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Physical activity has positive health implications for individuals living with neurodegenerative diseases. The success of physical activity programs, particularly in culturally and linguistically diverse populations, is typically dependent on their alignment with the culture, lifestyle and environmental context of those involved. Aboriginal families living in remote communities in the Top End of Australia invited researchers to collaborate with them to co-design a physical activity and lifestyle program to keep individuals with Machado-Joseph disease (MJD) walking and moving around. The knowledge of Aboriginal families living with MJD, combined with findings from worldwide MJD research, formed the foundation for the co-design. An experience-based co-design (EBCD) approach, drawing from Indigenous and Participatory methodologies, was used. An expert panel of individuals with lived experience of MJD participated in a series of co-design phases. Prearranged and spontaneous co-design meetings were led by local community researchers within each phase. Data was collected using a culturally responsive ethnographic approach and analysed thematically. Sixteen panel members worked to develop the ‘Staying Strong Toolbox’ to cater for individuals with MJD who are ‘walking strong’; or ‘wobbly’; or ‘in a wheelchair’. Based on the ‘Staying Strong Framework’, the Toolbox was developed as a spiral bound A3 book designed to guide the user to select from a range of activities to keep them walking and moving around and to identify those activities most important to them to work on. The ‘Staying Strong Toolbox’ is a community driven, evidence based resource for a physical activity and lifestyle program for Aboriginal families with MJD. The Toolbox provides a guide for health professionals and support workers to deliver person-centred support to Aboriginal families with MJD, and that can be modified for use by other families with MJD or people with other forms of ataxia around the world.

Machado Joseph Disease (MJD) (spinocerebellar ataxia 3) is a hereditary neurodegenerative disease causing progressive ataxia and loss of mobility. It is the most common spinocerebellar ataxia worldwide. Among Aboriginal families of Groote Eylandt and related communities across Australia's Top End, MJD is estimated to be more prevalent than anywhere else in the world. This study explored lived experiences of individuals and families with MJD to determine what is important and what works best to keep walking and moving around. A collaborative qualitative exploratory study, drawing from constructivist grounded theory methods, was undertaken for data collection and analysis. Semi-structured in-depth interviews were conducted with individuals with MJD (n = 8) and their family members (n = 4) from the Groote Eylandt Archipelago where ~1500 Aboriginal people (Warnumamalya) live. Interviews were led by Warnumamalya community research partners in participants' preferred language(s). Participants described their experience of living with MJD, from 'knowing about MJD', 'protecting yourself from MJD' and 'adjusting to life with MJD'. While the specific importance of walking and moving around differed widely between participants, all perceived that walking and moving around enabled them to do what mattered most to them in life. 'Staying strong on the inside and outside' (physically, mentally, emotionally, spiritually) was perceived to work best to keep walking and moving around as long as possible. A framework that included personal and environmental strategies for staying strong emerged: 'Exercising your body', 'having something important to do', 'keeping yourself happy', 'searching for good medicine', 'families helping each other' and 'going country'. This study, the first to explore lived experiences of MJD in Australia, highlights the importance of maintaining mobility as long as possible. Strategies perceived to work best address physical and psychosocial needs in an integrated manner. Services supporting families with MJD need flexibility to provide individualised, responsive and holistic care.

ObjectivesMachado-Joseph disease (MJD) is the most common spinocerebellar ataxia worldwide. Prevalence is highest in affected remote Aboriginal communities of the Top End of Australia. Aboriginal families with MJD from Groote Eylandt believe ‘staying strong on the inside and outside’ works best to keep them walking and moving around, in accordance with six key domains that form the ‘Staying Strong’ Framework. The aim of this current study was to review the literature to: (1) map the range of interventions/strategies that have been explored to promote walking and moving around (functional mobility) for individuals with MJD and; (2) align these interventions to the ‘Staying Strong’ Framework described by Aboriginal families with MJD.DesignScoping review.Data sourcesSearches were conducted in July 2018 in MEDLINE, EMBASE, CINAHL, PsychINFO and Cochrane Databases.Eligibility criteria for selecting studiesPeer-reviewed studies that (1) included adolescents/adults with MJD, (2) explored the effects of any intervention on mobility and (3) included a measure of mobility, function and/or ataxia were included in the review.ResultsThirty studies were included. Few studies involved participants with MJD alone (12/30). Most studies explored interventions that aligned with two ‘Staying Strong’ Framework domains, ‘exercising your body’ (n=13) and ‘searching for good medicine’ (n=17). Few studies aligned with the domains having ‘something important to do’ (n=2) or ‘keeping yourself happy’ (n=2). No studies aligned with the domains ‘going country’ or ‘families helping each other’.ConclusionsEvidence for interventions to promote mobility that align with the ‘Staying Strong’ Framework were focused on staying strong on the outside (physically) with little reflection on staying strong on the inside (emotionally, mentally and spiritually). Findings suggest future research is required to investigate the benefits of lifestyle activity programmes that address both physical and psychosocial well-being for families with MJD.

Antarctic supraglacial lakes (SGLs) have been linked to ice shelf collapse and the subsequent acceleration of inland ice flow, but observations of SGLs remain relatively scarce and their interannual variability is largely unknown. This makes it difficult to assess whether some ice shelves are close to thresholds of stability under climate warming. Here, we present the first observations of SGLs across the entire East Antarctic Ice Sheet over multiple melt seasons (2014–2020). Interannual variability in SGL volume is >200% on some ice shelves, but patterns are highly asynchronous. More extensive, deeper SGLs correlate with higher summer (December-January-February) air temperatures, but comparisons with modelled melt and runoff are complex. However, we find that modelled January melt and the ratio of November firn air content to summer melt are important predictors of SGL volume on some potentially vulnerable ice shelves, suggesting large increases in SGLs should be expected under future atmospheric warming. Antarctic supraglacial lakes (SGLs) have been linked to ice-shelf collapse and the subsequent acceleration of inland ice flow, but observations of SGLs remain relatively scarce and their interannual variability is largely unknown. This new study shows that lake area and volume vary substantially from year-to-year around the East Antarctic Ice Sheet and between ice shelves.

AbstractObjectivesTo provide accurate risk estimates of serious adverse events after elective shoulder replacement surgery for arthritis, including age and sex specific estimates of the lifetime risk of revision surgery.DesignPopulation based cohort study.SettingHospital episode statistics for NHS England, including civil registration mortality data.Participants58 054 elective shoulder replacements in 51 895 adults (aged ≥50 years) between April 1998 and April 2017.Main outcome measuresThe lifetime risk of revision surgery, calculated using an actuarial life table approach and the cumulative probability method. Rates of serious adverse events at 30 and 90 days post-surgery: pulmonary embolism, myocardial infarction, lower respiratory tract infection, acute kidney injury, urinary tract infection, cerebrovascular events, and all cause death. Secondary outcome measures were the number of surgeries performed each year and Kaplan-Meier estimates of revision risk at 3, 5, 10, and 15 years.ResultsThe number of shoulder replacements performed each year increased 5.6-fold between 1998 and 2017. Lifetime risks of revision surgery ranged from 1 in 37 (2.7%, 95% confidence interval 2.6% to 2.8%) in women aged 85 years and older to 1 in 4 (23.6%, 23.2% to 24.0%) in men aged 55-59 years. The risks of revision were highest during the first five years after surgery. The risk of any serious adverse event at 30 days post-surgery was 1 in 28 (3.5%, 3.4% to 3.7%), and at 90 days post-surgery was 1 in 22 (4.6%, 4.4% to 4.8%). At 30 days, the relative risk of pulmonary embolism compared with baseline population risk was 61 (95% confidence interval 50 to 73) for women aged 50-64. Serious adverse events were associated with increasing age, comorbidity, and male sex. 1 in 5 (21.2%, 17.9% to 25.1%) men aged 85 years and older experienced at least one serious adverse event within 90 days.ConclusionsYounger patients, particularly men, need to be aware of a higher likelihood of early failure of shoulder replacement and the need for further and more complex revision replacement surgery. All patients should be counselled about the risks of serious adverse events. These risks are higher than previously considered, and for some could outweigh any potential benefits. Our findings caution against unchecked expansion of shoulder replacement surgery in both younger and older patients. The more accurate age and sex specific estimates of risk from this study are long overdue and should improve shared decision making between patients and clinicians.Study registrationClinicalTrials.gov NCT03573765.

Supraglacial lakes (SGLs) enhance surface melting and can flex and fracture ice shelves when they grow and subsequently drain, potentially leading to ice shelf disintegration. However, the seasonal evolution of SGLs and their influence on ice shelf stability in East Antarctica remains poorly understood, despite some potentially vulnerable ice shelves having high densities of SGLs. Using optical satellite imagery, air temperature data from climate reanalysis products and surface melt predicted by a regional climate model, we present the first long-term record (2000–2020) of seasonal SGL evolution on Shackleton Ice Shelf, which is Antarctica's northernmost remaining ice shelf and buttresses Denman Glacier, a major outlet of the East Antarctic Ice Sheet. In a typical melt season, we find hundreds of SGLs with a mean area of 0.02 km2, a mean depth of 0.96 m and a mean total meltwater volume of 7.45×106 m3. At their most extensive, SGLs cover a cumulative area of 50.7 km2 and are clustered near to the grounding line, where densities approach 0.27 km2 km−2. Here, SGL development is linked to an albedo-lowering feedback associated with katabatic winds, together with the presence of blue ice and exposed rock. Although below-average seasonal (December–January–February, DJF) temperatures are associated with below-average peaks in total SGL area and volume, warmer seasonal temperatures do not necessarily result in higher SGL areas and volumes. Rather, peaks in total SGL area and volume show a much closer correspondence with short-lived high-magnitude snowmelt events. We therefore suggest seasonal lake evolution on this ice shelf is instead more sensitive to snowmelt intensity associated with katabatic-wind-driven melting. Our analysis provides important constraints on the boundary conditions of supraglacial hydrology models and numerical simulations of ice shelf stability.

Identifying immunodominant T cell epitopes remains a significant challenge in the context of infectious disease, autoimmunity, and immuno-oncology. To address the challenge of antigen discovery, we developed a quantitative proteomic approach that enabled unbiased identification of major histocompatibility complex class II (MHCII)–associated peptide epitopes and biochemical features of antigenicity. On the basis of these data, we trained a deep neural network model for genome-scale predictions of immunodominant MHCII-restricted epitopes. We named this model bacteria originated T cell antigen (BOTA) predictor. In validation studies, BOTA accurately predicted novel CD4 T cell epitopes derived from the model pathogen Listeria monocytogenes and the commensal microorganism Muribaculum intestinale . To conclusively define immunodominant T cell epitopes predicted by BOTA, we developed a high-throughput approach to screen DNA-encoded peptide–MHCII libraries for functional recognition by T cell receptors identified from single-cell RNA sequencing. Collectively, these studies provide a framework for defining the immunodominance landscape across a broad range of immune pathologies. A quantitative proteomic approach overcomes a major bottleneck in translational immunology, namely the identification of autologous and bacterial immunodominant major histocompatibility complex class II epitopes based on genomic sequences.

The host protein viperin is an interferon stimulated gene (ISG) that is up-regulated during a number of viral infections. In this study we have shown that dengue virus type-2 (DENV-2) infection significantly induced viperin, co-incident with production of viral RNA and via a mechanism requiring retinoic acid-inducible gene I (RIG-I). Viperin did not inhibit DENV-2 entry but DENV-2 RNA and infectious virus release was inhibited in viperin expressing cells. Conversely, DENV-2 replicated to higher tires earlier in viperin shRNA expressing cells. The anti-DENV effect of viperin was mediated by residues within the C-terminal 17 amino acids of viperin and did not require the N-terminal residues, including the helix domain, leucine zipper and S-adenosylmethionine (SAM) motifs known to be involved in viperin intracellular membrane association. Viperin showed co-localisation with lipid droplet markers, and was co-localised and interacted with DENV-2 capsid (CA), NS3 and viral RNA. The ability of viperin to interact with DENV-2 NS3 was associated with its anti-viral activity, while co-localisation of viperin with lipid droplets was not. Thus, DENV-2 infection induces viperin which has anti-viral properties residing in the C-terminal region of the protein that act to restrict early DENV-2 RNA production/accumulation, potentially via interaction of viperin with DENV-2 NS3 and replication complexes. These anti-DENV-2 actions of viperin show both contrasts and similarities with other described anti-viral mechanisms of viperin action and highlight the diverse nature of this unique anti-viral host protein.

Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs) and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter (226 gene panel) and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. We performed correlation analyses of gene expression between samples and across platforms. We then specifically assessed whole transcriptome expression of lincRNA and discovery of eSNVs and fusion transcripts in the FFPE RNA-Seq data. For gene expression in the manually degraded samples, we observed Pearson correlations of >0.94 and >0.80 with NanoString and ScriptSeq protocols, respectively. Gene expression data for matched fresh-frozen and FFPE samples yielded mean Pearson correlations of 0.874 and 0.783 for NanoString (226 genes) and ScriptSeq whole transcriptome protocols respectively, p<2x10(-16). Specifically for lincRNAs, we observed superb Pearson correlation (0.988) between matched fresh-frozen and FFPE pairs. FFPE samples across NanoString and RNA-Seq platforms gave a mean Pearson correlation of 0.838. In FFPE libraries, we detected 53.4% of high confidence SNVs and 24% of high confidence fusion transcripts. Sensitivity of fusion transcript detection was not overcome by an increase in depth of sequencing up to 3-fold (increase from ~56 to ~159 million reads). Both NanoString and ScriptSeq RNA-Seq technologies yield reliable gene expression data for degraded and FFPE material. The high degree of correlation between NanoString and RNA-Seq platforms suggests discovery based whole transcriptome studies from FFPE material will produce reliable expression data. The RiboZeroGold ScriptSeq protocol performed particularly well for lincRNA expression from FFPE libraries, but detection of eSNV and fusion transcripts was less sensitive.

Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines. Prediction of HLA class I epitopes is improved in accuracy and breath with peptidomes from 95 mono-allelic cell lines.