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Aims/hypothesis Among white European children developing type 1 diabetes, the otherwise common HLA haplotype DR15-DQ6 is rare, and highly protective. Adult-onset type 1 diabetes is now known to represent more overall cases than childhood onset, but it is not known whether DR15-DQ6 is protective in older-adult-onset type 1 diabetes. We sought to quantify DR15-DQ6 protection against type 1 diabetes as age of onset increased. Methods In two independent cohorts we assessed the proportion of type 1 diabetes cases presenting through the first 50 years of life with DR15-DQ6, compared with population controls. In the After Diabetes Diagnosis Research Support System-2 (ADDRESS-2) cohort (n = 1458) clinician-diagnosed type 1 diabetes was confirmed by positivity for one or more islet-specific autoantibodies. In UK Biobank (n = 2502), we estimated type 1 diabetes incidence rates relative to baseline HLA risk for each HLA group using Poisson regression. Analyses were restricted to white Europeans and were performed in three groups according to age at type 1 diabetes onset: 0–18 years, 19–30 years and 31–50 years. Results DR15-DQ6 was protective against type 1 diabetes through to age 50 years (OR p Conclusions/interpretation HLA DR15-DQ6 confers dominant protection from type 1 diabetes across the first five decades of life. Graphical abstract

The complexity of each Coupled Model Intercomparison Project grows with every new generation. The Phase 5 effort saw a dramatic increase in the number of experiments that were performed and the number of variables that were requested compared to its previous generation, Phase 3. The large increase in data volume stressed the resources of several centers including at the National Center for Atmospheric Research. During Phase 5, we missed several deadlines and we struggled to get the data out to the community for analysis. In preparation for the current generation, Phase 6, we examined the weaknesses in our workflow and addressed the performance issues with new software tools. Through this investment, we were able to publish approximately 565 TB of compressed data to the community, with another 30 TB yet to be published. When compared to the volumes we produced in the previous generation, 165 TB of uncompressed data, we were able to provide 6 times the amount of data and we accomplish this within one-third of the time. This provided us with an approximate 18 times faster speedup. While this paper discusses the improvements we have made to our own workflow for the Coupled Model Intercomparison Project Phase 6 (CMIP6), we hope to encourage other centers to evaluate and invest in their own workflows in order to be successful in these types of modeling campaigns.

OBJECTIVE To describe the relationship between type 2 diabetes and all-cause mortality among adults with coronavirus disease 2019 (COVID-19) in the critical care setting. RESEARCH DESIGN AND METHODS This was a nationwide retrospective cohort study in people admitted to hospital in England with COVID-19 requiring admission to a high dependency unit (HDU) or intensive care unit (ICU) between 1 March 2020 and 27 July 2020. Cox proportional hazards models were used to estimate 30-day in-hospital all-cause mortality associated with type 2 diabetes, with adjustment for age, sex, ethnicity, obesity, and other major comorbidities (chronic respiratory disease, asthma, chronic heart disease, hypertension, immunosuppression, chronic neurological disease, chronic renal disease, and chronic liver disease). RESULTS A total of 19,256 COVID-19–related HDU and ICU admissions were included in the primary analysis, including 13,809 HDU (mean age 70 years) and 5,447 ICU (mean age 58 years) admissions. Of those admitted, 3,524 (18.3%) had type 2 diabetes and 5,077 (26.4%) died during the study period. Patients with type 2 diabetes were at increased risk of death (adjusted hazard ratio [aHR] 1.23 [95% CI 1.14, 1.32]), and this result was consistent in HDU and ICU subsets. The relative mortality risk associated with type 2 diabetes decreased with higher age (age 18–49 years aHR 1.50 [95% CI 1.05, 2.15], age 50–64 years 1.29 [1.10, 1.51], and age ≥65 years 1.18 [1.09, 1.29]; P value for age–type 2 diabetes interaction = 0.002). CONCLUSIONS Type 2 diabetes may be an independent prognostic factor for survival in people with severe COVID-19 requiring critical care treatment, and in this setting the risk increase associated with type 2 diabetes is greatest in younger people.

Despite the known heterogeneity of type 2 diabetes and variable response to glucose lowering medications, current evidence on optimal treatment is predominantly based on average effects in clinical trials rather than individual-level characteristics. A precision medicine approach based on treatment response would aim to improve on this by identifying predictors of differential drug response for people based on their characteristics and then using this information to select optimal treatment. Recent research has demonstrated robust and clinically relevant differential drug response with all noninsulin treatments after metformin (sulfonylureas, thiazolidinediones, dipeptidyl peptidase 4 [DPP-4] inhibitors, glucagon-like peptide 1 [GLP-1] receptor agonists, and sodium–glucose cotransporter 2 [SGLT2] inhibitors) using routinely available clinical features. This Perspective reviews this current evidence and discusses how differences in drug response could inform selection of optimal type 2 diabetes treatment in the near future. It presents a novel framework for developing and testing precision medicine–based strategies to optimize treatment, harnessing existing routine clinical and trial data sources. This framework was recently applied to demonstrate that “subtype” approaches, in which people are classified into subgroups based on features reflecting underlying pathophysiology, are likely to have less clinical utility compared with approaches that combine the same features as continuous measures in probabilistic “individualized prediction” models.

ObjectiveTo establish whether clinical patient characteristics routinely measured in primary care can identify people with differing short-term benefits and risks for SGLT2-inhibitor and DPP4-inhibitor therapies, and to derive and validate a treatment selection algorithm to identify the likely optimal therapy for individual patients.DesignProspective cohort study.SettingRoutine clinical data from United Kingdom general practice (Clinical Practice Research Datalink [CPRD]), and individual-level clinical trial data from 14 multi-country trials of SGLT2-inhibitor and DPP4-inhibitor therapies.Participants26,877 new users of SGLT2-inhibitor and DPP4-inhibitor therapy in CPRD over 2013-2019, and 10,414 participants randomised to SGLT2-inhibitor or DPP4-inhibitor therapy in 14 clinical trials, including 3 head-to-head trials of the two therapies (n=2,499).Main outcome measuresThe primary outcome was achieved HbA1c 6 months after initiating therapy. Clinical features associated with differential HbA1c outcomes with SGLT2-inhibitor and DPP4-inhibitor therapies were identified in routine clinical data, with associations then tested in trial data. A multivariable treatment selection algorithm to predict differential HbA1c outcomes was developed in a CPRD derivation cohort (n=14,069), with validation in a CPRD validation cohort (n=9,376) and the head-to-head trials. In CPRD, we further explored the relationship between model predictions and secondary outcomes of weight loss and treatment discontinuation.ResultsThe final treatment selection algorithm included HbA1c, eGFR, ALT, age, and BMI, which were identified as predictors of differential HbA1c outcomes with SGLT2-inhibitor and DPP4-inhibitor therapies using both routine and trial data. In validation cohorts, patient strata predicted to have a ≥5 mmol/mol HbA1c reduction with SGLT2-inhibitor therapy compared with DPP4-inhibitor therapy (38.8% of CPRD validation sample) had an observed greater reduction of 8.8 mmol/mol [95%CI 7.8-9.8] in the CPRD validation sample, a 5.8 mmol/mol (95%CI 3.9-7.7) greater reduction in the Cantata D/D2 trials, and a 6.6 mmol/mol [95%CI 2.2-11.0]) greater reduction in the BI1245.20 trial. In CPRD, there was a greater weight reduction with SGLT2-inhibitor therapy regardless of predicted glycaemic benefit. Strata predicted to have greater reduction in HbA1c on SGLT2-inhibitor therapy had a similar risk of discontinuation as on DPP4-inhibitor therapy. In contrast, strata predicted to have greater reduction in HbA1c with DPP4-inhibitor therapy were half as likely to discontinue DPP4-inhibitor therapy than SGLT2-inhibitor therapy.ConclusionsRoutinely measured clinical features are robustly associated with differential glycaemic responses to SGLT2-inhibitor and DPP4-inhibitor therapies. Combining features into a treatment selection algorithm can inform clinical decisions concerning optimal type 2 diabetes treatment choices.Key messagesWhat is already known on this subjectDespite there being multiple glucose-lowering treatment options available for people with type 2 diabetes, current guidelines do not provide clear advice on selecting the optimal treatment for most patients.It is unknown whether routinely measured clinical features modify the risks and benefits of two common treatment options, DPP4-inhibitor or SGLT2-inhibitor therapy, and which could be used to target these treatments to those patients most likely to benefit.What this study addsUsing data from 10,414 participants in 14 randomised trials, and 26,877 patients in UK primary care, we show several routinely available clinical features, notably glycated haemoglobin (HbA1c) and kidney function, are robustly associated with differential HbA1c responses to initiating SGLT2-inhibitor and DPP4-inhibitor therapies.Combining clinical features into a multivariable treatment selection model identifies validated patient strata with 1) a >5 mmol/mol HbA1c benefit for SGLT2-i therapy compared with DPP4-inhibitor therapy ; 2) a 50% reduced risk of early treatment discontinuation with DPP4-inhibitor therapy compared with SGLT2-inhibitor therapy.Our findings demonstrate a precision medicine approach based on routine clinical features can inform clinical decisions concerning optimal type 2 diabetes treatment choices.

Among white European children developing type 1 diabetes, the otherwise common HLA haplotype DR15-DQ6 is rare, and highly protective. Adult-onset type 1 diabetes is now known to represent more overall cases than childhood onset, but it is not known whether DR15-DQ6 is protective in older-adult-onset type 1 diabetes. We sought to quantify DR15-DQ6 protection against type 1 diabetes as age of onset increased.In two independent cohorts we assessed the proportion of type 1 diabetes cases presenting through the first 50 years of life with DR15-DQ6, compared with population controls. In the After Diabetes Diagnosis Research Support System-2 (ADDRESS-2) cohort (n = 1458) clinician-diagnosed type 1 diabetes was confirmed by positivity for one or more islet-specific autoantibodies. In UK Biobank (n = 2502), we estimated type 1 diabetes incidence rates relative to baseline HLA risk for each HLA group using Poisson regression. Analyses were restricted to white Europeans and were performed in three groups according to age at type 1 diabetes onset: 0-18 years, 19-30 years and 31-50 years.DR15-DQ6 was protective against type 1 diabetes through to age 50 years (OR 1 for each age group, all p 0.001). The following ORs for type 1 diabetes, relative to a neutral HLA genotype, were observed in ADDRESS-2: age 5-18 years OR 0.16 (95% CI 0.08, 0.31); age 19-30 years OR 0.10 (0.04, 0.23); and age 31-50 years OR 0.37 (0.21, 0.68). DR15-DQ6 also remained highly protective at all ages in UK Biobank. Without DR15-DQ6, the presence of major type 1 diabetes high-risk haplotype (either DR3-DQ2 or DR4-DQ8) was associated with increased risk of type 1 diabetes.HLA DR15-DQ6 confers dominant protection from type 1 diabetes across the first five decades of life.

Background Type 2 diabetes (T2D) is common and increasing in prevalence. It is possible to prevent or delay T2D using lifestyle intervention programmes. Entry to these programmes is usually determined by a measure of glycaemia in the ‘intermediate’ range. This paper investigated the relationship between HbA1c and future diabetes risk and determined the impact of varying thresholds to identify those at high risk of developing T2D. Methods We studied 4227 participants without diabetes aged ≥ 40 years recruited to the Exeter 10,000 population cohort in South West England. HbA1c was measured at study recruitment with repeat HbA1c available as part of usual care. Absolute risk of developing diabetes within 5 years, defined by HbA1c ≥ 48 mmol/mol (6.5%), according to baseline HbA1c, was assessed by a flexible parametric survival model. Results The overall absolute 5-year risk (95% CI) of developing T2D in the cohort was 4.2% (3.6, 4.8%). This rose to 7.1% (6.1, 8.2%) in the 56% (n = 2358/4224) of participants classified ‘high-risk’ with HbA1c ≥ 39 mmol/mol (5.7%; ADA criteria). Under IEC criteria, HbA1c ≥ 42 mmol/mol (6.0%), 22% (n = 929/4277) of the cohort was classified high-risk with 5-year risk 14.9% (12.6, 17.2%). Those with the highest HbA1c values (44–47 mmol/mol [6.2–6.4%]) had much higher 5-year risk, 26.4% (22.0, 30.5%) compared with 2.1% (1.5, 2.6%) for 39–41 mmol/mol (5.7–5.9%) and 7.0% (5.4, 8.6%) for 42–43 mmol/mol (6.0–6.1%). Changing the entry criterion to prevention programmes from 39 to 42 mmol/mol (5.7–6.0%) reduced the proportion classified high-risk by 61%, and increased the positive predictive value (PPV) from 5.8 to 12.4% with negligible impact on the negative predictive value (NPV), 99.6% to 99.1%. Increasing the threshold further, to 44 mmol/mol (6.2%), reduced those classified high-risk by 59%, and markedly increased the PPV from 12.4 to 23.2% and had little impact on the NPV (99.1% to 98.5%). Conclusions A large proportion of people are identified as high-risk using current thresholds. Increasing the risk threshold markedly reduces the number of people that would be classified as high-risk and entered into prevention programmes, although this must be balanced against cases missed. Raising the entry threshold would allow limited intervention opportunities to be focused on those most likely to develop T2D.

Objectives Electronic health records (EHR) provide a valuable resource for assessing drug side-effects, but treatments are not randomly allocated in routine care creating the potential for bias. We conduct a case study using the Prior Event Rate Ratio (PERR) Pairwise method to reduce unmeasured confounding bias in side-effect estimates for two second-line therapies for type 2 diabetes, thiazolidinediones, and sulfonylureas. Study Design and Settings Primary care data were extracted from the Clinical Practice Research Datalink (n = 41,871). We utilized outcomes from the period when patients took first-line metformin to adjust for unmeasured confounding. Estimates for known side-effects and a negative control outcome were compared with the A Diabetes Outcome Progression Trial (ADOPT) trial (n = 2,545). Results When on metformin, patients later prescribed thiazolidinediones had greater risks of edema, HR 95% CI 1.38 (1.13, 1.68) and gastrointestinal side-effects (GI) 1.47 (1.28, 1.68), suggesting the presence of unmeasured confounding. Conventional Cox regression overestimated the risk of edema on thiazolidinediones and identified a false association with GI. The PERR Pairwise estimates were consistent with ADOPT: 1.43 (1.10, 1.83) vs. 1.39 (1.04, 1.86), respectively, for edema, and 0.91 (0.79, 1.05) vs. 0.94 (0.80, 1.10) for GI. Conclusion The PERR Pairwise approach offers potential for enhancing postmarketing surveillance of side-effects from EHRs but requires careful consideration of assumptions.

OBJECTIVES: To determine whether the previously described trend of improving mortality in people with coronavirus disease 2019 in critical care during the first wave was maintained, plateaued, or reversed during the second wave in United Kingdom, when B117 became the dominant strain. DESIGN: National retrospective cohort study. SETTING: All English hospital trusts (i.e., groups of hospitals functioning as single operational units), reporting critical care admissions (high dependency unit and ICU) to the Coronavirus Disease 2019 Hospitalization in England Surveillance System. PATIENTS: A total of 49,862 (34,336 high dependency unit and 15,526 ICU) patients admitted between March 1, 2020, and January 31, 2021 (inclusive). INTERVENTIONS: Not applicable. MEASUREMENTS AND MAIN RESULTS: The primary outcome was inhospital 28-day mortality by calendar month of admission, from March 2020 to January 2021. Unadjusted mortality was estimated, and Cox proportional hazard models were used to estimate adjusted mortality, controlling for age, sex, ethnicity, major comorbidities, social deprivation, geographic location, and operational strain (using bed occupancy as a proxy). Mortality fell to trough levels in June 2020 (ICU: 22.5% [95% CI, 18.2-27.4], high dependency unit: 8.0% [95% CI, 6.4-9.6]) but then subsequently increased up to January 2021: (ICU: 30.6% [95% CI, 29.0-32.2] and high dependency unit, 16.2% [95% CI, 15.3-17.1]). Comparing patients admitted during June-September 2020 with those admitted during December 2020-January 2021, the adjusted mortality was 59% (CI range, 39-82) higher in high dependency unit and 88% (CI range, 62-118) higher in ICU for the later period. This increased mortality was seen in all subgroups including those under 65. CONCLUSIONS: There was a marked deterioration in outcomes for patients admitted to critical care at the peak of the second wave of coronavirus disease 2019 in United Kingdom (December 2020-January 2021), compared with the post-first-wave period (June 2020-September 2020). The deterioration was independent of recorded patient characteristics and occupancy levels. Further research is required to determine to what extent this deterioration reflects the impact of the B117 variant of concern.

Linear mixed effects models are frequently used in biomedical statistics to model the trajectory of a repeatedly measured longitudinal variable, such as a biomarker, over time. However, population-level estimates may be biased by censoring bias resulting from exit criteria that depend on the variable in question. A joint longitudinal-survival model, in which the exit criteria and longitudinal variable are modelled simultaneously, may address this bias. Using blood glucose progression (change in HbA1c) in type 2 diabetes patients on metformin monotherapy as an example, we study the potential benefit of using joint models to model trajectory of a biomarker in observational data. 7,712 patients with type 2 diabetes initiating metformin monotherapy were identified in UK Biobank’s general practice (GP) linked records. Genetic information was extracted from UK Biobank, and prescription records, baseline clinical features and biomarkers, and longitudinal HbA1c measures were extracted from GP records. Exit criteria for follow-up for a patient was defined as progression to an additional glucose-lowering drug (which is more likely in patient with higher HbA1c). Estimates of HbA1c trajectory over time were compared using linear mixed effect model approaches (which do not account for censoring bias) and joint models. In the primary analysis, a 0.19 mmol/mol per year higher (p = 0.01) HbA1c gradient was estimated using the joint model compared to the linear mixed effects model. This difference between models was attenuated (0.13 mmol/mol per year higher, p=0.43) when baseline clinical features and biomarkers were included as additional covariates.Censoring bias should be carefully considered when modelling trajectories of repeatedly measured longitudinal variables in observational data. Joint longitudinal-survival models are a useful approach to identify and potentially correct for censoring bias when estimating population-level trajectories.Author SummaryModelling biomarkers that change over time in real world data is a challenging statistical problem due to many potential sources of bias. For example, when studying a chronic disease using a biomarker or other measurement that represents disease severity, medication intended to affect that measurement has a profound effect on how it will change over time. One common way to control for this is to study a cohort on the same treatment strategy. That way, results are not influenced by treatment change. If a patient progresses to stronger medication, then future data is no longer used. However, this approach introduces its own bias. Patients whose condition progress particularly quickly are more likely to change treatment more rapidly (and therefore be removed from further analysis, or ‘censored’), so the cohort is biased towards those whose condition progresses slower. In this paper we apply a technique called joint longitudinal-survival modelling which can adjust for this censoring bias and produce less biased estimates of progression rates. We use HbA1c (a widely used measure of glucose control) in type 2 diabetes as an example, however our methods are theoretically applicable to a range of problems across medicine in which a biomarker or feature is repeatedly measured in an individual.

Background The literature paints a complex picture of the association between mortality risk and ICU strain. In this study, we sought to determine if there is an association between mortality risk in intensive care units (ICU) and occupancy of beds compatible with mechanical ventilation, as a proxy for strain. Methods A national retrospective observational cohort study of 89 English hospital trusts (i.e. groups of hospitals functioning as single operational units). Seven thousand one hundred thirty-three adults admitted to an ICU in England between 2 April and 1 December, 2020 (inclusive), with presumed or confirmed COVID-19, for whom data was submitted to the national surveillance programme and met study inclusion criteria. A Bayesian hierarchical approach was used to model the association between hospital trust level (mechanical ventilation compatible), bed occupancy, and in-hospital all-cause mortality. Results were adjusted for unit characteristics (pre-pandemic size), individual patient-level demographic characteristics (age, sex, ethnicity, deprivation index, time-to-ICU admission), and recorded chronic comorbidities (obesity, diabetes, respiratory disease, liver disease, heart disease, hypertension, immunosuppression, neurological disease, renal disease). Results One hundred thirty-five thousand six hundred patient days were observed, with a mortality rate of 19.4 per 1000 patient days. Adjusting for patient-level factors, mortality was higher for admissions during periods of high occupancy (> 85% occupancy versus the baseline of 45 to 85%) [OR 1.23 (95% posterior credible interval (PCI): 1.08 to 1.39)]. In contrast, mortality was decreased for admissions during periods of low occupancy ( Conclusion Increasing occupancy of beds compatible with mechanical ventilation, a proxy for operational strain, is associated with a higher mortality risk for individuals admitted to ICU. Further research is required to establish if this is a causal relationship or whether it reflects strain on other operational factors such as staff. If causal, the result highlights the importance of strategies to keep ICU occupancy low to mitigate the impact of this type of resource saturation.

Objectives: \ud To measure temporal trends in survival over time in people with severe coronavirus disease 2019 requiring critical care (high dependency unit or ICU) management, and to assess whether temporal variation in mortality was explained by changes in patient demographics and comorbidity burden over time.\ud \ud Design: \ud Retrospective observational cohort; based on data reported to the COVID-19 Hospitalisation in England Surveillance System. The primary outcome was in-hospital 30-day all-cause mortality. Unadjusted survival was estimated by calendar week of admission, and Cox proportional hazards models were used to estimate adjusted survival, controlling for age, sex, ethnicity, major comorbidities, and geographical region.\ud \ud Setting: \ud One hundred eight English critical care units.\ud \ud Patients: \ud All adult (18 yr +) coronavirus disease 2019 specific critical care admissions between March 1, 2020, and June 27, 2020.\ud \ud Interventions: \ud Not applicable.\ud \ud Measurements and Main Results:\ud Twenty-one thousand eighty-two critical care patients (high dependency unit n = 15,367; ICU n = 5,715) were included. Unadjusted survival at 30 days was lowest for people admitted in late March in both high dependency unit (71.6% survival) and ICU (58.0% survival). By the end of June, survival had improved to 92.7% in high dependency unit and 80.4% in ICU. Improvements in survival remained after adjustment for patient characteristics (age, sex, ethnicity, and major comorbidities) and geographical region.\ud \ud Conclusions:\ud There has been a substantial improvement in survival amongst people admitted to critical care with coronavirus disease 2019 in England, with markedly higher survival rates in people admitted in May and June compared with those admitted in March and April. Our analysis suggests this improvement is not due to temporal changes in the age, sex, ethnicity, or major comorbidity burden of admitted patients.

Objectives To determine if there is an association between survival rates in intensive care units (ICU) and occupancy of the unit on the day of admission. Design National retrospective observational cohort study spanning the first wave of the England’s COVID-19 pandemic. Setting 114 hospital trusts (groups of hospitals functioning as single operational units). Participants 4,032 adults admitted to an ICU in England between 2nd April and 1st June, 2020, with presumed or confirmed COVID-19, for whom data was submitted to the national surveillance programme and met study inclusion criteria. Interventions N/A Main Outcomes and Measures A Bayesian hierarchical approach was used to model the association between hospital trust level (mechanical ventilation compatible) bed occupancy, and in-hospital all-cause mortality. Results were adjusted for unit characteristics (pre-pandemic size), individual patient-level demographic characteristics (age, sex, ethnicity, time-to-ICU admission), and recorded chronic comorbidities (obesity, diabetes, respiratory disease, liver disease, heart disease, hypertension, immunosuppression, neurological disease, renal disease). Results 79,793 patient-days were observed, with a mortality rate of 19.4 per 1,000 patient days. Adjusting for patient-level factors, mortality was higher for admissions during periods of high occupancy (>85% occupancy versus the baseline of 45 to 85%) [OR 1.19 (95% posterior credible interval (PCI): 1.00 to 1.44)]. In contrast, mortality was decreased for admissions during periods of low occupancy ( Conclusion and Relevance Increasing occupancy of beds compatible with mechanical ventilation, a proxy for operational strain, is associated with a higher mortality risk for individuals admitted to ICU. Public health interventions (such as expeditious vaccination programmes and non-pharmaceutical interventions) to control both incidence and prevalence of COVID-19, and therefore keep ICU occupancy low in the context of the pandemic, are necessary to mitigate the impact of this type of resource saturation. Trial Registration N/A Summary Box What is already known on this topic Pre-pandemic, higher occupancy of intensive care units was shown to be associated with increased mortality risk. However, there is limited data on the extent to which occupancy levels impacted patient outcomes during the first wave of COVID-19, especially in light of the mobilisation of significant additional resources. A recent study from Belgium reported a 42% higher mortality during periods of ICU surge capacity deployment, although in the analysis surge capacity was evaluated only as a binary variable. Although, this contradicts earlier results from smaller studies in Australia and Wales, where no association between ICU occupancy and mortality was identified. What this study adds The results of this study suggest that survival rates for patients with COVID-19 in intensive care settings appears to deteriorate as the occupancy of (surge capacity) beds compatible with mechanical ventilation (a proxy for operational pressure), increases. Moreover, this risk doesn’t occur above a specific threshold, but rather appears linear; whereby going from 0% occupancy to 100% occupancy increases risk of mortality by 92% (after adjusting for relevant individual-level factors). Furthermore, risk of mortality based on occupancy on the date of recorded outcome is even higher; OR 4.74 (95% posterior credible interval: 3.54 – 6.34). As such, this national-level cohort study of England provides compelling evidence for a relationship between occupancy and critical care mortality, and highlights the needs for decisive action to control the incidence and prevalence of COVID-19.

IntroductionAtopic dermatitis (AD) is one of the most common inflammatory skin conditions in both children and adults. Despite this, contemporary descriptions of the incidence, prevalence and current management of the condition in the UK are lacking.Methods and analysisWe will perform a series of retrospective studies using a large population-based cohort derived from the Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) network database to explore two key research themes: AD epidemiology and AD management.In the epidemiology theme, we will describe the incidence and prevalence of AD in children and adults in England from 2009 to 2018 inclusive. We will stratify findings by age, national Index of Multiple Deprivation (IMD), ethnicity, urban-rural environment and geographic location; and explore independent associations of these features with AD in multivariable models.In the management theme, we will explore healthcare utilisation and treatment in people with AD. Regarding healthcare utilisation, we will evaluate rates of AD-associated primary care visits and specialist dermatology referrals in people with AD. Rates will be stratified by age, gender, socioeconomic IMD quintile and ethnicity. We will describe contemporary treatment by estimating prescribing rates across medication classes used in AD (emollients, topical corticosteroids by potency, topical calcineurin inhibitors, topical antimicrobials, antihistamines, oral corticosteroids and systemic immunomodulatory therapies) overall, and by age and sociodemographic groupings. We will also examine trends in prescribing over the study period. In people first diagnosed with AD during the study period, we will describe differences in treatment escalation by sociodemographic factors using time-to-event analysis.Ethics and disseminationThe Health Research Authority decision tool classed this a study of ‘usual practice’, ethics approval was not required. Study approval was granted by the RCGP RSC Study Approval Committee. Results will be disseminated through peer-reviewed publications.Trial registration numberNCT03823794.

ObjectivesTo determine the trend in mortality risk over time in people with severe COVID-19 requiring critical care (high intensive unit [HDU] or intensive care unit [ICU]) management.MethodsWe accessed national English data on all adult COVID-19 specific critical care admissions from the COVID-19 Hospitalisation in England Surveillance System (CHESS), up to the 29th June 2020 (n=14,958). The study period was 1st March until 30th May, meaning every patient had 30 days of potential follow-up available. The primary outcome was in-hospital 30-day all-cause mortality. Hazard ratios for mortality were estimated for those admitted each week using a Cox proportional hazards models, adjusting for age (non-linear restricted cubic spline), sex, ethnicity, comorbidities, and geographical region.Results30-day mortality peaked for people admitted to critical care in early April (peak 29.1% for HDU, 41.5% for ICU). There was subsequently a sustained decrease in mortality risk until the end of the study period. As a linear trend from the first week of April, adjusted mortality risk decreased by 11.2% (adjusted HR 0.89 [95% CI 0.87 - 0.91]) per week in HDU, and 9.0% (adjusted HR 0.91 [95% CI 0.88 - 0.94]) in ICU.ConclusionsThere has been a substantial mortality improvement in people admitted to critical care with COVID-19 in England, with markedly lower mortality in people admitted in mid-April and May compared to earlier in the pandemic. This trend remains after adjustment for patient demographics and comorbidities suggesting this improvement is not due to changing patient characteristics. Possible causes include the introduction of effective treatments as part of clinical trials and a falling critical care burden.

BackgroundNon-pharmacological interventions were introduced based on modelling studies which suggested that the English National Health Service (NHS) would be overwhelmed by the COVID-19 pandemic. In this study, we describe the pattern of bed occupancy across England during the first wave of the pandemic, January 31st to June 5th 2020.MethodsBed availability and occupancy data was extracted from daily reports submitted by all English secondary care providers, between 27-Mar and 5-June. Two thresholds for ‘safe occupancy’ were utilized (85% as per Royal College of Emergency Medicine and 92% as per NHS Improvement).FindingsAt peak availability, there were 2711 additional beds compatible with mechanical ventilation across England, reflecting a 53% increase in capacity, and occupancy never exceeded 62%. A consequence of the repurposing of beds meant that at the trough, there were 8·7% (8,508) fewer general and acute (G&A) beds across England, but occupancy never exceeded 72%. The closest to (surge) capacity that any trust in England reached was 99·8% for general and acute beds. For beds compatible with mechanical ventilation there were 326 trust-days (3·7%) spent above 85% of surge capacity, and 154 trust-days (1·8%) spent above 92%. 23 trusts spent a cumulative 81 days at 100% saturation of their surge ventilator bed capacity (median number of days per trust = 1 [range: 1 to 17]). However, only 3 STPs (aggregates of geographically co-located trusts) reached 100% saturation of their mechanical ventilation beds.InterpretationThroughout the first wave of the pandemic, an adequate supply of all bed-types existed at a national level. Due to an unequal distribution of bed utilization, many trusts spent a significant period operating above ‘safe-occupancy’ thresholds, despite substantial capacity in geographically co-located trusts; a key operational issue to address in preparing for a potential second wave.FundingThis study received no funding.Research In ContextEvidence Before This StudyWe identified information sources describing COVID-19 related bed and mechanical ventilator demand modelling, as well as bed occupancy during the first wave of the pandemic by performing regular searches of MedRxiv, PubMed and Google, using the terms ‘COVID-19’, ‘mechanical ventilators’, ‘bed occupancy’, ‘England’, ‘UK’, ‘demand’, and ‘non-pharmacological interventions (NPIs)’, until June 20th, 2020. Two UK-specific studies were found that modelled the demand for mechanical ventilators, one of which incorporated sensitivity analysis based on the introduction of NPIs and found that their effects might prevent the healthcare system being overwhelmed. Separately, several news reports were found pertaining to a single hospital that reached ventilator capacity in England during the first wave of the pandemic, however, no single authoritative source was identified detailing impact across all hospital sites in England.Added Value of This StudyThis national study of hospital-level bed occupancy in England provides unique and timely insight into bed-specific resource utilization during the first wave of the COVID-19 pandemic, nationally, and by specific (geographically defined) health footprints. We found evidence of an unequal distribution of resource utilization across England. Although occupancy of beds compatible with mechanical ventilation never exceeded 62% at the national level, 52 (30%) hospitals across England reached 100% saturation at some point during the first wave of the pandemic. Close examination of the geospatial data revealed that in the vast majority of circumstances there was relief capacity in geographically co-located hospitals. Over the first wave it was theoretically possible to markedly reduce (by 95.1%) the number of hospitals at 100% saturation of their mechanical ventilator bed capacity by redistributing patients to nearby hospitals.Implications Of All The Available EvidenceNow-casting using routinely collected administrative data presents a robust approach to rapidly evaluate the effectiveness of national policies introduced to prevent a healthcare system being overwhelmed in the context of a pandemic illness. Early investment in operational field hospital and an independent sector network may yield more overtly positive results in the winter, when G&A occupancy-levels regularly exceed 92% in England, however, during the first wave of the pandemic they were under-utilized. Moreover, in the context of the non-pharmacological interventions utilized during the first wave of COVID-19, demand for beds and mechanical ventilators was much lower than initially predicted, but despite this many trust spent a significant period of time operating above ‘safe-occupancy’ thresholds. This finding demonstrates that it is vital that future demand (prediction) models reflect the nuances of local variation within a healthcare system. Failure to incorporate such geographical variation can misrepresent the likelihood of surpassing availability thresholds by averaging out over regions with relatively lower demand, and presents a key operational issue for policymakers to address in preparing for a potential second wave.

The complexity of each Coupled Model Intercomparison Project grows with every new generation. The Phase 5 effort saw a large increase in the number of experiments that were performed and the number of variables that were requested compared to its previous generation, Phase 3. Many centers were not prepared for the large demand and this stressed the resources of several centers including at the National Center for Atmospheric Research. During Phase 5, we missed several deadlines and we struggled to get the data out to the community for analysis. In preparation for the current generation, Phase 6, we examined the weaknesses in our workflow and addressed the performance issues with new software tools. Through this investment, we were able to publish approximately six times the amount of data to the community compared to the volumes we produced in the previous generation and we were able to accomplish this within one-third of the time, providing an 18 times speedup. This paper discusses the improvements we have made to accomplish this success for Phase 6 and further improvements we hope to make for the next generation.

OBJECTIVE To evaluate the association between metformin use and anemia risk in type 2 diabetes, and the time-course for this, in a randomized controlled trial (RCT) and real-world population data. RESEARCH DESIGN AND METHODS Anemia was defined as a hemoglobin measure of RESULTS In ADOPT, compared with sulfonylureas, the odds ratio (OR) (95% CI) for anemia was 1.93 (1.10, 3.38) for metformin and 4.18 (2.50, 7.00) for thiazolidinediones. In UKPDS, compared with diet, the OR (95% CI) was 3.40 (1.98, 5.83) for metformin, 0.96 (0.57, 1.62) for sulfonylureas, and 1.08 (0.62, 1.87) for insulin. In ADOPT, hemoglobin and hematocrit dropped after metformin initiation by 6 months, with no further decrease after 3 years. In UKPDS, hemoglobin fell by 3 years in the metformin group compared with other treatments. At years 6 and 9, hemoglobin was reduced in all treatment groups, with no greater difference seen in the metformin group. In GoDARTS, each 1 g/day of metformin use was associated with a 2% higher annual risk of anemia. CONCLUSIONS Metformin use is associated with early risk of anemia in individuals with type 2 diabetes, a finding consistent across two RCTs and replicated in one real-world study. The mechanism for this early fall in hemoglobin is uncertain, but given the time course, is unlikely to be due to vitamin B12 deficiency alone.

OBJECTIVE A precision approach to type 2 diabetes therapy would aim to target treatment according to patient characteristics. We examined if measures of insulin resistance and secretion were associated with glycemic response to dipeptidyl peptidase 4 (DPP-4) inhibitor therapy. RESEARCH DESIGN AND METHODS We evaluated whether markers of insulin resistance and insulin secretion were associated with 6-month glycemic response in a prospective study of noninsulin-treated participants starting DPP-4 inhibitor therapy (Predicting Response to Incretin Based Agents [PRIBA] study; n = 254), with replication for routinely available markers in U.K. electronic health care records (Clinical Practice Research Datalink [CPRD]; n = 23,001). In CPRD, we evaluated associations between baseline markers and 3-year durability of response. To test the specificity of findings, we repeated analyses for glucagon-like peptide 1 (GLP-1) receptor agonists (PRIBA, n = 339; CPRD, n = 4,464). RESULTS In PRIBA, markers of higher insulin resistance (higher fasting C-peptide [P = 0.03], HOMA2 insulin resistance [P = 0.01], and triglycerides [P < 0.01]) were associated with reduced 6-month HbA1c response to DPP-4 inhibitors. In CPRD, higher triglycerides and BMI were associated with reduced HbA1c response (both P < 0.01). A subgroup defined by obesity (BMI ≥30 kg/m2) and high triglycerides (≥2.3 mmol/L) had reduced 6-month response in both data sets (PRIBA HbA1c reduction 5.3 [95% CI 1.8, 8.6] mmol/mol [0.5%] [obese and high triglycerides] vs. 11.3 [8.4, 14.1] mmol/mol [1.0%] [nonobese and normal triglycerides]; P = 0.01). In CPRD, the obese, high- triglycerides subgroup also had less durable response (hazard ratio 1.28 [1.16, 1.41]; P < 0.001). There was no association between markers of insulin resistance and response to GLP-1 receptor agonists. CONCLUSIONS Markers of higher insulin resistance are consistently associated with reduced glycemic response to DPP-4 inhibitors. This finding provides a starting point for the application of a precision diabetes approach to DPP-4 inhibitor therapy.

To describe the measurement of heart rate turbulence (HRT) after ventricular premature beats and compare HRT in healthy Doberman pinschers and those with dilated cardiomyopathy (DCM), with and without congestive heart failure (CHF).Sixty-five client-owned Dobermans: 20 healthy (NORMAL), 31 with preclinical DCM and 14 with DCM and CHF (DCM + CHF).A retrospective study of data retrieved from clinical records and ambulatory ECG (Holter) archives, including data collected previously for a large-scale prospective study of Dobermans with preclinical DCM. Holter data were reanalysed quantitatively, including conventional time-domain heart rate variability and the HRT parameters turbulence onset and turbulence slope.Heart rate turbulence could be measured in 58/65 dogs. Six Holter recordings had inadequate ventricular premature contractions (VPCs) and one exhibited VPCs too similar to sinus morphology. Heart rate turbulence parameter, turbulence onset, was significantly reduced in DCM dogs, whereas conventional heart rate variability measures were not. Heart rate variability and HRT markers were reduced in DCM + CHF dogs as expected.Heart rate turbulence can be measured from the majority of good quality standard canine 24-hour Holter recordings with >5 VPCs. Turbulence onset is significantly reduced in Dobermans with preclinical DCM which indicates vagal withdrawal early in the course of disease. Heart rate turbulence is a powerful prognostic indicator in human cardiac disease which can be measured from standard 24-hour ambulatory ECG (Holter) recordings using appropriate computer software. Further studies are warranted to assess whether HRT may be of prognostic value in dogs with preclinical DCM and in other canine cardiac disease.

Background:The importance of diabetes as a prognostic factor in people admitted to hospital critical care with COVID-19 is poorly understood and has not been qu

Background There is much interest in the use of prognostic and diagnostic prediction models in all areas of clinical medicine. The use of machine learning to improve prognostic and diagnostic accuracy in this area has been increasing at the expense of classic statistical models. Previous studies have compared performance between these two approaches but their findings are inconsistent and many have limitations. We aimed to compare the discrimination and calibration of seven models built using logistic regression and optimised machine learning algorithms in a clinical setting, where the number of potential predictors is often limited, and externally validate the models. Methods We trained models using logistic regression and six commonly used machine learning algorithms to predict if a patient diagnosed with diabetes has type 1 diabetes (versus type 2 diabetes). We used seven predictor variables (age, BMI, GADA islet-autoantibodies, sex, total cholesterol, HDL cholesterol and triglyceride) using a UK cohort of adult participants (aged 18–50 years) with clinically diagnosed diabetes recruited from primary and secondary care (n = 960, 14% with type 1 diabetes). Discrimination performance (ROC AUC), calibration and decision curve analysis of each approach was compared in a separate external validation dataset (n = 504, 21% with type 1 diabetes). Results Average performance obtained in internal validation was similar in all models (ROC AUC ≥ 0.94). In external validation, there were very modest reductions in discrimination with AUC ROC remaining ≥ 0.93 for all methods. Logistic regression had the numerically highest value in external validation (ROC AUC 0.95). Logistic regression had good performance in terms of calibration and decision curve analysis. Neural network and gradient boosting machine had the best calibration performance. Both logistic regression and support vector machine had good decision curve analysis for clinical useful threshold probabilities. Conclusion Logistic regression performed as well as optimised machine algorithms to classify patients with type 1 and type 2 diabetes. This study highlights the utility of comparing traditional regression modelling to machine learning, particularly when using a small number of well understood, strong predictor variables.

Objectives To describe the relationship between reported serious operational problems (SOPs), and mortality for patients with COVID-19 admitted to intensive care units (ICUs). Design English national retrospective cohort study. Setting 89 English hospital trusts (i.e. small groups of hospitals functioning as single operational units). Patients All adults with COVID-19 admitted to ICU between 2nd April and 1st December, 2020 (n = 6,737). Interventions N/A Main outcomes and measures Hospital trusts routinely submit declarations of whether they have experienced ‘serious operational problems’ in the last 24 hours (e.g. due to staffing issues, adverse weather conditions, etc.). Bayesian hierarchical models were used to estimate the association between in-hospital mortality (binary outcome) and: 1) an indicator for whether a SOP occurred on the date of a patient’s admission, and; 2) the proportion of the days in a patient’s stay that had a SOP occur within their trust. These models were adjusted for individual demographic characteristics (age, sex, ethnicity), and recorded comorbidities. Results Serious operational problems (SOPs) were common; reported in 47 trusts (52.8%) and were present for 2,701 (of 21,716; 12.4%) trust days. Overall mortality was 37.7% (2,539 deaths). Admission during a period of SOPs was associated with a substantially increased mortality; adjusted odds ratio (OR) 1.34 (95% posterior credible interval (PCI): 1.07 to 1.68). Mortality was also associated with the proportion of a patient’s admission duration that had concurrent SOPs; OR 1.47 (95% PCI: 1.10 to 1.96) for mortality where SOPs were present for 100% compared to 0% of the stay. Conclusion and relevance Serious operational problems at the trust-level are associated with a significant increase in mortality in patients with COVID-19 admitted to critical care. The link isn’t necessarily causal, but this observation justifies further research to determine if a binary indicator might be a valid prognostic marker for deteriorating quality of care.

This tutorial presents the details of the interconnection network utilized in many high performance computing (HPC) systems today. “InfiniBand” is the hardware interconnect utilized by over 35% of the top 500 supercomputers in the world as of June, 2017. “Verbs” is the term used for both the semantic description of the interface in the InfiniBand architecture specifications, and the name used for the functions defined in the widely used OpenFabrics alliance implementation of the software interface to InfiniBand. “Message passing interface” is the primary software library by which HPC applications portably pass messages between processes across a wide range of interconnects including InfiniBand. Our goal is to explain how these three components are designed and how they interact to provide a powerful, efficient interconnect for HPC applications. We provide a succinct look into the inner technical workings of each component that should be instructive to both novices to HPC applications as well as to those who may be familiar with one component, but not necessarily the others, in the design and functioning of the total interconnect. A supercomputer interconnect is not a monolithic structure, and this tutorial aims to give non-experts a “big-picture” overview of its substructure with an appreciation of how and why features in one component influence those in others. We believe this is one of the first tutorials to discuss these three major components as one integrated whole. In addition, we give detailed examples of practical experience and typical algorithms used within each component in order to give insights into what issues and trade-offs are important.

ObjectiveIn this study, we describe the pattern of bed occupancy across England during the peak of the first wave of the COVID-19 pandemic.DesignDescriptive survey.SettingAll non-specialist secondary care providers in England from 27 March27to 5 June 2020.ParticipantsAcute (non-specialist) trusts with a type 1 (ie, 24 hours/day, consultant-led) accident and emergency department (n=125), Nightingale (field) hospitals (n=7) and independent sector secondary care providers (n=195).Main outcome measuresTwo thresholds for ‘safe occupancy’ were used: 85% as per the Royal College of Emergency Medicine and 92% as per NHS Improvement.ResultsAt peak availability, there were 2711 additional beds compatible with mechanical ventilation across England, reflecting a 53% increase in capacity, and occupancy never exceeded 62%. A consequence of the repurposing of beds meant that at the trough there were 8.7% (8508) fewer general and acute beds across England, but occupancy never exceeded 72%. The closest to full occupancy of general and acute bed (surge) capacity that any trust in England reached was 99.8% . For beds compatible with mechanical ventilation there were 326 trust-days (3.7%) spent above 85% of surge capacity and 154 trust-days (1.8%) spent above 92%. 23 trusts spent a cumulative 81 days at 100% saturation of their surge ventilator bed capacity (median number of days per trust=1, range: 1–17). However, only three sustainability and transformation partnerships (aggregates of geographically co-located trusts) reached 100% saturation of their mechanical ventilation beds.ConclusionsThroughout the first wave of the pandemic, an adequate supply of all bed types existed at a national level. However, due to an unequal distribution of bed utilisation, many trusts spent a significant period operating above ‘safe-occupancy’ thresholds despite substantial capacity in geographically co-located trusts, a key operational issue to address in preparing for future waves.

Background: Recent research using data-driven cluster analysis has proposed five subgroups of diabetes with different diabetes progression and complication risk. We aimed to compare the clinical utility of this subgroup-based approach with an alternative strategy using specific outcome models that use routine clinical features. Methods: We identified clusters in the ADOPT (n=4,351) trial cohort using the cluster analysis reported by Ahlqvist and colleagues (Lancet Diabetes Endocrinology 2018;6:361-69). Differences between clusters in glycaemic and renal progression were evaluated, and contrasted with stratification using routine measures (age at diagnosis and baseline renal function). We tested the performance of a strategy of selecting glucose lowering therapy using clusters with one using simple clinical features (sex, BMI, age at diagnosis, baseline HbA1c) in an independent trial cohort (RECORD (n=4,447)). Findings: Clusters identified in trial data were similar to those described in the original study. Clusters showed differences in glycaemic progression, but a model with age at diagnosis alone had similar predictive ability. We found differences in CKD incidence between clusters however baseline eGFR was a better predictor of time to CKD. Clusters differed in glycaemic response, with a particular benefit for cluster 3 (insulin-resistant) with thiazolidinediones and cluster 5 (older) with sulfonylureas. However simple clinical features outperformed clusters to select therapy for individual patients. Interpretation: Precision medicine in type 2 diabetes is likely to have most clinical utility if based on an approach of using specific continuous clinical measures to predict specific outcomes, rather than stratifying patients into subgroups. Funding Statement: This work was supported by the Medical Research Council (UK) (MR/N00633X/1). Data for both ADOPT and RECORD trials were accessed through the Clinical Trial Data Transparency Portal under approval from GSK (Proposal 930). ATH is a NIHR Senior Investigator and a Wellcome Trust Senior Investigator (098395/Z/12/Z). AGJ is supported by an NIHR Clinician Scientist award (CS-2015-15- 018). JMD, ATH and BMS are supported by the NIHR Exeter Clinical Research Facility. The views expressed are those of the authors and not necessarily those of the MRC, the NIHR or the Wellcome Trust Declaration of Interests: WEH declares a grant from IQVIA. All other authors declare no competing interests. Ethics Approval Statement: Individual-level participant data from the ADOPT and RECORD trials were accessed through the Clinical Trial Data Transparency Portal, with study approval from GlaxoSmithKline (Proposal 930). Both trials were conducted according to Good Clinical (Research) Practice guidelines and the Declaration of Helsinki (1996).

OBJECTIVE The choice of therapy for type 2 diabetes after metformin is guided by overall estimates of glycemic response and side effects seen in large cohorts. A stratified approach to therapy would aim to improve on this by identifying subgroups of patients whose glycemic response or risk of side effects differs markedly. We assessed whether simple clinical characteristics could identify patients with differing glycemic response and side effects with sulfonylureas and thiazolidinediones. RESEARCH DESIGN AND METHODS We studied 22,379 patients starting sulfonylurea or thiazolidinedione therapy in the U.K. Clinical Practice Research Datalink (CPRD) to identify features associated with increased 1-year HbA1c fall with one therapy class and reduced fall with the second. We then assessed whether prespecified patient subgroups defined by the differential clinical factors showed differing 5-year glycemic response and side effects with sulfonylureas and thiazolidinediones using individual randomized trial data from ADOPT (A Diabetes Outcome Progression Trial) (first-line therapy, n = 2,725) and RECORD (Rosiglitazone Evaluated for Cardiovascular Outcomes and Regulation of Glycemia in Diabetes) (second-line therapy, n = 2,222). Further replication was conducted using routine clinical data from GoDARTS (Genetics of Diabetes Audit and Research in Tayside Scotland) (n = 1,977). RESULTS In CPRD, male sex and lower BMI were associated with greater glycemic response with sulfonylureas and a lesser response with thiazolidinediones (both P < 0.001). In ADOPT and RECORD, nonobese males had a greater overall HbA1c reduction with sulfonylureas than with thiazolidinediones (P < 0.001); in contrast, obese females had a greater HbA1c reduction with thiazolidinediones than with sulfonylureas (P < 0.001). Weight gain and edema risk with thiazolidinediones were greatest in obese females; however, hypoglycemia risk with sulfonylureas was similar across all subgroups. CONCLUSIONS Patient subgroups defined by sex and BMI have different patterns of benefits and risks on thiazolidinedione and sulfonylurea therapy. Subgroup-specific estimates can inform discussion about the choice of therapy after metformin for an individual patient. Our approach using routine and shared trial data provides a framework for future stratification research in type 2 diabetes.

Climate simulation codes, such as the Community Earth System Model (CESM), are especially complex and continually evolving. Their ongoing state of development requires frequent software verification in the form of quality assurance to both preserve the quality of the code and instill model confidence. To formalize and simplify this previously subjective and computationally expensive aspect of the verification process, we have developed a new tool for evaluating climate consistency. Because an ensemble of simulations allows us to gauge the natural variability of the model's climate, our new tool uses an ensemble approach for consistency testing. In particular, an ensemble of CESM climate runs is created, from which we obtain a statistical distribution that can be used to determine whether a new climate run is statistically distinguishable from the original ensemble. The CESM ensemble consistency test, referred to as CESM-ECT, is objective in nature and accessible to CESM developers and users. The tool has proven its utility in detecting errors in software and hardware environments and providing rapid feedback to model developers.

This paper presents a measurement study of congestion on a production, highly utilized, 72K-core InfiniBand cluster called Yellowstone. The measurement study consists of a 23-day data collection phase in which port counters of the Yellowstone switches were read multiple times every hour to check for stalls during which the port is unable to send data due to a lack of flow-control credits. A total of 30M data records were obtained and analyzed. Results showed that a significant number of the 100-ms intervals over which a port counter was observed, there were transmission stalls. For example, out of 6M observations of Top-of-Rack (ToR) switch uplink ports, we found that the port was forced to wait for credits in 60% of these 100-ms intervals. Such transmission stalls could increase application execution time, and also decrease cluster utilization. The latter will occur when Message Passing Interface (MPI) Barrier calls are issued for synchronization and communication delays cause one or more MPI ranks to be slower than others.

ObjectiveTo develop and validate multivariable clinical diagnostic models to assist distinguishing between type 1 and type 2 diabetes in adults aged 18–50.DesignMultivariable logistic regression analysis was used to develop classification models integrating five pre-specified predictor variables, including clinical features (age of diagnosis, body mass index) and clinical biomarkers (GADA and Islet Antigen 2 islet autoantibodies, Type 1 Diabetes Genetic Risk Score), to identify type 1 diabetes with rapid insulin requirement using data from existing cohorts.SettingUK cohorts recruited from primary and secondary care.Participants1352 (model development) and 582 (external validation) participants diagnosed with diabetes between the age of 18 and 50 years of white European origin.Main outcome measuresType 1 diabetes was defined by rapid insulin requirement (within 3 years of diagnosis) and severe endogenous insulin deficiency (C-peptide 600 pmol/L at ≥5 years diabetes duration). Model performance was assessed using area under the receiver operating characteristic curve (ROC AUC), and internal and external validation.ResultsType 1 diabetes was present in 13% of participants in the development cohort. All five predictor variables were discriminative and independent predictors of type 1 diabetes (pConclusionsClinical diagnostic models integrating clinical features with biomarkers have high accuracy for identifying type 1 diabetes with rapid insulin requirement, and could assist clinicians and researchers in accurately identifying patients with type 1 diabetes.

We have developed a new parallel Python tool for the standardization of Earth System Model (ESM) data for publication as part of Model Intercomparison Projects (MIPs). It was specifically designed to aid Community Earth System Model (CESM) scientists at the National Center for Atmospheric Research (NCAR) in preparation for the Coupled Model Intercomparison Project, Phase 6 (CMIP6), expected to start in early 2017. However, the tool is general to any and all MIPs and ESMs. The tool is implemented with MPI parallelism using mpi4py, and it performs the data standardization computation with a directed acyclic graph (DAG) data structure capable of streaming data from ESM input data to standardized output files. In this paper, we describe the tool, its design and testing.

This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation.

While the InfiniBand link-by-link flow control helps avoid packet loss, it unfortunately causes the effects of congestion to spread through a network. Flows whose paths do not even pass through congested ports could suffer from reduced throughput. We propose a Dynamic Congestion Management System (DCMS) to address this problem. Without per-flow information, the DCMS leverages performance counters of switch ports to detect onset of congestion, and determines whether-or-not victim flows are present. The DCMS then takes actions to cause an aggressive reduction in the sending rates of congestion-causing (contributor) flows if victim flows are present. On the other hand, in the absence of victim flows, the DCMS allows the contributor flows to maintain high sending rates and finish as quickly as possible.Our results show that dynamic congestion management can enable a network to serve both contributor flows and victim flows effectively. The DCMS solution operates within the constraints of the InfiniBand Standard.

With the fourth release of the Community Climate System Model, the ability to perform ultra-high-resolution climate simulations is now possible, enabling eddy-resolving ocean and sea-ice models to be coupled to a finite-volume atmosphere model for a range of atmospheric resolutions. This capability was made possible by enabling the model to use large scale parallelism, which required a significant refactoring of the software infrastructure. We describe the scalability of two ultra-high-resolution coupled configurations on leadership class computing platforms. We demonstrate the ability to utilize over 30,000 processor cores on a Cray XT5 system and over 60,000 cores on an IBM Blue Gene/P system to obtain climatologically relevant simulation rates for these configurations.

We examine the ability of the IBM Blue Gene/L™ (BG/L) architecture to provide ultrahigh-resolution climate simulation capability. Our investigations show that it is possible to scale climate models to more than 32,000 processors on a 20-rack BG/L system using a variety of commonly employed techniques. One novel contribution is our load-balancing strategy that is based on newly developed space-filling curve partitioning algorithms. Here, we examine three models: the Parallel Ocean Program (POP), the Community Ice CodE (CICE), and the High-Order Method Modeling Environment (HOMME). The POP and CICE models are components of the next-generation Community Climate System Model (CCSM), which is based at the National Center for Atmospheric Research and is one of the leading coupled climate system models. HOMME is an experimental dynamical "core" (i.e., the CCSM component that calculates atmosphere dynamics) currently being evaluated within the Community Atmospheric Model, the atmospheric component of CCSM. For our scaling studies, we concentrate on 1/10° resolution simulations for CICE and POP, and 1/3° resolution for HOMME. The ability to simulate high resolutions on the massively parallel systems, which will dominate high-performance computing for the foreseeable future, is essential to the advancement of climate science.

Objective To examine mortality in members of the two UK Houses of Parliament compared with the general population, 1945-2011. Design Retrospective cohort analysis of death rates and predictors of mortality in Members of Parliament (MPs) and members of the House of Lords (Lords). Setting UK. Participants 4950 MPs and Lords first joining the UK parliament in 1945-2011. Main outcome measure Standardised mortality ratios, comparing all cause death rates of MPs and Lords from first election or appointment with those in the age, sex, and calendar year matched general population. Results Between 1945 and 2011, mortality was lower in MPs (standardised mortality ratio 0.72, 95% confidence interval 0.67 to 0.76) and Lords (0.63, 0.60 to 0.67) than in the general population. Over the same period, death rates among MPs also improved more quickly than in the general population. For every 100 expected deaths, 22 fewer deaths occurred among MPs first elected in 1990-99 compared with MPs first elected in 1945-49. Labour party MPs had 19% higher death rates compared with the general population than did Conservative MPs (relative mortality ratio 1.19, 95% confidence interval 1.01 to 1.40). The effect of political party on mortality disappeared when controlling for education level. Conclusions From 1945 to 2011, MPs and Lords experienced lower mortality than the UK general population, and, at least until 1999, the mortality gap between newly elected MPs and the general population widened. Even among MPs, educational background was an important predictor of mortality, and education possibly explains much of the mortality difference between Labour and Conservative MPs. Social inequalities are alive and well in UK parliamentarians, and at least in terms of mortality, MPs are likely to have never had it so good.

This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation. The main computational objectives were: 1. To develop computationally efficient, but physically based, parameterizations of estuary and continental shelf mixing processes for use in an Earth System Model (CESM). 2. To develop a two-way nested regional modeling framework in order to dynamically downscale the climate response of particular coastal ocean regions and to upscale the impact of the regional coastal processes to the global climate in an Earth System Model (CESM). 3. To develop computational infrastructure to enhance the efficiency of data transfer between specific sources and destinations, i.e., a point-to-point communication capability, (used in objective 1) within POP, the ocean component of CESM.

The InfiniBand Congestion Control (CC) mechanism is able to reduce congestion and improve performance in many situations. In this paper we study the characteristics of congestion in InfiniBand by monitoring and analyzing the CC mechanism with a hardware analyzer. To the best of our knowledge, this is the first paper that presents experience with, and analysis of, the InfiniBand CC with such a tool. We found that there can be more than one “root of congestion”, as defined by the IBTA specification, existing at the same time in the congestion tree, and a “root of congestion” can be converted to a “victim of congestion” as its nature changes. We also observed that even with constant traffic flows, the “root of congestion” will shift from one place to another within the congestion tree, with corresponding consequence for packets from various traffic sources: traffic that might be negatively impacted by tree spreading and might be not contributing to the “root of congestion” before, will be treated as a congestion contributor and then be throttled by the CC mechanism.

Advances in software parallelism and high-performance systems have resulted in an order of magnitude increase in the volume of output data produced by the Community Earth System Model (CESM). As the volume of data produced by CESM increases, the single-threaded script-based software packages traditionally used to post-process model output data have become a bottleneck in the analysis process. This paper presents a parallel version of the CESM atmosphere model data analysis workflow implemented using the Swift scripting language.Using the Swift implementation of the workflow, the time to analyze a 10-year atmosphere simulation on a typical cluster is reduced from 95 to 32 minutes on a single 8-core node and to 20 minutes on two nodes. The parallelized workflow is then used to evaluate several new data-intensive computational systems that feature RAM-based and flash-based storage. Even when constraining parallelism to limit the amount of file system space used by intermediate temporary data, our results show that the Swift-based implementation significantly reduces data analysis time.

Previous efforts aimed at improving direct volume rendering performance have focused largely on time-invariant, 3D data. Little work has been done in the area of interactive direct volume rendering of time-varying data, such as is commonly found in Computational Fluid Dynamics (CFD) simulations. Until recently, the additional costs imposed by time-varying data have made consideration of interactive direct volume rendering impractical. We present a volume rendering system based on a parallel implementation of the Shear-Warp Factorization algorithm that is capable of rendering time-varying 1283 data at interactive speeds.

Two years ago we recorded our findings in 122 patients with proved acoustic nerve tumors operated upon in the Hospital of the University of Pennsylvania, the Graduate Hospital of the University of Pennsylvania, and the Temple University Hospital (5). At that time we concerned ourselves only with eighth nerve tumors. The present report will bring our experiences with acoustic nerve tumors in the Hospitals of the University of Pennsylvania up to date. In addition, we have reviewed the records of all other patients operated upon for cerebellopontine angle tumor syndromes who proved to have neoplasms other than acoustic neuromas. The roentgen findings in these cases, also, will be recorded. The data for this report were taken from the records of the Neurosurgical Services of the Hospital of the University and the Graduate Hospital of the University of Pennsylvania, made available to us through the kindness of the neurosurgeons of these hospitals, Dr. Francis C. Grant and Dr. Robert A. Groff. Our present serie...

Three of the 38 cases reviewed in this retrospective study of pyogenic arthritis demonstrated the presence of dystrophic periarticular calcifications.These soft tissue calcifications, which are indicative of severe soft tissue disruption, occurred several weeks after the onset of the illness in those patients with severe and prolonged illnesses.

Large, complex codes such as earth system models are in a constant state of development, requiring frequent software quality assurance. The recently developed Community Earth System Model (CESM) Ensemble Consistency Test (CESM-ECT) provides an objective measure of statistical consistency for new CESM simulation runs, which has greatly facilitated error detection and rapid feedback for model users and developers. CESM-ECT determines consistency based on an ensemble of simulations that represent the same earth system model. Its statistical distribution embodies the natural variability of the model. Clearly the composition of the employed ensemble is critical to CESM-ECT's effectiveness. In this work we examine whether the composition of the CESM-ECT ensemble is adequate for characterizing the variability of a consistent climate. To this end, we introduce minimal code changes into CESM that should pass the CESM-ECT, and we evaluate the composition of the CESM-ECT ensemble in this context. We suggest an improved ensemble composition that better captures the accepted variability induced by code changes, compiler changes, and optimizations, thus more precisely facilitating the detection of errors in the CESM hardware or software stack as well as enabling more in-depth code optimization and the adoption of new technologies.