Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

Response-guided neoadjuvant sacituzumab govitecan for localized triple-negative breast cancer: results from the NeoSTAR trial

BACKGROUND

Sacituzumab govitecan (SG), a novel antibody-drug conjugate (ADC) targeting TROP2, is approved for pre-treated metastatic triple-negative breast cancer (mTNBC). We conducted an investigator-initiated clinical trial evaluating neoadjuvant (NA) SG (NCT04230109), and report primary results.

PATIENTS AND METHODS

Participants with early-stage TNBC received NA SG for four cycles. The primary objective was to assess pathological complete response (pCR) rate in breast and lymph nodes (ypT0/isN0) to SG. Secondary objectives included overall response rate (ORR), safety, event-free survival (EFS), and predictive biomarkers. A response-guided approach was utilized, and subsequent systemic therapy decisions were at the discretion of the treating physician.

RESULTS

From July 2020 to August 2021, 50 participants were enrolled (median age = 48.5 years; 13 clinical stage I disease, 26 stage II, 11 stage III). Forty-nine (98%) completed four cycles of SG. Overall, the pCR rate with SG alone was 30% [n = 15, 95% confidence interval (CI) 18% to 45%]. The ORR per RECIST V1.1 after SG alone was 64% (n = 32/50, 95% CI 77% to 98%). Higher Ki-67 and tumor-infiltrating lymphocytes (TILs) were predictive of pCR to SG (P = 0.007 for Ki-67 and 0.002 for TILs), while baseline TROP2 expression was not (P = 0.440). Common adverse events were nausea (82%), fatigue (76%), alopecia (76%), neutropenia (44%), and rash (48%). With a median follow-up time of 18.9 months (95% CI 16.3-21.9 months), the 2-year EFS for all participants was 95%. Among participants with a pCR with SG (n = 15), the 2-year EFS was 100%.

CONCLUSIONS

In the first NA trial with an ADC in localized TNBC, SG demonstrated single-agent efficacy and feasibility of response-guided escalation/de-escalation. Further research on optimal duration of SG as well as NA combination strategies, including immunotherapy, are needed.

Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes

SUMMARY

Sensory receptor gene families have undergone extensive expansion and loss across vertebrate evolution, leading to significant variation in receptor counts between species. However, due to their species-specific nature, conventional reference-based annotation tools often underestimate the true number of sensory receptors in a given species. While there has been an exponential increase in the taxonomic diversity of publicly available genome assemblies in recent years, only ∼30% of vertebrate species on the NCBI database are currently annotated. To overcome these limitations, we developed 'Sensommatic', an automated and accessible sensory receptor annotation pipeline. Sensommatic implements BLAST and AUGUSTUS to mine and predict sensory receptor genes from whole genome assemblies, adopting a one-to-many gene mapping approach. While designed for vertebrates, Sensommatic can be extended to run on non-vertebrate species by generating customized reference files, making it a scalable and generalizable tool.

AVAILABILITY AND IMPLEMENTATION

Source code and associated files are available at: https://github.com/GMHughes/Sensommatic.

Cementless versus cemented unicompartmental knee arthroplasty: a systematic review of comparative studies

There are still some controversies regarding the clinical use of cementless UKAs. The aim of this systematic review was to determine whether cementless medial UKA leads to similar outcomes compared to cemented medial UKA. This search was conducted in accordance with the Preferred Reporting Items for Systematic Reviews guidelines (PRISMA). The random effects model with 95% confidence interval (CI) was applied to the analysis. The I2 statistic was used to assess study heterogeneity. Six studies were eligible for inclusion (4784 UKAs, 4776 patients): 2947 cemented UKAs (61.6%) and 1837 cementless UKAs (38.4%). The overall mean follow-up was 4.9 years. The all-cause reoperation rate was 11.3% (80 of 706) at mean 5.7-year follow-up for cemented UKA and 6.9% (57 of 824) at mean 4.1-year follow-up for the cementless. The overall revision rate was 10.2% (303 of 2947) for the cemented and 5.8% (108 of 1837) for the cementless. Aseptic loosening was the most frequent reason of revision (2.3% cemented vs 0.5% cementless). The overall rate of radiolucent lines (RLL) was 28.3% (63 of 223) in the cemented cohort and 11.1% in the cementless (26 of 234). All the studies reported improved functional outcomes. Cementless UKA provides at least equivalent if not better results compared to cemented UKA. Despite the use of cemented UKA outnumber cementless fixation, available data shows that cementless UKA had a reduced midterm revision rate, while providing similar functional outcomes.

Evolutionary constraint and innovation across hundreds of placental mammals

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Evolutionary constraint and innovation across hundreds of placental mammals

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Integrating gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

The contribution of historical processes to contemporary extinction risk in placental mammals

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (N_e) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical N_e carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Mammalian evolution of human cis-regulatory elements and transcription factor binding sites

Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). We identified 439,461 cCREs and 2,024,062 TFBSs under evolutionary constraint. Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. About 20% of TFBSs are transposable element-derived and exhibit intricate patterns of gains and losses during primate evolution whereas sequence variants associated with complex traits are enriched in constrained TFBSs. Our annotations illuminate the regulatory functions of the human genome.

A genomic timescale for placental mammal evolution

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

The functional and evolutionary impacts of human-specific deletions in conserved elements

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Asthma medication adherence and exacerbations and lung function in children managed in Leicester primary care

Poor adherence to asthma preventer medication is associated with life-threatening asthma attacks. The quality and outcomes framework mandated primary care annual asthma review does not include adherence monitoring and the effect of poor adherence on lung function in paediatric primary care patients is unknown. The aim was to investigate the link between inhaled corticosteroid (ICS) adherence and spirometry, fraction of exhaled nitric oxide (FeNO) and asthma control in asthmatic school-age children in this cross-sectional observational study involving three Leicestershire general practices. Children 5-16 years on the practice's asthma registers, were invited for a routine annual asthma review between August 2018 and August 2019. Prescription and clinical data were extracted from practice databases. Spirometry, bronchodilator reversibility (BDR) and FeNO testing were performed as part of the review. 130 of 205 eligible children (63.4%) attended their review. Mean adherence to ICS was 36.2% (SEM 2.1%) and only 14.6% of children had good adherence (≥75% prescriptions issued). We found no differences in asthma exacerbations in the preceding 12 months between the adherence quartiles. 28.6% of children in the lowest and 5.6% in the highest adherence quartile had BDR ≥ 12% but this was not statistically significant (p = 0.55). A single high FeNO value did not predict adherence to ICS. Adherence to ICS in children with asthma in primary care is poor. The link between adherence to ICS and asthma exacerbations, spirometry and FeNO is complex but knowledge of adherence to ICS is critical in the management of children with asthma.

"What are you doing here?": Narratives of border crossings among diverse Afghans going to the UK at different times

Through the "hostile environment" migration policy, the UK government has expressed its commitment to do whatever possible to deter and expel unwanted migrants. Faced with the loss of power in the context of globalization, the Conservative administration, elected in 2010, presented itself as a guarantor of citizens' security. The political discourse of "taking back control" of the nation's borders has resulted in increasingly restrictive immigration and asylum policies. In this paper, we present narratives of Afghans who arrived in the UK at different times and through different routes. As well as those evacuated from Kabul airport in 2021, we also interviewed participants who traveled via insecure routes over land and sea often taking months, or even years, and involving expensive people smugglers. While the evacuation from Kabul was a very public and highly reported event, often with celebratory tones in the international media as Western governments sought to "rescue" Afghan allies, those Afghans who travel to the UK via illegal routes are often stigmatized; demonized in press and political discourses. Building on the emerging body of literature that uses "journey as a narrative device" and drawing upon our novel dataset, we analyze how diverse migrants tell their stories and present agency, within contexts of extreme hazards, to achieve their imagined future. Moreover, applying a spatio-temporal lens we advance understanding of the intersection of place and time in how Afghans traveling to the UK, including recent evacuees, are framed differently with resultant consequences for how border crossings are negotiated and narrated. In so doing, we complicate simplistic categories of deserving vs. undeserving, genuine vs. fraudulent, evacuees vs. irregularised migrants.

A novel programme of supportive two-exchange assisted continuous ambulatory peritoneal dialysis for frail patients with end-stage kidney disease

We have developed a supportive two-exchange assisted continuous ambulatory peritoneal dialysis (asCAPD) programme for the older frail person who cannot do autonomous PD and do not want or are considered to be too high risk for haemodialysis (HD). Evaluation of the programme was determined by data collected retrospectively from patient records. Primary outcome was comparison of symptoms at start of dialysis and 3 months following dialysis start. Secondary outcomes were survival and peritonitis rate. Over a 4-year period (2016-2020), 49 patients with mean age 79.6 years (range 47-90) enrolled in the programme with eGFR 7.7 ± 2.6 ml/min (mean ± SD) at dialysis start. Forty-one patients had been on asCAPD for >3 months. There was an improvement in all symptoms at 3 months compared to baseline: anorexia (46% to 15%), fatigue (46% to 15%), shortness of breath (27% to 2%) and oedema (51% to 32%). One-year survival was 55%. Peritonitis rate was 0.52 episodes per patient year. The novel supportive two-exchange asCAPD programme shows potential improvement of symptoms after 3 months and may provide an acceptable dialysis modality for the frail co-morbid person with established kidney failure. More detailed study and evaluation are needed.

265 A PHYSIOTHERAPY-LED TRANSITION TO HOME INTERVENTION FOR OLDER ADULTS FOLLOWING EMERGENCY DEPARTMENT DISCHARGE: A PILOT FEASIBILITY RANDOMISED-CONTROLLED TRIAL

Background

Older adults frequently attend the Emergency Department (ED) and experience high rates of adverse outcomes following ED presentation including functional decline, ED re-presentation and unplanned hospital admission. The development of effective interventions to prevent such outcomes is a key priority for research and service provision. A presentation to an ED can be viewed as an opportunity to assess those at risk of adverse outcomes and initiate a care plan in those deemed as ‘high risk'. Our aim was to evaluate the feasibility of a physiotherapy led integrated care intervention for older adults discharged from the ED (ED-PLUS).

Methods

Older adults presenting to the ED with undifferentiated medical complaints and discharged within 72 hours were computer randomised in a ratio of 1:1:1 to deliver usual care, Comprehensive Geriatric Assessment (CGA) in the ED, or ED-PLUS (Trial registration: NCT04983602). ED-PLUS is an evidence-based and stakeholder-informed intervention to bridge the care transition between the ED and community by initiating a CGA in the ED and implementing a six-week, multi-component, self-management programme in the patient’s own home. Feasibility (recruitment and retention rates) and acceptability of the programme were assessed quantitatively and qualitatively. Functional decline was examined post-intervention using the Barthel Index. All outcomes were assessed by a research nurse blinded to group allocation.

Results

29 participants were recruited, indicating 97% of our recruitment target. 90% of participants completed the ED-PLUS intervention. All participants expressed positive feedback about the intervention. The incidence of functional decline at 6 weeks was 10% in the ED-PLUS group versus 70-89% in the usual care and CGA-only groups.

Conclusion

High adherence and retention rates were observed among participants and preliminary findings indicate a lower incidence of functional decline in the ED-PLUS group. Recruitment challenges existed in the context of COVID-19. Data collection is ongoing for six-month outcomes.

Forecasting Multiple Groundwater Time Series with Local and Global Deep Learning Networks

Time series data from environmental monitoring stations are often analysed with machine learning methods on an individual basis, however recent advances in the machine learning field point to the advantages of incorporating multiple related time series from the same monitoring network within a 'global' model. This approach provides the opportunity for larger training data sets, allows information to be shared across the network, leading to greater generalisability, and can overcome issues encountered in the individual time series, such as small datasets or missing data. We present a case study involving the analysis of 165 time series from groundwater monitoring wells in the Namoi region of Australia. Analyses of the multiple time series using a variety of different aggregations are compared and contrasted (with single time series, subsets, and all of the time series together), using variations of the multilayer perceptron (MLP), self-organizing map (SOM), long short-term memory (LSTM), and a recently developed LSTM extension (DeepAR) that incorporates autoregressive terms and handles multiple time series. The benefits, in terms of prediction performance, of these various approaches are investigated, and challenges such as differing measurement frequencies and variations in temporal patterns between the time series are discussed. We conclude with some discussion regarding recommendations and opportunities associated with using networks of environmental data to help inform future resource-related decision making.

729 INCORPORATING PATIENTS’ VIEWS IN THE DESIGN OF AN EDUCATIONAL LEAFLET FOR FRAIL, OLDER PATIENTS WITH KIDNEY DISEASE

Introduction

There are an increasing number of older people live with advanced kidney disease. These individuals tend to have a higher number of co-morbidities, including frailty. This group experience multiple challenges in understanding and managing their co-existing conditions. This quality improvement project aimed to incorporate patient and carers views and experiences to improve their understanding and support self-management.

Method

Semi-structured interviews were conducted with older patients with advanced kidney disease and their carers. Interviews explored their views on ageing and frailty, how it affects them, coping strategies, resource awareness and opinions on structure and content for an educational leaflet for older people with kidney disease. The interviews were transcribed verbatim then coded into themes to inform key topics for the leaflet. These were used to generate reader-friendly questions and answers. The leaflet was reviewed and approved by the Clinical Committee and Patient Information Board in Kidney Care UK.

Results

10 individuals (8 patients and 2 carers) were interviewed. Patients were aged 62–88 years. Three were receiving haemodialysis, two peritoneal dialysis, two had a kidney transplant and three attended the advanced kidney care clinic. The five most common codes identified were ‘physical exercise’, ‘losing abilities’, ‘mobility’, ‘prevention and safety’ and ‘medical problems’. Themes identified were 1. Mood and memory, 2. Mobility and medical problems, 3. Self-help and supports, 4. Determination, 5. Impact on self and other. The leaflet title was chosen by patients and carers. Figure 1 shows the completed, published leaflet.

Conclusion

This quality improvement project used semi-structured interviews with older patients and carers affected by advanced kidney disease. The main issues they identified in relation to getting older with kidney disease were included in an educational leaflet. Partnership with Kidney Care UK has made the leaflet available across the UK. We hope it will directly address their everyday concerns.

"You still want to go lots of places": Exploring walking interviews in research with older migrants

BACKGROUND AND OBJECTIVES

Walking interviews have become prevalent in social sciences, however, their use in research with older people is limited. This article offers a reflexive account of our ethical and methodological choices and practices while conducting walking interviews with older migrants, and considers the potential of this method in researching migrants' aging in place.

RESEARCH DESIGN AND METHODS

The study had a longitudinal, multi-sited (London and Yorkshire), qualitatively driven multi-method research design. In 2018-19, in-depth interviews were conducted with 45 older migrants originally from the Caribbean, Ireland and Poland; followed by walking interviews with a sub-sample of 9 participants 6-12 months later. The majority of participants were over 80 years old.

RESULTS

Our study demonstrated that walking interviews are a promising method to explore in-depth a variety of relevant issues including older migrants' mobility, health and wellbeing; navigating places through everyday activities; interactions with local neighbourhoods over time, and the meanings associated with such experiences. Through direct exposure to the physicality of places, walking interviews can elicit rich and complex data that would be difficult to collect through other methods.

DISCUSSION AND IMPLICATIONS

Conducting walking interviews with older migrants has unique thematic potential. However, a range of ethical and practical challenges need to be considered, including a risk to revealing participants' identities and adopting an ethics-in-practice approach. The method has some limitations, especially with less mobile participants. Implications for researchers, policymakers and practitioners are suggested.

Two separate, large cohorts reveal potential modifiers of age-associated variation in visual reaction time performance

To identify potential factors influencing age-related cognitive decline and disease, we created MindCrowd. MindCrowd is a cross-sectional web-based assessment of simple visual (sv) reaction time (RT) and paired-associate learning (PAL). svRT and PAL results were combined with 22 survey questions. Analysis of svRT revealed education and stroke as potential modifiers of changes in processing speed and memory from younger to older ages (n_total = 75,666, n_women = 47,700, n_men = 27,966; ages 18-85 years old, mean (M)_Age = 46.54, standard deviation (SD)_Age = 18.40). To complement this work, we evaluated complex visual recognition reaction time (cvrRT) in the UK Biobank (n_total = 158,249 n_women = 89,333 n_men = 68,916; ages 40-70 years old, M_Age = 55.81, SD_Age = 7.72). Similarities between the UK Biobank and MindCrowd were assessed using a subset of MindCrowd (UKBb MindCrowd) selected to mirror the UK Biobank demographics (n_total = 39,795, n_women = 29,640, n_men = 10,155; ages 40-70 years old, M_Age = 56.59, SD_Age = 8.16). An identical linear model (LM) was used to assess both cohorts. Analyses revealed similarities between MindCrowd and the UK Biobank across most results. Divergent findings from the UK Biobank included (1) a first-degree family history of Alzheimer's disease (FHAD) was associated with longer cvrRT. (2) Men with the least education were associated with longer cvrRTs comparable to women across all educational attainment levels. Divergent findings from UKBb MindCrowd included more education being associated with shorter svRTs and a history of smoking with longer svRTs from younger to older ages.

A cohort study to investigate sex-specific differences in ANCA-associated glomerulonephritis outcomes

Data surrounding sex-specific differences in ANCA-associated vasculitis glomerulonephritis (ANCA-GN) outcomes is sparse. We hypothesised that the previously observed increased risk of end-stage kidney disease (ESKD) in males is driven by sex-specific variation in immunosuppression dosing. Patients were recruited to the Irish Rare Kidney Disease Registry or followed by the Royal Free Hospital vasculitis team (2012–2020). Inclusion criteria: prior diagnosis of ANCA-GN (biopsy proven pauci-immune glomerulonephritis) and positive serology for anti-MPO or -PR3 antibodies. Renal and patient survival, stratified by sex and Berden histological class, was analysed. The cumulative- and starting dose/kilogram of induction agents and prednisolone, respectively, was compared between sexes. 332 patients were included. Median follow-up was time 40.2 months (IQR 17.3–69.2). 73 (22%) reached ESKD and 47 (14.2%) died. Overall 1- and 5-year renal survival was 82.2% and 76.7% in males and 87.1% and 82.0% in females, respectively (p 0.13). The hazard ratio for ESKD in males versus females, after adjustment for age, ANCA serology, baseline creatinine and histological class was 1.07 (95% CI 0.59–1.93). There was no difference between sexes in the dose/kilogram of any induction agent. We did not observe a strong impact of sex on renal outcome in ANCA-GN. Treatment intensity does not vary by sex.

Smoking is associated with impaired verbal learning and memory performance in women more than men

Vascular contributions to cognitive impairment and dementia (VCID) include structural and functional blood vessel injuries linked to poor neurocognitive outcomes. Smoking might indirectly increase the likelihood of cognitive impairment by exacerbating vascular disease risks. Sex disparities in VCID have been reported, however, few studies have assessed the sex-specific relationships between smoking and memory performance and with contradictory results. We investigated the associations between sex, smoking, and cardiovascular disease with verbal learning and memory function. Using MindCrowd, an observational web-based cohort of ~ 70,000 people aged 18-85, we investigated whether sex modifies the relationship between smoking and cardiovascular disease with verbal memory performance. We found significant interactions in that smoking is associated with verbal learning performance more in women and cardiovascular disease more in men across a wide age range. These results suggest that smoking and cardiovascular disease may impact verbal learning and memory throughout adulthood differently for men and women.

Long Chain Omega-3 Fatty Acid Intervention in Ageing Adults at Risk of Dementia Following Repeated Head Trauma. Low-level Support or an Opportunity for an Unanswered Question?

Emerging evidence of brain injury on risk of neurodegenerative diseases such as Alzheimer's disease (AD) and chronic traumatic encephalopathy (CTE) have resulted in interest in therapeutic potential of omega-3 fatty acids (n-3FA). We conducted a systematic review of n-3FA therapeutic efficacy for ageing adults at risk of AD/CTE following a history of repeated head trauma. Databases for articles between 1980-June 2020 were examined for studies reporting on n-3 FAs in adults (≥ 45 years) with a history of repeated brain injury. Following an initial screen of 175 articles, 12 studies were considered but were eventually rejected, as they did not meet inclusion criteria. Our review could find no evidence to support, or disprove, effectiveness of n-3FA intervention in older adults with a history of head trauma. With animal studies showing neuro-restorative potential of n-3FA following brain injury, this review highlights the urgent need for human research in this area.

P1733MINERAL BONE DISEASE (MBD) IS THE POST KIDNEY TRANSPLANTATION POPULATION

Background and Aims

Patients with ESRD have a 4-fold higher risk of fracture compared to the general population. (1) Transplant bone disease is a combination of mineral bone disease sustained pre transplantation and damage incurred post transplantation, risk factors for which include immunosuppression and immobility in the early post transplantation period. Given the high morbidity, mortality and financial burden associated with fractures, the management and prevent of osteoporosis is fundamental. (2) We aimed to compare the management of MBD in our patient cohort to international nephrology and rheumatology guidelines. (1, 3)

Method

A retrospective review of all patients post kidney transplantation attending our department was carried out. Information pertaining to patient demographics, renal history, osteoporosis investigation and management was collected. The results were analysed with Microsoft Excel.

Results

154 patient records (92 male, 62 female) were reviewed. Mean age was 52 years (range 19-80). Mean eGFR was 54ml/min (range 9-90). 82% of patients were taking corticosteroids, the mean dose was 5mg. 9% were taking corticosteroids pre-transplantation. 11 patients (7%) had a history of parathyroidectomy. 19% of patients had a history of a fracture. 26% of patients had a DEXA scan performed which demonstrated 50% had osteopenia and 29% had osteoporosis. The mean fracture risk assessment tool (FRAX) score (risk of having an osteoporosis-related fracture in the next 10 years) for a major osteoporotic fracture was 10.2% (range 2.1-34%) and for a hip fracture was 3.1% (range 0.2-18). Based on these scores 19% and 26% of patients respectively met the criteria for treatment. Overall, 58% of patients were on treatment for either osteoporosis prevention or management or for mineral bone disease. 74% of patients with osteopenia were on treatment (32% calcium supplementation, 5% alfacalcidol, and 63% cholecalciferol). 82% of patients with osteoporosis were on treatment (45% cinacalcet, 36% cholecalciferol, 18% bisphosphonate and 9% denosumab). 27% of patients with osteoporosis were managed in keeping the guidelines.

Conclusion

Our cohort have significant risk factors for osteoporosis including maintenance corticosteroid treatment and previous fractures. There is a high prevalence of osteoporosis in our cohort compared to that reported internationally (4) and they had a high predicted rate of future fractures. Increased screening with targeted treatment is required to reduce the risk of fractures in our post renal transplant patients.

Supporting and maintaining the frail patient on long-term renal replacement therapy

The number of frail patients reaching end-stage kidney disease is increasing. They have a high level of comorbidity and symptom burden which need to be considered when making management plans. For those who choose renal replacement therapy, it is important to establish goals and ceilings of care and to provide holistic care focusing on optimising quality of life. Advance care planning is the process of documenting the patient's preferences for their treatment in the event they lose capacity to make decisions about their treatment.

Unsettling Events: Understanding Migrants’ Responses to Geopolitical Transformative Episodes through a Life-Course Lens

Migration under the European Union’s (EU) Freedom of Movement is constructed as temporary and circular, implying that migrants respond to changing circumstances by returning home or moving elsewhere. This construction underpins predictions of an exodus of EU migrants from the United Kingdom (UK) in the context of Brexit. While migration data indicate an increase in outflows since the vote to leave the EU, the scale does not constitute a “Brexodus.” Moreover, EU migrants’ applications for UK citizenship have been increasing. The data, though, are not sufficiently detailed to reveal who is responding to Brexit in which way. This article aims to offer a deeper understanding of how migrants experience and respond to changing geopolitical episodes such as Brexit. Introducing the term “unsettling events,” we analyze data collected longitudinally, in the context of three moments of significant change: 2004 EU enlargement, 2008–09 economic recession, and Brexit. Examining our data, mainly on Polish migrants, through a life-course lens, our findings highlight the need to account for the situatedness of migrant experiences as lived in particular times (both personal and historical), places, and relationships. In so doing, we reveal various factors informing migrants’ experiences of and reactions to unsettling events and the ways in which their experiences and reactions potentially impact migration projects.

Urinary and serum soluble CD25 complements urinary soluble CD163 to detect active renal anti-neutrophil cytoplasmic autoantibody-associated vasculitis: a cohort study

Background

Early detection of renal involvement in anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) is of major clinical importance to allow prompt initiation of treatment and limit renal damage. Urinary soluble cluster of differentiation 163 (usCD163) has recently been identified as a potential biomarker for active renal vasculitis. However, a significant number of patients with active renal vasculitis test negative using usCD163. We therefore studied whether soluble CD25 (sCD25), a T cell activation marker, could improve the detection of renal flares in AAV.

Methods

sCD25 and sCD163 levels in serum and urine were measured by enzyme-linked immunosorbent assay in 72 patients with active renal AAV, 20 with active extrarenal disease, 62 patients in remission and 18 healthy controls. Urinary and blood CD4+ T and CD4+ T effector memory (TEM) cell counts were measured in 22 patients with active renal vasculitis. Receiver operating characteristics (ROC) curves were generated and recursive partitioning was used to calculate whether usCD25 and serum soluble CD25 (ssCD25) add utility to usCD163.

Results

usCD25, ssCD25 and usCD163 levels were significantly higher during active renal disease and significantly decreased after induction of remission. A combination of usCD25, usCD163 and ssCD25 outperformed all individual markers (sensitivity 84.7%, specificity 95.1%). Patients positive for sCD25 but negative for usCD163 (n = 10) had significantly higher C-reactive protein levels and significantly lower serum creatinine and proteinuria levels compared with the usCD163-positive patients. usCD25 correlated positively with urinary CD4+ T and CD4+ TEM cell numbers, whereas ssCD25 correlated negatively with circulating CD4+ T and CD4+ TEM cells.

Conclusion

Measurement of usCD25 and ssCD25 complements usCD163 in the detection of active renal vasculitis.

Statistical strategies for the analysis of massive data sets

The advent of the big data age has changed the landscape for statisticians. Public and private organizations alike these days are interested in capturing and analyzing complex customer data in order to improve their service and drive efficiency gains. However, the large volume of data involved often means that standard statistical methods fail and new ways of thinking are needed. Although great gains can be obtained through the use of more advanced computing environments or through developing sophisticated new statistical algorithms that handle data in a more efficient way, there are also many simpler things that can be done to handle large data sets in an efficient and intuitive manner. These include the use of distributed analysis methodologies, clever subsampling, data coarsening, and clever data reductions that exploit concepts such as sufficiency. These kinds of strategies represent exciting opportunities for statisticians to remain front and center in the data science world.

Comparing predictive abilities of longitudinal child growth models

The Bill and Melinda Gates Foundation's Healthy Birth, Growth and Development knowledge integration project aims to improve the overall health and well-being of children across the world. The project aims to integrate information from multiple child growth studies to allow health professionals and policy makers to make informed decisions about interventions in lower and middle income countries. To achieve this goal, we must first understand the conditions that impact on the growth and development of children, and this requires sensible models for characterising different growth patterns. The contribution of this paper is to provide a quantitative comparison of the predictive abilities of various statistical growth modelling techniques based on a novel leave-one-out validation approach. The majority of existing studies have used raw growth data for modelling, but we show that fitting models to standardised data provide more accurate estimation and prediction. Our work is illustrated with an example from a study into child development in a middle income country in South America.

‘Drunken Tans’: Representations of Sex and Violence in the Anglo-Irish War (1919–21)

War is a highly gendered experience which is both informed by and informs constructions of masculinity and femininity. The dominant depiction of masculine heroes and feminine victims simplifies the complex intersections of militarism, nationalism and gendered roles and identities. Focusing on a case study of the Anglo-Irish War or War of Independence (1919–1921), this paper examines how violence against women, especially sexual violence, was written about and reported in ways which framed representations of Irish and British masculinity and Irish femininity.

In addition, by analysing a range of varied sources including newspapers, autobiographical accounts and recorded testimonies, this paper attempts to assess the extent to which violence against women formed a key aspect of military practice in the war. In conclusion, I engage with some of the difficulties faced by researchers today in exploring evidence of gendered violence in specific historical, cultural and militarized contexts.

Antimicrobial resistance and molecular epidemiology using whole-genome sequencing of Neisseria gonorrhoeae in Ireland, 2014-2016: focus on extended-spectrum cephalosporins and azithromycin

High-level resistance and treatment failures with ceftriaxone and azithromycin, the first-line agents for gonorrhoea treatment are reported and antimicrobial-resistant Neisseria gonorrhoeae is an urgent public health threat. Our aims were to determine antimicrobial resistance rates, resistance determinants and phylogeny of N. gonorrhoeae in Ireland, 2014-2016. Overall, 609 isolates from four University Hospitals were tested for susceptibility to extended-spectrum cephalosporins (ESCs) and azithromycin by the MIC Test Strips. Forty-three isolates were whole-genome sequenced based on elevated MICs. The resistance rate to ceftriaxone, cefixime, cefotaxime and azithromycin was 0, 1, 2.1 and 19%, respectively. Seven high-level azithromycin-resistant (HLAzi-R) isolates were identified, all susceptible to ceftriaxone. Mosaic penA alleles XXXIV, X and non-mosaic XIII, and G120K plus A121N/D/G (PorB1b), H105Y (MtrR) and A deletion (mtrR promoter) mutations, were associated with elevated ESC MICs. A2059G and C2611T mutations in 23S rRNA were associated with HLAzi-R and azithromycin MICs of 4-32 mg/L, respectively. The 43 whole-genome sequenced isolates belonged to 31 NG-MAST STs. All HLAzi-R isolates belonged to MLST ST1580 and some clonal clustering was observed; however, the isolates differed significantly from the published HLAzi-R isolates from the ongoing UK outbreak. There is good correlation between previously described genetic antimicrobial resistance determinants and phenotypic susceptibility categories for ESCs and azithromycin in N. gonorrhoeae. This work highlights the advantages and potential of whole-genome sequencing to be applied at scale in the surveillance of antibiotic resistant strains of N. gonorrhoeae, both locally and internationally.

Smooth individual level covariates adjustment in disease mapping

Spatial models for disease mapping should ideally account for covariates measured both at individual and area levels. The newly available "indiCAR" model fits the popular conditional autoregresssive (CAR) model by accommodating both individual and group level covariates while adjusting for spatial correlation in the disease rates. This algorithm has been shown to be effective but assumes log-linear associations between individual level covariates and outcome. In many studies, the relationship between individual level covariates and the outcome may be non-log-linear, and methods to track such nonlinearity between individual level covariate and outcome in spatial regression modeling are not well developed. In this paper, we propose a new algorithm, smooth-indiCAR, to fit an extension to the popular conditional autoregresssive model that can accommodate both linear and nonlinear individual level covariate effects while adjusting for group level covariates and spatial correlation in the disease rates. In this formulation, the effect of a continuous individual level covariate is accommodated via penalized splines. We describe a two-step estimation procedure to obtain reliable estimates of individual and group level covariate effects where both individual and group level covariate effects are estimated separately. This distributed computing framework enhances its application in the Big Data domain with a large number of individual/group level covariates. We evaluate the performance of smooth-indiCAR through simulation. Our results indicate that the smooth-indiCAR method provides reliable estimates of all regression and random effect parameters. We illustrate our proposed methodology with an analysis of data on neutropenia admissions in New South Wales (NSW), Australia.

Non-ignorable missingness in logistic regression

Nonresponses and missing data are common in observational studies. Ignoring or inadequately handling missing data may lead to biased parameter estimation, incorrect standard errors and, as a consequence, incorrect statistical inference and conclusions. We present a strategy for modelling non-ignorable missingness where the probability of nonresponse depends on the outcome. Using a simple case of logistic regression, we quantify the bias in regression estimates and show the observed likelihood is non-identifiable under non-ignorable missing data mechanism. We then adopt a selection model factorisation of the joint distribution as the basis for a sensitivity analysis to study changes in estimated parameters and the robustness of study conclusions against different assumptions. A Bayesian framework for model estimation is used as it provides a flexible approach for incorporating different missing data assumptions and conducting sensitivity analysis. Using simulated data, we explore the performance of the Bayesian selection model in correcting for bias in a logistic regression. We then implement our strategy using survey data from the 45 and Up Study to investigate factors associated with worsening health from the baseline to follow-up survey. Our findings have practical implications for the use of the 45 and Up Study data to answer important research questions relating to health and quality-of-life. Copyright © 2017 John Wiley & Sons, Ltd.

Antimicrobial-resistant Faecal Organisms in Algae Products Marketed as Health Supplements

Dietary supplements are increasingly popular in Irish society. One of these is blue-green algae which is used with a variety health benefits in mind. A batch of Chlorella powder was found to be contaminated with Salmonella species in Ireland in 2015. This prompted additional testing of a total of 8 samples of three different products (Chlorella, Spirulina and Super Greens), for other faecal flora and antimicrobial resistance in any bacteria isolated. All 8 samples cultured enteric flora such as Enterococci, Enterobacteriaceae and Clostridium species. Antimicrobial susceptibility testing revealed one isolate with extended-spectrum ?-lactamase (ESBL) activity and one with carbapenemase activity. Clinicians caring for vulnerable patients should be aware of the potential risk of exposure to antimicrobial resistant bacteria associated with these products.