Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data

The lived experience of discrimination by white women in committed interracial relationships with black men

Abstract: This study explores the experiences of discrimination by white women in committed interracial relationships with black men within the South African context from a descriptive phenomenological perspective. Three white females in committed interracial relationships with black males were recruited and interviewed. Open-ended interviews were conducted in order to elicit rich and in-depth first-person descriptions of the participants’ lived experiences of discrimination as a result of being in committed interracial relationships. The data analysis entailed a descriptive phenomenological content analysis and description. The results of this study suggest that white women in committed interracial relationships with black men experienced discrimination in various contexts where discrimination manifests as either a negative or a positive encounter; in addition, discrimination evokes various emotional responses and is coped with in either maladaptive or adaptive ways. Finally the experience of discrimination, although personal, necessarily impacts on the interracial relationship. Discrimination experienced by white women in committed interracial relationships with black men is thus multi-layered and both an intra-personal and inter-personal phenomenon

Generalisability of deep learning models in low-resource imaging settings: A fetal ultrasound study in 5 African countries

Most artificial intelligence (AI) research have concentrated in high-income countries, where imaging data, IT infrastructures and clinical expertise are plentiful. However, slower progress has been made in limited-resource environments where medical imaging is needed. For example, in Sub-Saharan Africa the rate of perinatal mortality is very high due to limited access to antenatal screening. In these countries, AI models could be implemented to help clinicians acquire fetal ultrasound planes for diagnosis of fetal abnormalities. So far, deep learning models have been proposed to identify standard fetal planes, but there is no evidence of their ability to generalise in centres with limited access to high-end ultrasound equipment and data. This work investigates different strategies to reduce the domain-shift effect for a fetal plane classification model trained on a high-resource clinical centre and transferred to a new low-resource centre. To that end, a classifier trained with 1,792 patients from Spain is first evaluated on a new centre in Denmark in optimal conditions with 1,008 patients and is later optimised to reach the same performance in five African centres (Egypt, Algeria, Uganda, Ghana and Malawi) with 25 patients each. The results show that a transfer learning approach can be a solution to integrate small-size African samples with existing large-scale databases in developed countries. In particular, the model can be re-aligned and optimised to boost the performance on African populations by increasing the recall to $0.92 \pm 0.04$ and at the same time maintaining a high precision across centres. This framework shows promise for building new AI models generalisable across clinical centres with limited data acquired in challenging and heterogeneous conditions and calls for further research to develop new solutions for usability of AI in countries with less resources

Socio-cultural influences on the behaviour of South Asian women with diabetes in pregnancy: qualitative study using a multi-level theoretical approach

BACKGROUND: Diabetes in pregnancy is common in South Asians, especially those from low-income backgrounds, and leads to short-term morbidity and longer-term metabolic programming in mother and offspring. We sought to understand the multiple influences on behaviour (hence risks to metabolic health) of South Asian mothers and their unborn child, theorise how these influences interact and build over time, and inform the design of culturally congruent, multi-level interventions. METHODS: Our sample for this qualitative study was 45 women of Bangladeshi, Indian, Sri Lankan, or Pakistani origin aged 21-45 years with a history of diabetes in pregnancy, recruited from diabetes and antenatal services in two deprived London boroughs. Overall, 17 women shared their experiences of diabetes, pregnancy, and health services in group discussions and 28 women gave individual narrative interviews, facilitated by multilingual researchers, audiotaped, translated, and transcribed. Data were analysed using the constant comparative method, drawing on sociological and narrative theories. RESULTS: Key storylines (over-arching narratives) recurred across all ethnic groups studied. Short-term storylines depicted the experience of diabetic pregnancy as stressful, difficult to control, and associated with negative symptoms, especially tiredness. Taking exercise and restricting diet often worsened these symptoms and conflicted with advice from relatives and peers. Many women believed that exercise in pregnancy would damage the fetus and drain the mother's strength, and that eating would be strength-giving for mother and fetus. These short-term storylines were nested within medium-term storylines about family life, especially the cultural, practical, and material constraints of the traditional South Asian wife and mother role and past experiences of illness and healthcare, and within longer-term storylines about genetic, cultural, and material heritage - including migration, acculturation, and family memories of food insecurity. While peer advice was familiar, meaningful, and morally resonant, health education advice from clinicians was usually unfamiliar and devoid of cultural meaning. CONCLUSIONS: 'Behaviour change' interventions aimed at preventing and managing diabetes in South Asian women before and during pregnancy are likely to be ineffective if delivered in a socio-cultural vacuum. Individual education should be supplemented with community-level interventions to address the socio-material constraints and cultural frames within which behavioural 'choices' are made

A 'third way' for football fandom research: Anthony Giddens and Structuration Theory

Although football fans actively discuss all of the 'big players' within their practice, the same cannot be said for sociologists of sport. Anthony Giddens is a world renowned intellectual and author of some of the most predominant sociological texts of the last millennium. He is the most frequently cited contemporary sociologist spanning all aspects of the social sciences, and yet his work is seldom referred to or used within the sociology of sport. In response to this and in reaction to calls from authors such as Williams to re-think football fandom, this article aims to explore the potential of Giddens 'Structuration Theory' (ST) for moving the sociology of sport closer towards meeting this end. It draws on in-depth qualitative interviews with thirty football fans. The findings of these and their implications are discussed in relation to the 'everyday' processes of fandom

Appraising empirical applications of Structuration Theory in management and organization studies

There is an increasing interest in the application of Structuration Theory in the fields of management and organization studies. Based upon a thorough literature review, we have come up with a data-set to assess how Structuration Theory has been used in empirical research. We use three key concepts of this theory (duality of structure, knowledgeability, and time-space) as sensitizing concepts for our analysis. We conclude that the greatest potential of Structuration Theory for management and organization studies is to view it as a process theory that offers a distinct building block for explaining intra and interorganizational change, as exemplified through concepts such as routine, script, genre, practice, and discourse

Beyond the martial façade: gender, heritage and medieval castles

Gendered interpretations are rare both within castle-studies and heritage discourses on medieval castles. Yet, castles hold potential to inform multi-vocal accounts of the medieval past and to inspire meaningful heritage interpretations to achieve greater societal impact. This article explores the role that gender currently plays in interpretations of medieval castles in Britain, supported by three case-studies written by heritage professionals. The enduring narrative of militarism at medieval castles sites is discussed, together with issues of authenticity in relation to the historical record, which is in itself biased and inherently gendered. Outcomes from a collaborative workshop highlight the need to address interpretative issues where gender is considered to equate to ‘making women visible’. Finally, we pose the question: What makes a ‘good gendered interpretation’ at a public heritage site

Can the feedback of patient assessments, brief training, or their combination, improve the interpersonal skills of primary care physicians? A systematic review

<p>Abstract</p> <p>Background</p> <p>Improving quality of primary care is a key focus of international health policy. Current quality improvement efforts place a large focus on technical, clinical aspects of quality, but a comprehensive approach to quality improvement should also include interpersonal care. Two methods of improving the quality of interpersonal care in primary care have been proposed. One involves the feedback of patient assessments of interpersonal care to physicians, and the other involves brief training and education programmes. This study therefore reviewed the efficacy of (i) feedback of real patient assessments of interpersonal care skills, (ii) brief training focused on the improvement of interpersonal care (iii) interventions combining both (i) and (ii)</p> <p>Methods</p> <p>Systematic review of randomised controlled trials. Three electronic databases were searched (CENTRAL, Medline and Embase) and augmented by searches of the bibliographies of retrieved articles. The quality of studies was appraised and results summarised in narrative form.</p> <p>Results</p> <p>Nine studies were included (two patient based feedback studies and seven brief training studies). Of the two feedback studies, one reported a significant positive effect. Only one training study reported a significant positive effect.</p> <p>Conclusion</p> <p>There is limited evidence concerning the effects of patient based feedback. There is reasonable evidence that brief training as currently delivered is not effective, although the evidence is not definitive, due to the small number of trials and the variation in the training methods and goals. The lack of effectiveness of these methods may reflect a number of issues, such as differences in the effectiveness of the interventions in experienced practitioners and those in training, the lack of theory linking feedback to behaviour change, failure to provide sufficient training or to use a comprehensive range of behaviour change techniques. Further research into both feedback and brief training interventions is required before these interventions are routinely introduced to improve patient satisfaction with interpersonal care in primary care. The interventions to be tested in future research should consider using insights from the wider literature on communication outside primary care, might benefit from a clearer theoretical basis, and should examine the use of combined brief training and feedback.</p

Pre-validation of the WHO organ dysfunction based criteria for identification of maternal near miss

<p>Abstract</p> <p>Background</p> <p>To evaluate the performance of the WHO criteria for defining maternal near miss and identifying deaths among cases of severe maternal morbidity (SMM) admitted for intensive care.</p> <p>Method</p> <p>Between October 2002 and September 2007, 673 women with SMM were admitted, and among them 18 died. Variables used for the definition of maternal near miss according to WHO criteria and for the SOFA score were retrospectively evaluated. The identification of at least one of the WHO criteria in women who did not die defined the case as a near miss. Organ failure was evaluated through the maximum SOFA score above 2 for each one of the six components of the score, being considered the gold standard for the diagnosis of maternal near miss. The aggregated score (Total Maximum SOFA score) was calculated using the worst result of the maximum SOFA score. Sensitivity, specificity, positive and negative predictive values of these WHO criteria for predicting maternal death and also for identifying cases of organ failure were estimated.</p> <p>Results</p> <p>The WHO criteria identified 194 cases of maternal near miss and all the 18 deaths. The most prevalent criteria among cases of maternal deaths were the use of vasoactive drug and the use of mechanical ventilation (≥1 h). For the prediction of maternal deaths, sensitivity was 100% and specificity 70.4%. These criteria identified 119 of the 120 cases of organ failure by the maximum SOFA score (Sensitivity 99.2%) among 194 case of maternal near miss (61.34%). There was disagreement in 76 cases, one organ failure without any WHO criteria and 75 cases with no failure but with WHO criteria. The Total Maximum SOFA score had a good performance (area under the curve of 0.897) for prediction of cases of maternal near miss according to the WHO criteria.</p> <p>Conclusions</p> <p>The WHO criteria for maternal near miss showed to be able to identify all cases of death and almost all cases of organ failure. Therefore they allow evaluation of the severity of the complication and consequently enable clinicians to build a plan of care or to provide an early transfer for appropriate reference centers.</p

Availability and quality of emergency obstetric care in Gambia's main referral hospital: women-users' testimonies

<p>Abstract</p> <p>Background</p> <p>Reduction of maternal mortality ratio by two-thirds by 2015 is an international development goal with unrestricted access to high quality emergency obstetric care services promoted towards the attainment of that goal. The objective of this qualitative study was to assess the availability and quality of emergency obstetric care services in Gambia's main referral hospital.</p> <p>Methods</p> <p>From weekend admissions a group of 30 women treated for different acute obstetric conditions including five main diagnostic groups: hemorrhage, hypertensive disorders, dystocia, sepsis and anemia were purposively selected. In-depth interviews with the women were carried out at their homes within two weeks of discharge.</p> <p>Results</p> <p>Substantial difficulties in obtaining emergency obstetric care were uncovered. Health system inadequacies including lack of blood for transfusion, shortage of essential medicines especially antihypertensive drugs considerably hindered timely and adequate treatment for obstetric emergencies. Such inadequacies also inflated the treatment costs to between 5 and 18 times more than standard fees. Blood transfusion and hypertensive treatment were associated with the largest costs.</p> <p>Conclusion</p> <p>The deficiencies in the availability of life-saving interventions identified are manifestations of inadequate funding for maternal health services. Substantial increase in funding for maternal health services is therefore warranted towards effective implementation of emergency obstetric care package in The Gambia.</p