Excursion to Strood and Halling

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Gene3D: modelling protein structure, function and evolution

The Gene3D release 4 database and web portal () provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives—including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein–protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers

The impact of inflammatory bowel disease on sexual health in men: A scoping review.

AIMS AND OBJECTIVES: To review the literature on the impact of inflammatory bowel disease on the sexual health of men, and make recommendations for nursing practice and research. BACKGROUND: Inflammatory bowel disease is a chronic condition of the gastrointestinal tract, causing symptoms that may impact upon sexual health. Specialist nurses are well positioned to assess and manage sexual health, but there is a lack of clinical guidance, especially in relation to men. DESIGN: A systematic scoping review following the Arksey and O'Malley (2005) framework reported in line with the PRISMA-ScR checklist (Tricco et al. 2018). METHODS: OVID MEDLINE ALL [R], OVID EMBASE [R], OVID PsychINFO, EBSCO CINAHL Complete, The Cochrane Library and ProQuest were searched. Inclusion and exclusion criteria were applied independently by two reviewers. Data was extracted, charted and summarised from eligible studies. RESULTS: Thirty-one studies met the inclusion criteria. These were synthesised under three categories: mediators, moderators, and descriptors of sexual health. Depression, disease activity and surgery were the most commonly cited disease-related factors to affect sexual health in men. The most commonly used assessment tool was The International Index of Erectile Function. Descriptors of function included; frequency of intercourse, libido and the ability to maintain a desired sexual role. CONCLUSIONS: The effect of inflammatory bowel disease on sexual health in men involves a complex interaction of physical and psychosocial factors. Researchers must explore areas outside of erectile function to understand how the disease impacts sexuality, sexual well-being and masculinity. This can be achieved through qualitative exploration of patient, partner and health professional experiences. Relevance to clinical practice A holistic nursing assessment of men with inflammatory bowel disease should include sexual health. Developing understanding of how the disease influences sexual interaction and expression will facilitate support that is relevant, accessible and of value to men living with the disease

Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit

Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance

Assessing the impact of a combined nutrition counselling and cash transfer intervention on women’s empowerment in rural Bangladesh: a randomised control trial protocol

Introduction There is growing interest in assessing the impact of health interventions, particularly when women are the focus of the intervention, on women’s empowerment. Globally, research has shown that interventions targeting nutrition, health and economic development can affect women’s empowerment. Evidence suggests that women’s empowerment is also an underlying determinant of nutrition outcomes. Depending on the focus of the intervention, different domains of women’s empowerment will be influenced, for example, an increase in nutritional knowledge, or greater control over income and access to resources. Objective This study evaluates the impact of the Shonjibon Cash and Counselling (SCC) Trial that combines nutrition counselling and an unconditional cash transfer, delivered on a mobile platform, on women’s empowerment in rural Bangladesh. Methods and analysis We will use a mixed-methods approach, combining statistical analysis of quantitative data from 2840 women in a cluster randomised controlled trial examining the impact of nutrition behaviour change communications (BCCs) and cash transfers on child undernutrition. Pregnant participants will be given a smartphone with a customised app, delivering nutrition BCC messages, and will receive nutrition counselling via a call centre and an unconditional cash transfer. This study is a component of the SCC Trial and will measure women’s empowerment using a composite indicator based on the Project-Level Women’s Empowerment in Agriculture Index, with quantitative data collection at baseline and endline. Thematic analysis of qualitative data, collected through longitudinal interviews with women, husbands and mothers-in-law, will elicit a local understanding of women’s empowerment and the linkages between the intervention and women’s empowerment outcomes. This paper describes the study protocol to evaluate women’s empowerment in a nutrition-specific and sensitive intervention using internationally validated, innovative tools and will help fill the evidence gap on pathways of impact, highlighting areas to target for future programming. Ethics and dissemination Ethical approval has been obtained from the International Centre for Diarrhoeal Disease Research (Ref. PR 17106) and The University of Sydney (Ref: 2019/840). Findings from this study will be shared in Bangladesh with dissemination sessions in-country and internationally at conferences, and will be published in peer-reviewed journals

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

We report the latest release (version 3.0) of the CATH protein domain database (). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in diverse structural homologues being determined by the structural genomics initiatives, more sensitive methods have been developed for identifying boundaries in multi-domain proteins and for recognising homologues. The CATH classification update is now being driven by an integrated pipeline that links these automated procedures with validation steps, that have been made easier by the provision of information rich web pages summarising comparison scores and relevant links to external sites for each domain being classified. An analysis of the population of domains in the CATH hierarchy and several domain characteristics are presented for version 3.0. We also report an update of the CATH Dictionary of homologous structures (CATH-DHS) which now contains multiple structural alignments, consensus information and functional annotations for 1459 well populated superfamilies in CATH. CATH is directly linked to the Gene3D database which is a projection of CATH structural data onto ∼2 million sequences in completed genomes and UniProt

Shonjibon cash and counselling: a community-based cluster randomised controlled trial to measure the effectiveness of unconditional cash transfers and mobile behaviour change communications to reduce child undernutrition in rural Bangladesh.

BackgroundUndernutrition is strongly associated with poverty - levels of undernutrition are higher in poor countries than in better-off countries. Social protection especially cash transfer is increasingly recognized as an important strategy to accelerate progress in improving maternal and child nutrition. A critical method to improve nutrition knowledge and influence feeding practices is through behaviour change communication intervention. The Shonjibon Cash and Counselling study aims to assess the effectiveness of unconditional cash transfers combined with a mobile application on nutrition counselling and direct counselling through mobile phone in reducing the prevalence of stunting in children at 18 months.MethodThe study is a longitudinal cluster randomised controlled trial, with two parallel groups, and cluster assignment by groups of villages. The cohort of mother-child dyads will be followed-up over the intervention period of approximately 24 months, starting from recruitment to 18 months of the child's age. The study will take place in north-central Bangladesh. The primary trial outcome will be the percentage of stunted children at 18 m as measured in follow up assessments starting from birth. The secondary trial outcomes will include differences between treatment arms in (1) Mean birthweight, percentage with low birthweight and small for gestational age (2) Mean child length-for age, weight for age and weight-for-length Z scores (3) Prevalence of child wasting (4) Percentage of women exclusively breastfeeding and mean duration of exclusive breastfeeding (5) Percentage of children consuming > 4 food groups (6) Mean child intake of energy, protein, carbohydrate, fat and micronutrients (7) Percentage of women at risk of inadequate nutrient intakes in all three trimesters (8) Maternal weight gain (9) Household food security (10) Number of events for child suffering from diarrhoea, acute respiratory illness and fever (11) Average costs of mobile phone BCC and cash transfer, and benefit-cost ratio for primary and secondary outcomes.DiscussionThe proposed trial will provide high-level evidence of the efficacy and cost-effectiveness of mobile phone nutrition behavior change communication, combined with unconditional cash transfers in reducing child undernutrition in rural Bangladesh.Trial registrationThe study has been registered in the Australian New Zealand Clinical Trials Registry ( ACTRN12618001975280 )

From BIM towards digital twin: Strategy and future development for smart asset management

With the rising adoption of Building Information Model (BIM) for as-set management within architecture, engineering, construction and owner-operated (AECO) sector, BIM-enabled asset management has been increasingly attracting more attentions in both research and practice. This study provides a comprehensive review and analysis of the state-of-the-art latest research and industry standards development that impact upon BIM and asset management within the operations and maintenance (O&M) phase. However, BIM is not always enough in whole-life cycle asset management, especially in the O&M phase. Therefore, a framework for future development of smart asset management are proposed, integrating the concept of Digital Twin (DT). DT integrates artificial intelligence, machine learning and data analytics to create dynamic digital models that are able to learn and update the status of the physical counterpart from multiple sources. The findings will contribute to inspiring novel research ideas and promote wide-spread adoption of smart DT-enabled asset management within the O&M phaseCentre for Digital Built Britain, Innovate U

Co-designing inflammatory bowel disease (Ibd) services in Scotland : findings from a nationwide survey

Background: The Scottish Government’s ambition is to ensure that health services are co-designed with the communities they serve. Crohn’s and Colitis UK and the Scottish Government acknowledged the need to review and update the current IBD care model. An online survey was conducted asking IBD patients about their experiences of the NHS care they receive. This survey was the first step of co-designing and developing a national strategy for IBD service improvement in Scotland. Aim: To explore IBD patients’ experiences of current services and make recommendations for future service development. Methods: This study was part of a wider cross-sectional on-line survey. Participants were patients with IBD across Scotland. 777 people with IBD took part in the survey. Thematic analysis of all data was conducted independently by two researchers. Results: Three key themes emerged: Quality of life: Participants highlighted the impact the disease has on quality of life and the desperate need for IBD services to address this more holistically. IBD clinicians and access: Participants recognised the need for more IBD nurses and gastroenterologists along with better access to them. Those with a named IBD nurse reported to be more satisfied with their care. An explicit IBD care pathway: Patients with IBD identified the need of making the IBD care pathway more explicit to service users. Conclusions: Participants expressed the need for a more holistic approach to their IBD care. This includes integrating psychological, counselling and dietetic services into IBD care with better access to IBD clinicians and a more explicit IBD care pathway. Keywords: Inflammatory bowel disease, Co-designing, Qualitative study, Patient survey, Crohn’s disease, Ulcerative coliti

Determinants of exclusive breastfeeding in Nigeria

<p>Abstract</p> <p>Background</p> <p>Exclusive breast feeding (EBF) has important protective effects on the survival of infants and decreases risk for many early-life diseases. The purpose of this study was to assess the factors associated with EBF in Nigeria.</p> <p>Methods</p> <p>Data on 658 children less than 6 months of age were obtained from the Nigeria Demographic and Health Survey (NDHS) 2003. The 2003 NDHS was a multi-stage cluster sample survey of 7864 households. EBF rates were examined against a set of individual, household and community level variables using a backward stepwise multilevel logistic regression method.</p> <p>Results</p> <p>The average EBF rate among infants younger than 6 months of age was 16.4% (95%CI: 12.6%-21.1%) but was only 7.1% in infants in their fifth month of age. After adjusting for potential confounders, multivariate analyses revealed that the odds of EBF were higher in rich (Adjusted Odds Ratios (AOR) = 1.15, CI = 0.28-6.69) and middle level (AOR = 2.45, CI = 1.06-5.68) households than poor households. Increasing infant age was associated with significantly less EBF (AOR = 0.65, 95%CI: 0.51-0.82). Mothers who had four or more antenatal visits were significantly more likely to engage in EBF (AOR = 2.70, 95%CI = 1.04-7.01). Female infants were more likely to be exclusively breastfed than male infants (AOR = 2.13, 95%CI = 1.03-4.39). Mothers who lived in the North Central geopolitical region were significantly more likely to exclusively breastfeed their babies than those mothers who lived in other geopolitical regions.</p> <p>Conclusions</p> <p>The EBF rate in Nigeria is low and falls well short of the expected levels needed to achieve a substantial reduction in child mortality. Antenatal care was strongly associated with an increased rate of EBF. Appropriate infant feeding practises are needed if Nigeria is to reach the child survival Millennium Development Goal of reducing infant mortality from about 100 deaths per 1000 live births to a target of 35 deaths per 1000 live births by the year 2015.</p