A genomic mutational constraint map using variation in 76,156 human genomes

The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than that for non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.

Hopes and fears regarding care robots: Content analysis of newspapers in East Asia and Western Europe, 2001-2020

Background

As a type of welfare technology, care robotics is now widely seen as a potential aide to rehabilitation, increasing independence and enhancing the wellbeing of people with disabilities and older adults. Research into and development of care robots have both been vigorously promoted in North America, Europe and Asia, and the competition for technological advancement in robotics is becoming fierce. AI ethics and policy guidelines are being established. However, there are still differences in attitudes and perceptions, as well as national policies regarding this type of welfare technology. Moreover, despite the anticipated usefulness, it is believed that progress has been slow in the diffusion of care robots.

Purpose

In order to explore how public discourses support technological innovation, such as care robots, while preparing society for potential risks and impact, we sought to ascertain whether public discourse on care robots varies from region to region. For example, what are the hopes and promises associated with care robots and what are the concerns?

Methods

To address these questions, this article explored how care robots have been portrayed in five major broadsheet newspapers in five jurisdictions in Asia and Europe (France, Great Britain, Hong Kong SAR, Ireland and Japan). We obtained 545 articles for the period between January 2001 and September 2020, more than half of which originated in Japan. A thematic analysis was conducted of these articles written in four languages (Chinese, English, French and Japanese).

Results

Positive and negative narratives were teased out, alongside other key prominent themes identified, such as Japan as the land of robots, the pandemic, and the impact of robots on the economy. As the number of robot-related articles grew from the year 2012 onwards, narratives became more nuanced in European newspapers, but not in Asian ones. Furthermore, recent articles began to address the social and relational impact of care robots, while providing concrete examples of improvements in the quality of life for users. Further careful examination will be necessary in the future in order to establish the impact of robotics use in rehabilitation for people with disabilities, older adults, their carers and society at large.

43 EXPLORING STAFF PERCEPTIONS AND ATTITUDES TO CARE AND CAREBOTS: THE CASE OF AN ORIGINAL AIR-DISINFECTION ROBOT IN IRELAND

Background

The pandemic heightened the sense of security and safety in care settings, with cleanliness and infection control becoming an even more important aspect of care delivery. Although the impact of new welfare technology on health and social care has been discussed in recent years, few studies have reported the implementation processes or human-robot interactions in care facilities in different cultural settings. The aims of this interdisciplinary research therefore were to understand needs and aspects that have to be considered for implementing an assistive robot, and to explore user perceptions, and the process by which the robots are adopted in Ireland and Japan.

Methods

An original air-disinfection robot (V-Air) was developed by Akara Robotics, as part of research project “Harmonisation towards the establishment of Person-centred, Robotics-aided Care System” (Toyota Foundation, D18-ST-0005). Prior to its instalment in a rehabilitation centre in Dublin, semi-structured interviews were conducted, and observations carried out with seven care professionals, as they interacted with V-Air. The robot was then trialled for eight weeks (March-May 2022) in selected areas of the facility. After four weeks, the users filled out the System Usability Score and were asked questions at the end of the trial. Their scores and answers to the questions revealed staff perceptions and attitudes to care robots.

Results

Overall, the users had positive perceptions of V-Air and its usability. Initial differences existed in staff’s confidence levels, depending on prior experiences with technologies. Collective sensemaking was observed, particularly, around care delivery processes and robot functionalities. The adoption process was facilitated by several factors such as the timing of introduction, user-centred design, concept of care and organisational support.

Conclusion

The findings suggest that the introduction of care robots in care settings can offer an additional layer of organisational safety, while highlighting the significance of the iterative process in adopting assistive technologies.

134 ADULT SAFEGUARDING, HUMAN RIGHTS AND PEOPLE LIVING WITH DEMENTIA IN NURSING HOMES: CO-PRODUCING RECOMMENDATIONS FOR BEST PRACTICE

Background

People living with dementia (PLwD) in nursing homes have the right to be safe and to live a life free from harm and abuse; all persons are entitled to this right, regardless of their circumstances or where they live. PLwD are at greater risk of abuse and neglect than those without a diagnosis. Such abuse often goes unnoticed, because dementia may affect a person’s ability to recognise abuse or to report it. In 2021, the Alzheimer Society of Ireland’s Irish Dementia Working Group (IDGW) commissioned the development of a briefing paper to outline the key issues relating to upholding the human rights and safeguarding of PLwD in nursing homes including concrete recommendations for policy and practice.

Methods

A scoping review of the existing literature on this topic was carried out. This was supplemented by adopting a snowball strategy to identify additional relevant literature. Three co-design online sessions were convened with members of the IDWG in order to discuss and agree on the general content and members also provided suggestions for additional research or policy papers that should be included. Co-design sessions were also used to brainstorm and reach a consensus as a group on recommendations.

Results

This project identified a number of specific risk factors for PLwD, including organisational abuse, the need to move towards a restraint-free environment, addressing barriers to reporting of abuse and promoting agency and autonomy within safeguarding processes. A number of policy and legislative gaps in our current adult safeguarding framework were identified making it more difficult to adequately protect PLwD in nursing homes.

Conclusion

22 recommendations for best practice were developed by the IDWG for nursing home service providers (public and private), health and social care practitioners, policymakers, the Department of Health, HIQA and political representatives in order to collectively advocate for meaningful change.

63 USING CO-DESIGN TO DEVELOP A CORE COMPETENCY FRAMEWORK FOR INTERPROFESSIONAL COLLABORATION WITHIN INTEGRATED CARE TEAMS FOR OLDER PEOPLE IN IRELAND

Background

Fundamental to the successful delivery of integrated care for older people in Ireland and internationally, is sustainable interprofessional collaboration (IPC). Current evidence, however, offers little guidance in terms of how IPC can be fostered and sustained within the context of integrated care and older people. This research aimed to design a framework that describes core competencies for IPC within integrated care teams (ICTs) for older people, and outline mechanisms by which ICTs could start to develop the necessary knowledge, skills and behaviours to demonstrate proficiency.

Methods

Using a co-design approach, academic health systems researchers, members of the National Integrated Care Programme for Older People in Ireland (IPC subcommittee), and public and patient representatives (nominated by Age Friendly Ireland) collaborated across three studies to devise a core competency framework. Study 1 used co-design workshops to develop and gain consensus on core competencies; study 2 employed semi-structured interviews to explore current working practice within two existing interprofessional ICTs and study 3, combined findings from study 1 and 2, validated the agreed upon competencies and finalised the IPC competency framework.

Results

Six competencies, within three domains, were agreed. Domain one, knowledge of the team, includes the competencies, understanding roles and making referrals. Domain two, communication, includes sharing information and communicating effectively and domain three, shared decision-making, includes the final two competencies, supporting decision making with older people and collective clinical decision-making.

Conclusion

This co-designed framework provides the scaffold for curriculum development for the training of health and social care professionals around interdisciplinary team working for the care of older people. The core competencies prioritise mutual respect and active elicitation of input from all disciplines, thereby empowering disciplinary-specific expertise. Finally, and perhaps most critically, the will and preferences of the older person are deemed central to effective integrated interprofessional working within the developed IPC framework.

39 CAN CARE ROBOTS ASSIST OLDER PEOPLE AND LONG-TERM CARE SYSTEMS? KEY STAKEHOLDERS’ PERCEPTIONS IN HONG KONG SAR, CHINA AND IRELAND

Background

Robotics is now seen as part of the solution to the ageing population internationally, and is deployed in care settings. Care robots are designed to enable active ageing as well as ageing in place, with support to older persons, their families, and care professionals. The aim of this study was to understand the perceptions of stakeholders in Hong Kong and Ireland regarding the current state of affairs surrounding the use of care robots in their jurisdictions.

Methods

Semi-structured, in-depth interviews were conducted with 30 experts (15 from each jurisdiction). The participants included care professionals, service providers, researchers, and advocacy group representatives and policymakers. The questions explored their knowledge of and perceptions regarding the current use of assistive technologies, long-term care systems, and their own future vision of care provision for old age.

Results

In both jurisdictions, the use of care robots is relatively new, although many respondents were familiar with the seal robot PARO and the humanoid robot Pepper. In Hong Kong, a gerontechnology-specific exposition has become an annual feature in recent years, and the government’s investment has stepped up. In Ireland, a more general ehealth agenda has been adopted within the government’s planned care reform (Sláintecare). Older people in Hong Kong and Ireland are believed to fall through the cracks in their respective two-tier care systems, and many respondents stated that care robots are most needed in order to fill the gaps (e.g. safety monitoring, mobility support). Concerns regarding the impact of using robots included a possible reduction in human-to-human contact and deskilling of older people themselves.

Conclusion

There was a sense of urgency in both jurisdictions that more smart and digital technologies should be utilised to ease the pressures on care professionals and systems. However, a degree of optimism was noted for technological leapfrogging after the pandemic.

20 FALLING THROUGH THE CRACKS: AN EXPLORATION OF SOCIAL WORKERS’ PERCEPTIONS OF THE NEED FOR ADULT SAFEGUARDING LEGISLATION

Background

The investigation of, and interventions on, the alleged abuse of vulnerable adults, including older people,has become an important feature of social work.Policy and practice in adult safeguarding is characterised by competing debates about how regulators define core concepts and reporting systems. It has been argued that the introduction of specialist legislation could enhance responses to adult safeguarding (Montgomery et al.2016). This study sets out to shed light on how social work practitioners are navigating cases in the absence of primary legislation and to explore what benefits or challenges there might be should adult safeguarding legislation be fully enacted in the Irish context.

Methods

Focus Groups (N = 2) and face to face interviews (N = 14) were held with social work practitioners using a critical incident technique.An online survey questionnaire was also administered with N = 116 responses.

Results

Social workers reported that adults at risk were ‘falling through the cracks’ due to the absence of adult safeguarding legislation. In relation to older people, the issue of coercive control by another family member was repeatedly highlighted as a significant issue for which there was no legislative intervention available. Legislative powers such as a duty to cooperate, duty to share information and a duty to involve the adult at risk in the safeguarding process were deemed critically important but absent. In addition, social workers reported that the lack of access to support services for the adult at risk was significantly impacting on their ability to safeguard.

Conclusion

Whilst the current policy measures in place offer some protection, it is evident that social work practitioners believe that safeguarding procedures should be placed on a statutory basis to ensure the safeguarding process is applied in a consistent and effective way.

Reference

Montgomery, L., Anand, J., McKay, K., Taylor, B., Pearson, K. C., & Harper, C. M. (2016). Implications of divergences in Adult Protection legislation. Journal of Adult Protection, 18(3).

Empirical validation of an automated approach to data use oversight

The current paradigm for data use oversight of biomedical datasets is onerous, extending the timescale and resources needed to obtain access for secondary analyses, thus hindering scientific discovery. For a researcher to utilize a controlled-access dataset, a data access committee must review her research plans to determine whether they are consistent with the data use limitations (DULs) specified by the informed consent form. The newly created GA4GH data use ontology (DUO) holds the potential to streamline this process by making data use oversight computable. Here, we describe an open-source software platform, the Data Use Oversight System (DUOS), that connects with DUO terminology to enable automated data use oversight. We analyze dbGaP data acquired since 2006, finding an exponential increase in data access requests, which will not be sustainable with current manual oversight review. We perform an empirical evaluation of DUOS and DUO on selected datasets from the Broad Institute's data repository. We were able to structure 118/123 of the evaluated DULs (96%) and 52/52 (100%) of research proposals using DUO terminology, and we find that DUOS' automated data access adjudication in all cases agreed with the DAC manual review. This first empirical evaluation of the feasibility of automated data use oversight demonstrates comparable accuracy to human-based data access oversight in real-world data governance.

The Data Use Ontology to streamline responsible access to human biomedical datasets

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.

AB0805 A SURVEY OF RHEUMATOLOGY PATIENTS’ SATISFACTION TO SWITCHING FROM ORIGINATOR TO BIOSIMILAR AGENTS

Background:

The recent widespread switching of patients with inflammatory rheumatic conditions from originators to biosimilars has largely been driven by costs. The views of patients on switching are also important in the successful long term switching to biosimilars. We conducted a survey of patients views on patients satisfaction with the switch to biosimilar therapy.

Objectives:

To assess satisfaction and response after switching from originator (Humira or Enbrel) to biosimilar (Amgevita or Benepali respectively), and to describe efficacy, side effects and reactions to biosimilar.

Methods:

All patients diagnosed with an inflammatory arthritis and switched to biosimilar were identified using the Irish national HighTech electronic prescriptions system. Participants had been administered the biosimilar for > 3 months and were invited to take part via a telephone survey. This consisted of 4 questions (Question 1: satisfaction with the response to the new medication [Using 5 point Likert scale = 0: very dissatisfied; 1: dissatisfied; 2: neutral; 3 satisfied;4: very satisfied]; Question 2: overall satisfaction with biosimilar compared to originator if originator was 10 [satisfaction rating from 1 – 10 scale: 1,2: very dissatisfied; 3,4: dissatisfied; 5: neutral; 6,7,8: satisfied; 9,10: very satisfied]]; Question 3: adverse effects with biosimilars; Question 4: opinion on usage of new device [0: very difficult; 1: difficult; 2: same as previous device; 3: improvement compare to previous device).

Results:

Baseline characteristics of biosimilar switch patients with disease category were:

Category(n)GenderMale (39), Female (56)Mean age (years)56Rheumatoid arthritis58Psoriatic arthritis18Ankylosing spondylitis16Reactive arthritis1Enteropathic arthritis1Juvenile idiopathic arthritis1

48 switched from Humira to Amgevita.

The majority of the patients had positive view towards the effectiveness of the biosimilar: 36% very satisfied; 28% satisfied; 13% neutral; 10% dissatisfied; 13% very dissatisfied.

45% of the patients gave score of 9 and 10 in the survey of overall satisfaction to biosimilar if originator was given a score of 10, followed by 32% of them gave a score from 6 to 8, 4% of the patients gave a score of 5 and 7% of them gave a score of 3 and 4. The rest of them gave a score of 1 and 2.

12 participants switched back to originator (Humira, n=5; Enbrel, n=7) for the reasons of unable to use the device, anxiety, hemoptysis, nose bleeding, tongue swelling, neck pain, lethargy and generalized itchiness.

The most common complaints were (12 patients) systemic side effects (tiredness, headache, nausea, skin rashes, hair loss, muscle ache, tongue swelling, mood swing, dizzy, nose bleed, erectile dysfunction, hypertension, hemoptysis and red sclera).

17% of the patients find the biosimilars device easier to use compare to originator and 55% of the patients find both device are similar. 24% and 4% of them find the new device is difficult to very difficult to use respectively.

Conclusion:

69% of patients from Amgevita group and 60% of patients from Benepali group were satisfied with the change. Only 28% of the patients found the new device difficult to use. Overall conclusion from the study showed less than one quarter of the participants showed dissatifaction towards biosimilar and less than 12 % experienced systemic side effects and whether biosimilar could be a next cost effective biologic therapy to replace originator in future requires a longer duration of study.

Disclosure of Interests:

None declared

COVID-19 infection in patients with intestinal failure: UK experience

BACKGROUND

The direct effect of the coronavirus disease 2019 (COVID-19) pandemic on patients with intestinal failure (IF) has not been described.

METHODS

We conducted a nationwide study of UK IF centers to evaluate the infection rates, presentations, and outcomes in patients with types 2 and 3 IF.

RESULTS

A total of 45 patients with IF contracted COVID-19 between March and August 2020; this included 26 of 2191 (1.2%) home parenteral nutrition (HPN)-dependent adults and 19 of 298 (6.4%) adults hospitalized with type 2 IF. The proportion of patients receiving nursing care for HPN administration was higher in those with community-acquired COVID-19 (66.7%) than the proportion in the entire HPN cohort (26.1%; P < .01). Two HPN-dependent and 1 hospitalized patient with type 2 IF died as a direct consequence of the virus (6.7% of 45 patients with types 2 or 3 infected).

CONCLUSION

This is the first study to describe the outcomes of COVID-19 in a large cohort of patients requiring long-term PN. Methods to reduce hospital and community nosocomial spread would likely be beneficial.

PARE0033 I’M HERE BUT I’M NOT: A PHOTOVOICE STUDY OF THE LIVED EXPERIENCE OF SELF-MANAGING RHEUMATOID ARTHRITIS

Background:

Rheumatoid arthritis (RA) is a widespread chronic disease affecting about 1% of the population in the West. It is characterised by pain, fatigue and inflammation that can flare-up without warning. This makes the condition difficult to predict and manage. Bury (1982) introduced the concept of chronic illness as a disruptive experience to one’s self-identity. This is often an invisible part of managing the illness and taken for granted by others, such as family members, friends and health care professionals. Thus, there is a need to raise awareness of the patients’ lived experiences of self-managing this long-term chronic illness.

Objectives:

We aimed to collaborate with people with RA to (i) record and reflect the community’s strengths and concerns; (ii) raise awareness of the lived experience of self-managing RA (iii) spark a dialogue among key stakeholders around the self-management of RA.

Methods:

A purposeful sample of people with RA (n=12) was recruited. An innovative qualitative methodology, Photovoice, was used (Wang & Burris, 1997). A series of small group workshops took place. Participants were provided with cameras and appropriate training. They were asked to take photographs of the“challenges and solutions to living with RA” over approximately two weeks. Semi-structured interviews were conducted incorporating photo elicitation. As a group, the participants, a visual artist and researcher co-created a photo exhibition for the public.

Results:

Participants selected 32 photographs for the exhibition. They carried out a thematic analysis of the photos identifying four themes:

•I’m Here but I’m Not– this theme reflected feelings of alienation and social isolation.

•Medicine in all its forms –this theme captured attitudes towards medication and devices, as well as the creative ways people coped with RA.

•Visible illness– this concerned the recognition of RA. It captures the experience of RA as a “contested illness” and the challenge of gaining medical and cultural legitimacy.

•Mind yourself –this theme highlighted the value of self-care, often closely connected with the natural world and engagement with social activities.

Exhibitions were held at a community arts centre and a large central hospital in Dublin city. A plain language report was also collaboratively produced.

Conclusion:

This study shows how participatory methods can be used to explore the hidden experience of living with an invisible illness. This research design enabled participants to use photographs to reflect on their experiences and the meaning they intended to convey, thereby increasing trustworthiness of the findings through individual and group member checking. This approach extends beyond traditional written and verbal responses to share the worldview of participants. It demonstrates how to work with patients to create opportunities to improve awareness and spark dialogue among those who play a role in supporting the self-management of chronic illness. The integration of creative arts and participatory methods can have a positive impact for those involved in research and can enhance public engagement with research.

References:

[1]Bury, Michael (1982) Chronic Illness as Biographical Disruption. Sociology of Health & Illness. 4. 167-82.

[2]Wang, C., & Burris, M. A. (1997). Photovoice: Concept, Methodology, and Use for Participatory Needs Assessment.Health Education & Behavior,24(3), 369–387.

Acknowledgments:

Funding is awarded from the UCD Wellcome Trust Institutional Strategic Support Fund as part of a Medical Humanities and Social Science Collaboration Scheme (ref 204844/Z/16/Z).

As part of a Patient and Public Involvement (PPI) strand, a Research Advisory Group composed of people living with RA was supported the design and execution of this project.

Disclosure of Interests:

None declared

FRI0297 COMPARISON OF EFFICACY OF SECUKINUMAB VS ANTI-TNF AS SECOND LINE BIOLOGIC THERAPY IN AXIAL SPONDYLOARTHROPATHY BASED ON BASDAI RESPONSE IN AN OBSERVATIONAL STUDY

Background:

Modern biologic therapies have demonstrated encouraging results in the treatment of axial spondylarthropathy (AxSpA). The benefits of interleukin-17 inhibitors (IL-17i), as first and second line therapies, are well established [1, 2]. A systematic literature review by Navarro-Compán has shown some benefit of second line therapies using both anti-tumour necrosis factor (anti-TNF) and IL-17i [3]. To our knowledge, there are currently no studies that have directly compared which pathway has a better overall outcome. This is therefore the first observational study directly comparing both treatment arms after anti-TNF had been administered as first line therapy.

Objectives:

To investigate which second line therapy is superior, anti TNF or IL-17i (secukinumab), in patients with AxSpA, that have failed first line anti-TNF therapy.

Methods:

Patient data was extracted from the Whipps Cross Hospital Rheumatology biologics registry database. All patients selected were required to have a diagnosis of AxSpA on magnetic resonance imaging (MRI). The patient cohort that was selected had previously been treated with anti-TNF as a first line therapy and were being considered for second line therapy with either anti-TNF or IL-17i. Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) scores were recorded at 3, 6 and 12 months to assess treatment response. The unpaired t-test was used to assess the significance between the treatment groups and were analysed using the R statistical package.

Results:

Seventy patients were identified for this study of which, 57% (46/70) were male and 37% (26/70) were female. The age ranged from 30-97 years, with an average age of 72. The HLA-B27 gene association in this cohort was 71% (50/70). Three patients out of the cohort had psoriatic spondylarthropathy and the remaining had isolated AxSpA. There were an equal number of secukinumab and anti-TNF patients. The anti-TNF patients were subdivided into their respective anti-TNF drug (listed in Table 1).

Table 1.

Frequency of individual anti-TNF drugs used in this cohort.

Anti-TNF drugFrequency usedAdalimumab9/35Certolizumab8/35Etanercept17/35Golimumab1/35

This study revealed that the patients experienced an average of a 52% reduction in the BASDAI score after 6 months of anti-TNF treatment compared to only a 6% reduction in patients on secukinumab (P 0.009). However, the disease activity improvement at 12 months was not sustained in the anti-TNF group and at this stage there was no difference between the groups. Overall both treatment groups showed an average reduction in the BASDAI score by more than 30% at each 3 monthly interval.

Figure 1.

BASDAI percentage reduction at 3 monthly intervals between the two second line treatment groups using anti-TNF and Secukinumab.

Conclusion:

A significant difference could not be demonstrated between the anti-TNF and secukinumab groups in this observational cohort. Interestingly, at 6 months, anti-TNF demonstrated better outcomes according to BASDAI scores than Secukinumab but this efficacy was lost at 12 months. It was difficult to interpret these isolated results without further testing, as this is a small non-randomised study. We observed similar outcomes to the Navarro-Compán review where there was a low percentage change in the BASDAI improvement in patients on second line therapy when compared to first line treatment BASDAI scores. Therefore, exploring the mechanism for the reduction in the BASDAI response would be an interesting future study. Moreover, to fully understand these results, randomised controlled studies would need to be conducted.

References:

[1]Baeten el al. NEJM 2015.

[2]van der Heijde et al. ARD 2018.

[3]Navarro-Compán et al. RMD Open 2017.

Disclosure of Interests:

None declared

The mutational constraint spectrum quantified from variation in 141,456 humans

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes1. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.

Substrate Supporting Disc Method for Confirmed Detection of Total Coliforms and E. coli in all Foods: Collaborative Study

The Coli Complete® substrate supporting disc (SSD) method for simultaneous confirmed total coliform count and Escherichia coli determination in all foods was compared with AOAC most probable number (MPN) methods, 966.23 and 966.24. Twenty-nine laboratories participated in this collaborative study in which 6 food types were analyzed. Four food types, raw ground beef, pork sausage, raw liquid milk, and nut meats, were naturally contaminated with coliform bacteria. Two foods, dry egg and fresh frozen vegetables, were seeded with coliforms. Three food types, ground beef, raw liquid milk, and pork sausage, were naturally contaminated with E. coli. Although pork sausage was naturally contaminated, the level was very low (&lt;10/50 g); therefore, additional E. coli were inoculated into 1 lot of this food type. Three food types, nut meats, dry egg, and fresh frozen vegetables, were inoculated with E. coli. For naturally contaminated samples, duplicate determinations were made on 3 separate lots for each food type. For inoculated samples, low, medium, and high contamination levels plus uninoculated control samples were examined in duplicate. Data were analyzed separately for total coliform bacteria and for E. coli. Mean log MPN counts were determined by the SSD method and the appropriate AOAC MPN method. Results were then analyzed for repeatability, reproducibility, and mean log MPN statistical equivalence. Results were statistically equivalent for all total coliform levels in all food types except frozen vegetable and raw nut meat uninoculated control samples and 1 lot of pork sausage where the SSD method produced statistically significant greater numbers. For the E. coli determinations, results were statistically equivalent across all samples and all levels for each food type. The SSD method has been adopted first action by AOAC International for confirmed detection of total coliforms and E. coli in all foods.

Shrinking lung syndrome and systemic lupus erythematosus: a case series and literature review

Shrinking lung syndrome (SLS) is a rare manifestation of systemic lupus erythematosus, characterized by progressive dsypnoea, reduced lung volumes and associated restrictive lung physiology. Here, we provide two previously unreported cases, and review the available literature on the pathophysiology, clinical features and management of SLS. Effective treatment can prevent further deterioration or lead to improvement in abnormal lung function. A heightened awareness of SLS and its management is therefore required to prevent disease progression and increased morbidity.

Risk Factors for the Development of Cephalic Arch Stenosis

Purpose

The creation of a vascular access is necessary in hemodialysis patients, including those with marginal vessels. Upper arm fistulae are attractive due to the ease of creation and of achieving high access flow rates. Cephalic arch stenosis (CAS) can lead to failure of upper arm fistulae and is increasingly identified. We hypothesized that CAS is promoted by high blood flow rates, brachiocephalic fistulae, and an angle of cephalic vein insertion approaching 90 degrees.

Methods

All patients requiring a fistulogram between January 2004 and May 2006 had surveillance fluoroscopy of the central veins. Demographic, clinical and laboratory parameters were collected and the angle of the cephalic vein insertion measured by 3 blinded independent observers.

Results

Fifty-eight patients had fistulograms and CAS was detected in 18 subjects. Significant differences between the CAS and non-CAS groups were brachiocephalic fistula site (p=0.046), access flow (mL/min) (p=0.012), and absence of diabetes (p=0.03). Univariate predictors of CAS include access flow (per 100 mL/min) (p=0.042), platelet count (p=0.031) and calcium-phosphate product (p=0.026). The relationship of brachiocephalic site and CAS was confounded by access flow [(per 100 mL/min)*brachiocephalic fistula site (p=0.016)] and fistula age [brachiocephalic fistula site*fistula age (p=0.017)]. In multivariate analysis, renovascular disease, calcium-phosphate product, platelet count and access flow (per 100 mL/min)*brachiocephalic fistula predicted CAS (p<0.001, Negelkerke's R-Square= 0.55). The angle of insertion of the cephalic vein was not predictive for CAS.

Conclusions

CAS may be a long-term consequence of high blood flow rates. The interaction of access flow and brachiocephalic fistula supports the hypothesis that high flow through a brachiocephalic fistula promotes CAS. The multiple factors influencing cephalic arch remodeling require further research.

Analysis of protein-coding genetic variation in 60,706 humans

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

Extended interval dosing of natalizumab in multiple sclerosis

BACKGROUND

Natalizumab (NTZ), a monoclonal antibody to human α4β1/β7 integrin, is an effective therapy for multiple sclerosis (MS), albeit associated with progressive multifocal leukoencephalopathy (PML). Clinicians have been extending the dose of infusions with a hypothesis of reducing PML risk. The aim of the study is to evaluate the clinical consequences of reducing NTZ frequency of infusion up to 8 weeks 5 days.

METHODS

A retrospective chart review in 9 MS centres was performed in order to identify patients treated with extended interval dosing (EID) regimens of NTZ. Patients were stratified into 3 groups based on EID NTZ treatment schedule in individual centres: early extended dosing (EED; n=249) every 4 weeks 3 days to 6 weeks 6 days; late extended dosing (LED; n=274) every 7 weeks to 8 weeks 5 days; variable extended dosing (n=382) alternating between EED and LED. These groups were compared with patients on standard interval dosing (SID; n=1093) every 4 weeks.

RESULTS

17% of patients on SID had new T2 lesions compared with 14% in EID (p=0.02); 7% of patients had enhancing T1 lesions in SID compared with 9% in EID (p=0.08); annualised relapse rate was 0.14 in the SID group, and 0.09 in the EID group. No evidence of clinical or radiographic disease activity was observed in 62% of SID and 61% of EID patients (p=0.83). No cases of PML were observed in EID group compared with 4 cases in SID cohort.

CONCLUSIONS

Dosing intervals up to 8 weeks 5 days did not diminish effectiveness of NTZ therapy. Further monitoring is ongoing to evaluate if the risk of PML is reduced in patients on EID.

A prospective view of animal and human Fasciolosis

Fasciolosis, a food-borne trematodiasis, results following infection with the parasites, Fasciola hepatica and Fasciola gigantica. These trematodes greatly affect the global agricultural community, infecting millions of ruminants worldwide and causing annual economic losses in excess of US $3 billion. Fasciolosis, an important zoonosis, is classified by WHO as a neglected tropical disease with an estimated 17 million people infected and a further 180 million people at risk of infection. The significant impact on agriculture and human health together with the increasing demand for animal-derived food products to support global population growth demonstrate that fasciolosis is a major One Health problem. This review details the problematic issues surrounding fasciolosis control, including drug resistance, lack of diagnosis and the threat that hybridization of the Fasciola species poses to future animal and human health. We discuss how these parasites may mediate their long-term survival through regulation and modulation of the host immune system, by altering the host immune homeostasis and/or by influencing the intestinal microbiome particularly in respect to concurrent infections with other pathogens. Large genome, transcriptome and proteomic data sets are now available to support an integrated One Health approach to develop novel diagnostic and control strategies for both animal and human disease.

Fasciola hepatica tegumental antigens indirectly induce an M2 macrophage-like phenotype in vivo

The M2 subset of macrophages has a critical role to play in host tissue repair, tissue fibrosis and modulation of adaptive immunity during helminth infection. Infection with the helminth, Fasciola hepatica, is associated with M2 macrophages in its mammalian host, and this response is mimicked by its excretory-secretory products (FhES). The tegumental coat of F. hepatica (FhTeg) is another major source of immune-modulatory molecules; we have previously shown that FhTeg can modulate the activity of both dendritic cells and mast cells inhibiting their ability to prime a Th1 immune response. Here, we report that FhTeg does not induce Th2 immune responses but can induce M2-like phenotype in vivo that modulates cytokine production from CD4(+) cells in response to anti-CD3 stimulation. FhTeg induces a RELMα expressing macrophage population in vitro, while in vivo, the expression of Arg1 and Ym-1/2 but not RELMα in FhTeg-stimulated macrophages was STAT6 dependent. To support this finding, FhTeg induces RELMα expression in vivo prior to the induction of IL-13. FhTeg can induce IL-13-producing peritoneal macrophages following intraperitoneal injection This study highlights the important role of FhTeg as an immune-modulatory source during F. hepatica infection and sheds further light on helminth-macrophage interactions.

Relatives' matched with staff's experience of the moment of death in a tertiary referral hospital

BACKGROUND

Although the majority of deaths occur in hospital it has been suggested that dying in hospital is largely a negative experience.

AIM

To explore the experience of relatives and staff of patients dying in hospital using qualitative grounded theory.

METHODS

Patients receiving palliative care were identified who were likely to die in hospital. Family members were met by the researcher prior to the patient's death. The ward nurse and doctor (excluding palliative care team) most involved at that time were interviewed within 48 h of the death. The family were interviewed 2 weeks later. Interviewees described their experience of the patient's dying and death. Recruitment and thematic analysis of interviews occurred concurrently.

RESULTS

Twelve triads over 6 months (relative, nurse and doctor) were interviewed in relation to 12 patients. Dying patients and families need a guide to attend to their needs. Every detail is remembered by the family who take up residence in the hospital. Families value acts of kindness by staff. Hospital may offer benefits for the dying patient and family. However, there are gaps in care identified by families and staff. After death is critical time for the family. Junior doctors are often uncertain of their role, expressing grief and guilt. Young nurses inexperienced in care of dying patients value support and guidance by senior colleagues.

CONCLUSION

Leadership from nursing and medical staff is required for seamless provision of competent and compassionate care at this life changing time for grieving families.

Peroxiredoxin: a central player in immune modulation

Peroxiredoxins (Prx) are a family of anti-oxidants that protect cells from metabolically produced reactive oxygen species (ROS). The presence of these enzymes in the secretomes of many parasitic helminths suggests they provide protection against ROS released by host immune effector cells. However, we recently reported that helminth-secreted Prx also contribute to the development of Th2-responses via a mechanism involving the induction of alternatively activated macrophages. In this review, we discuss the role helminth Prx may play in modulating the immune responses of their hosts.

Paraoxonase 1 arylesterase activity and mass are reduced and inversely related to C-reactive protein in patients on either standard or home nocturnal hemodialysis

Human serum paraoxonase (PON1) activity is reduced in standard hemodialysis (SHD) (4 hours, 3 days/week) patients. Home nocturnal hemodialysis (HNHD) (8 hours, 6 days/week), provides a greater dialysis dose resulting in a greater clearance of metabolites. Whether improvements in the metabolic milieu of HNHD patients results in different PON1 activity levels compared to SHD patients is unclear. We determined serum PON1 mass and arylesterase activities in a group of HNHD patients and compared them to SHD patients and a group of healthy controls (HC).

PATIENTS AND METHODS

We measured PON1 arylesterase activity and mass, C-reactive protein (CRP), cystatin C, total and high-density lipoprotein (HDL) cholesterol, triglycerides, apolipoproteins A-I and B in 15 HNHD, 15 SHD and 15 HC participants.

RESULTS

PON1 arylesterase activity (p < 0.001) and mass (p < 0.05) were significantly higher in HC participants compared to SHD and HNHD participants, although no significant differences were noted between HD groups. CRP (p < 0.05) was significantly higher in SHD compared to HC participants and there were no significant differences noted between HD groups. Cystatin C (p < 0.001) was significantly different among the 3 groups. There were no significant differences noted in any lipoprotein parameters among the groups. PON1 activity (r = -0.636, p < 0.001) and mass (r = -0.425, p = 0.019) were inversely correlated with CRP in HD patients.

CONCLUSION

PON1 is reduced in HNHD patients compared to HC subjects, independent of the concentration of HDL cholesterol. Within subjects on HD, the combination of increased CRP and reduced PON1 may identify subjects at a high risk for cardiovascular complications.

Validation of the confusion assessment method in the palliative care setting

The Confusion Assessment Method (CAM) is widely used in the palliative care setting despite the fact that its performance in this population has not been validated. The aim of the study was to determine the sensitivity and specificity of the CAM when used by Non-Consultant Hospital Doctors (NCHDs) working in a specialist palliative care unit. A pilot phase was performed in which NCHDs received a 1-hour training session based on the original CAM training manual. 32 patients underwent 33 assessments in the pilot phase but the sensitivity of the CAM was only 0.5 (0.22-0.78) and specificity was 1.0 (0.81-1.0). An 'enhanced' training programme was devised that took place over two 1-hour sessions and involved case-based learning focused on the areas where the NCHDs were experiencing difficulty. 52 patients underwent 54 assessments in the main phase of the study and the performance of the CAM improved significantly. Sensitivity was 0.88 (0.62-0.98) and specificity was 1.0 (0.88-1.0). The results suggest that the CAM is a valid screening tool for delirium in the palliative care setting but its performance is dependent on the skill of the operator. NCHDs require a certain standard of training before becoming proficient in its use.

Reversibility of delirium in terminally ill patients and predictors of mortality

In this study, factors related to reversibility and mortality in consecutive cases of Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) delirium [n = 121] occurring in palliative care patients were evaluated. Delirium was assessed with the revised Delirium Rating Scale (DRS-R98) and Cognitive Test for Delirium (CTD). Patients were followed until recovery from delirium or death. In all, 33 patients (27%) recovered from delirium before death. Mean time until death was 39.7 +/- 69.8 days in patients with reversible delirium [n = 33] versus 16.8 +/- 10.0 days in those with irreversible delirium [n = 88; P < 0.01]. DRS-R98 and CTD scores were higher in irreversible delirium (P < 0.001) with greater disturbances of sleep, language, long-term memory, attention, vigilance and visuospatial ability. Irreversible delirium was associated with greater disturbance of CTD attention and higher DRS-R98 visuospatial function. Survival time was predicted by CTD score (P < 0.001), age (P = 0.01) and organ failure (P = 0.01). Delirium was not necessarily a harbinger of imminent death. Less reversible delirium involved greater impairment of attention, vigilance and visuospatial function. Survival time is related to age, severity of cognitive impairment and evidence of organ failure.

Risk factors for the development of cephalic arch stenosis

PURPOSE

The creation of a vascular access is necessary in hemodialysis patients, including those with marginal vessels. Upper arm fistulae are attractive due to the ease of creation and of achieving high access flow rates. Cephalic arch stenosis (CAS) can lead to failure of upper arm fistulae and is increasingly identified. We hypothesized that CAS is promoted by high blood flow rates, brachiocephalic fistulae, and an angle of cephalic vein insertion approaching 90 degrees.

METHODS

All patients requiring a fistulogram between January 2004 and May 2006 had surveillance fluoroscopy of the central veins. Demographic, clinical and laboratory parameters were collected and the angle of the cephalic vein insertion measured by 3 blinded independent observers.

RESULTS

Fifty-eight patients had fistulograms and CAS was detected in 18 subjects. Significant differences between the CAS and non-CAS groups were brachiocephalic fistula site (p = 0.046), access flow (mL/min) (p = 0.012), and absence of diabetes (p = 0.03). Univariate predictors of CAS include access flow (per 100 mL/min) (p = 0.042), platelet count (p = 0.031) and calcium-phosphate product (p = 0.026). The relationship of brachiocephalic site and CAS was confounded by access flow [(per 100 mL/min)*brachiocephalic fistula site (p = 0.016)] and fistula age [brachiocephalic fistula site*fistula age (p = 0.017)]. In multivariate analysis, renovascular disease, calcium-phosphate product, platelet count and access flow (per 100 mL/min)*brachiocephalic fistula predicted CAS (p < 0.001, Negelkerke's R-Square = 0.55). The angle of insertion of the cephalic vein was not predictive for CAS.

CONCLUSIONS

CAS may be a long-term consequence of high blood flow rates. The interaction of access flow and brachiocephalic fistula supports the hypothesis that high flow through a brachiocephalic fistula promotes CAS. The multiple factors influencing cephalic arch remodeling require further research.

The Role of the Kidney in Blood Volume Regulation: The Kidney as a Regulator of the Hematocrit

The kidney plays a pivotal role in the regulation of blood volume by controlling the plasma volume and red blood cell (RBC) mass. Further, it is proposed that the kidney coordinates the relative volumes of these 2 blood components and in so doing regulates the hematocrit. This novel function as proposed is a functional concept whereby the kidney does not simply produce erythropoietin, but that the kidney regulates the hematocrit is termed the critmeter function. The kidney is unique in that it can indirectly report on blood volume as a tissue oxygen signal. It is proposed that the kidneys detect small changes in tissue oxygen tension for erythropoietin production at the critmeter, a functional unit of marginal oxygen tension within the kidneys. As the production of erythropoietin is modulated by angiotensin II, the renin-angiotensin system entrains the production of erythropoietin as part of the effector signals of the feedback loop of blood volume regulation. Collectively, the consideration of these points generates a paradigm shift in our understanding of blood volume regulation in that the role of the kidney may be expanded from simply "producing" erythropoietin to regulating the hematocrit. Further, this concept broadens the scope of the traditionally identified effector mechanisms of plasma volume regulation to include the modulation of erythropoietin production and hence RBC mass. The inclusion of both plasma volume and RBC mass as factors targeted by the effector signals recapitulates that whole blood volume is sensed and reported in the afferent signals. In summary, distinct sensing and effector mechanisms for regulating the volume of the two components of whole blood (plasma and red cell mass) are recognized. The coupling of the regulation of these 2 components of blood volume is highlighted.

Ordered-subset analysis of savant skills in autism for 15q11-q13

Autism is a complex disorder characterized by genetic and phenotypic heterogeneity. Analysis of phenotypically homogeneous subtypes has been used to both confirm and narrow potential autism linkage regions such as the chromosomal region 15q11-q13. Increased evidence for linkage in this region had been found in a subgroup of 21 autism families (total families = 94) stratified based on a savant skill factor (SSF) from the Autism Diagnostic Interview, Revised (ADI-R). We examined the savant phenotypic finding in our sample of 91 multiplex autism families. Using two-point parametric analysis in stratification with a cutoff point of a savant skill score of 0.16, our families failed to demonstrate linkage to 15q11-q13. In addition, ordered subset analysis (OSA) using SSF as a covariate also failed to show evidence for linkage. Our findings do not support savant skills as an informative phenotypic subset for linkage in our sample.