in any exploratory subgroup analyses (all pinteraction>0·05). INTERPRETATION: Our findings exclude all but a very modest harmful effect of antiplatelet therapy on recurrent intracerebral haemorrhage in the presence of cerebral microbleeds. Further randomised trials are needed to replicate these findings and investigate them with greater precision. FUNDING: British Heart Foundation

Model and experiences of initiating collaboration with traditional healers in validation of ethnomedicines for HIV/AIDS in Namibia

Many people with Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS) in Namibia have access to antiretroviral drugs but some still use traditional medicines to treat opportunistic infections and offset side-effects from antiretroviral medication. Namibia has a rich biodiversity of indigenous plants that could contain novel anti-HIV agents. However, such medicinal plants have not been identified and properly documented. Various ethnomedicines used to treat HIV/AIDS opportunistic infections have not been scientifically validated for safety and efficacy. These limitations are mostly attributable to the lack of collaboration between biomedical scientists and traditional healers. This paper presents a five-step contextual model for initiating collaboration with Namibian traditional healers in order that candidate plants that may contain novel anti-HIV agents are identified, and traditional medicines used to treat HIV/AIDS opportunistic infections are subjected to scientific validation. The model includes key structures and processes used to initiate collaboration with traditional healers in Namibia; namely, the National Biosciences Forum, a steering committee with the University of Namibia (UNAM) as the focal point, a study tour to Zambia and South Africa where other collaborative frameworks were examined, commemorations of the African Traditional Medicine Day (ATMD), and consultations with stakeholders in north-eastern Namibia. Experiences from these structures and processes are discussed. All traditional healers in north-eastern Namibia were willing to collaborate with UNAM in order that their traditional medicines could be subjected to scientific validation. The current study provides a framework for future collaboration with traditional healers and the selection of candidate anti-HIV medicinal plants and ethnomedicines for scientific testing in Namibia

Fall Armyworm (Spodoptera frugiperda)

The fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), originated from America but is reported recently from Africa and the Asia-Pacific. FAW has caused huge international concern since its outbreak in Africa since 2016 and in Asia since mid-2018. The chapter mainly reviews its global distribution, life cycle, identification characters, strains, host plants, nature of damage, economic damage, and integrated pest management strategies available. The pest completes its life cycle on maize in 30 days (in warm summer months); in cooler temperatures, it may extend up to 60–90 days. For effective management of fall armyworm, different tools, viz., cultural control, agronomic management, breeding for resistance, natural enemies, and eco-friendly insecticides, should be used in an integrated approach. As the insect is recently introduced to Africa and the Asia-Pacific, possible management strategies and future cases of action are discussed

The influence of refuge sharing on social behaviour in the lizard Tiliqua rugosa

Refuge sharing by otherwise solitary individuals during periods of inactivity is an integral part of social behaviour and has been suggested to be the precursor to more complex social behaviour. We compared social association patterns of active versus inactive sheltering individuals in the social Australian sleepy lizard, Tiliqua rugosa, to empirically test the hypothesis that refuge sharing facilitates social associations while individuals are active. We fitted 18 neighbouring lizards with Global Positioning System (GPS) recorders to continuously monitor social associations among all individuals, based on location records taken every 10 min for 3 months. Based on these spatial data, we constructed three weighted, undirected social networks. Two networks were based on empirical association data (one for active and one for inactive lizards in their refuges), and a third null model network was based on hypothetical random refuge sharing. We found patterns opposite to the predictions of our hypothesis. Most importantly, association strength was higher in active than in inactive sheltering lizards. That is, individual lizards were more likely to associate with other lizards while active than while inactive and in shelters. Thus, refuge sharing did not lead to increased frequencies of social associations while lizards were active, and we did not find any evidence that refuge sharing was a precursor to sleepy lizard social behaviour. Our study of an unusually social reptile provides both quantitative data on the relationship between refuge sharing and social associations during periods of activity and further insights into the evolution of social behaviour in vertebrates

The Use of Unusual Psychological Theories in Psychobiography: A Case Study and Discussion

This chapter argues for the use of ‘unusual’ theories in psychobiographical research through the presentation of a case study using such a theory. Historically, psychobiographical research has predominantly made use of the work of psychoanalytic and psychodynamic theorists and developmental theorists, while more recent psychobiographical approaches have preferred more modern, empirically based. However, over reliance on a few theories within psychobiographical research creates the possibility for narrow explanations of complex lives. Given the proliferation of theoretical modes in psychology the current use of theory barely scratches the surface of available explanatory paradigms. This chapter argues for the value of casting the explanatory net wider, and for the inclusion of more psychological theories in psychobiographical work. Using a psychobiographical case study, the chapter illustrates how a ‘forgotten’ psychological theory (script theory, based on the work of Tomkins) can serve as an extremely useful explanatory paradigm for a complex religious figure. The case study focuses on Gordon Hinckley (b. 1910, d. 2008), the fifteenth president of The Church of Jesus Christ of Latter-Day Saints (commonly referred to as the Mormon Church), who remains a prominent figure in contemporary Mormonism and played a key role in the rapid growth and increasingly positive public profile of the Religion throughout the twentieth and twenty-first centuries. Using Tomkins’ script theory in conjunction with a psychobiographical method and the analysis of data gathered from published speeches, this study explores Hinckley’s personality structure and identifies three core psychological scripts

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil1. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 20162) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 20162). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease3. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus