Chronogram:an R package for data curation and analysis of infection and vaccination cohort studies

Motivation: Observational cohort studies that track vaccine and infection responses offer real-world data to inform pandemic policy. Translating biological hypotheses, such as whether different patterns of accumulated antigenic exposures confer differing antibody responses, into analysis code can be onerous, particularly when source data is dis-aggregated. Results: The R package chronogram introduces the class chronogram, where metadata is seamlessly aggregated with sparse infection episode, clinical and laboratory data. Each experimental modality is added sequentially, allowing the incorporation of new data, such as specialized time-consuming research assays, or their downstream analyses. Source data can be any rectangular data format, including database tables (such as structured query language databases). This supports annotations that aggregate data types/sources, for example, combining symptoms, molecular testing, and sequencing of one or more infectious episodes in a pathogen-agnostic manner. Chronogram arranges observational data to allow the translation of biological hypotheses into their corresponding code via a shared vocabulary. Availability and implementation: Chronogram is implemented R and available under an MIT licence at: https://www.github.com/FrancisCrickInstitute/chronogram; a user manual is available at: https://franciscrickinstitute.github.io/chronogram

Chronogram:an R package for data curation and analysis of infection and vaccination cohort studies

Motivation: Observational cohort studies that track vaccine and infection responses offer real-world data to inform pandemic policy. Translating biological hypotheses, such as whether different patterns of accumulated antigenic exposures confer differing antibody responses, into analysis code can be onerous, particularly when source data is dis-aggregated. Results: The R package chronogram introduces the class chronogram, where metadata is seamlessly aggregated with sparse infection episode, clinical and laboratory data. Each experimental modality is added sequentially, allowing the incorporation of new data, such as specialized time-consuming research assays, or their downstream analyses. Source data can be any rectangular data format, including database tables (such as structured query language databases). This supports annotations that aggregate data types/sources, for example, combining symptoms, molecular testing, and sequencing of one or more infectious episodes in a pathogen-agnostic manner. Chronogram arranges observational data to allow the translation of biological hypotheses into their corresponding code via a shared vocabulary. Availability and implementation: Chronogram is implemented R and available under an MIT licence at: https://www.github.com/FrancisCrickInstitute/chronogram; a user manual is available at: https://franciscrickinstitute.github.io/chronogram

Hyper-compressions: The rise of flash fiction in “post-transitional” South Africa

Blair, P. (2020). Hyper-compressions: The rise of flash fiction in “post-transitional” South Africa', The Journal of Commonwealth Literature, 55(1), 38-60. Copyright © 2018. Reprinted by permission of SAGE Publications.This article begins with a survey of flash fiction in “post-transitional” South Africa, which it relates to the nation’s post-apartheid canon of short stories and short-short stories, to the international rise of flash fiction and “sudden fiction”, and to the historical particularities of South Africa’s “post-transition”. It then undertakes close readings of three flash fictions republished in the article, each less than 450 words: Tony Eprile’s “The interpreter for the tribunal” (2007), which evokes the psychological and ethical complexities, and long-term ramifications, of the Truth and Reconciliation Commission; Michael Cawood Green’s “Music for a new society” (2008), a carjacking story that invokes discourses about violent crime and the “‘new’ South Africa”; and Stacy Hardy’s “Kisula” (2015), which maps the psychogeography of cross-racial sex and transnational identity-formation in an evolving urban environment. The article argues that these exemplary flashes are “hyper-compressions”, in that they compress and develop complex themes with a long literary history and a wide contemporary currency. It therefore contends that flash fiction of South Africa’s post-transition should be recognized as having literary-historical significance, not just as an inherently metonymic form that reflects, and alludes to, a broader literary culture, but as a genre in its own right

Counselling formerly heterosexually partnered gay fathers raised with religion

Formerly heterosexually partnered gay fathers raised with religion are an under-researched group of LGBTQ parents. This group have potentially complex coming out journeys, which can result in them seeking counselling. This research explores the counselling experiences of such men and offers suggestions for working therapeutically with them. Twelve self-identified gay fathers participated in qualitative interviews. These men all had children in the context of a heterosexual marriage or committed partnership, and a religious upbringing of some kind in the US, Canada, the UK or Ireland. The key finding of the qualitative analysis was that participants wanted therapists to not assume a ‘best’ outcome for them as either gay or ‘straight’. Instead, they wanted therapists to respect and assist them to explore their own individual sense-making around their identities and to reject fixed notions from both ex-gay and (some versions of) gay affirmative therapy of what it means to be a ‘well-adjusted’ (gay) father

Reflections on the challenges of understanding racial, cultural and sexual differences in couple relationship research

In the field of systemic psychotherapy there has been much recent interest in the areas of culture and reflexivity, and in working with couples. In this article we reflect on the process of conducting research in these areas. Drawing on findings from a large, national, empirical mixed-methods study on long-term relationships, we use two examples from the data to illustrate the complexity of researching across racial, cultural and sexual differences, in terms of research design and sampling, fieldwork and research practice, and making sense of multidimensional data. We point to findings that suggest that notions of coupledom are culturally constructed and thus challenge straightforward ideas of the procreative, sexually active couple dyad, separate from intergenerational extended families. The clinical significance of the findings for both lesbian, gay, bisexual or queer and culturally diverse couples and families are discussed

Molecular diagnosis of Pneumocystis pneumonia in dogs

Pneumocystis pneumonia (PCP) is a life-threatening fungal disease that can occur in dogs. The aim of this study was to provide a preliminary genetic characterisation of Pneumocystis carinii f. sp. 'canis' (P. canis) in dogs and thereby develop a reliable molecular protocol to definitively diagnose canine PCP. We investigated P. canis in a variety of lung specimens from dogs with confirmed or strongly suspected PCP (Group 1, n = 16), dogs with non-PCP lower respiratory tract problems (Group 2, n = 65) and dogs not suspected of having PCP or other lower respiratory diseases (Group 3, n = 11). Presence of Pneumocystis DNA was determined by nested PCR of the large and small mitochondrial subunit rRNA loci and by a real-time quantitative polymerase chain reaction (qPCR) assay developed using a new set of primers. Molecular results were correlated with the presence of Pneumocystis morphotypes detected in cytological/histological prepa rations. Pneumocystis DNA was amplified from 13/16 PCP-suspected dogs (Group 1) and from 4/76 dogs of control Groups 2 and 3 (combined). The latter four dogs were thought to have been colonized by P. canis. Comparison of C-T values in 'infected' versus 'colonized' dogs was consistent with this notion, with a distinct difference in molecular burden between groups (C-T <= 26 versus C-T range (26 < C-T < 35), respectively). Phylogenetic analyses showed that P. canis is specifically 'canine' associated, being separated from other mammalian Pneumocystis species, thereby confirming the accuracy of qPCR amplicon for Pneumocystis in dogs. Using qPCR, Pneumocystis DNA can be detected in specimens from the respiratory tract and a C-T value can be interpreted to distinguish infection versus colonization

Effect of three different dental health preventive programmes on young adult individuals: a randomized, blinded, parallel group, controlled evaluation of oral hygiene behaviour on plaque and gingivitis

AIM: To evaluate, in young adults, the effect of different preventive programmes on oral hygiene and to determine whether the variables investigated are predictors of gingival health. MATERIAL AND METHODS: This randomized, blinded, parallel, controlled clinical study examined the effectiveness of three dental health programmes. Four hundred subjects aged 20-27 years, 211 males and 189 females, participated in the study. They were recruited from a Public Dental Service clinic and from a private dental practice in Jönköping, Sweden. The effect of the programmes on plaque and gingivitis was evaluated over a 3-year period. The programmes included activities that were adapted for individuals as well as for groups. The plaque indices (PLI) and gingival indices (GI) were used to evaluate the programmes. RESULTS: All programmes resulted in a decrease in PLI and GI. The greatest decrease was found in the group that was followed-up every 2 months. Professional tooth cleaning was non-significant for the clinical result. Gingival health at baseline, participation in any of the test programmes, and knowledge of the dental diseases caries, gingivitis or periodontitis were significant predictors of good gingival health. CONCLUSIONS: The study confirms the efficacy of three different preventive programmes in reducing supragingival plaque and gingival inflammation. Professional tooth cleaning provided no clinical benefit beyond that derived from individual and group-based health education