Logistic regression has similar performance to optimised machine learning algorithms in a clinical setting: application to the discrimination between type 1 and type 2 diabetes in young adults

This is the final version. Available from the publisher via the DOI in this record.The data that support the findings of this study are available from University of Exeter Medical School/Oxford University but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of University of Exeter Medical School/Oxford University. R code is made available in supplementary file (see Additional file 2).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.National Institute for Health Research (NIHR

Architecture of the AP2:clathrin coat on the membranes of clathrin-coated vesicles

AbstractClathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell’s plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which cargo-selecting clathrin adaptors are attached. AP2 is the key adaptor in CME. Crystallography has shown AP2 to adopt a range of conformations. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures, interactions and arrangements of clathrin and AP2 at the key steps of coat assembly, from AP2 in solution to membrane-assembled clathrin-coated vesicles (CCVs). AP2 binds cargo and PtdIns(4,5)P2-containing membranes via multiple interfaces, undergoing conformational rearrangement from its cytosolic state. The binding mode of AP2 β2-appendage into the clathrin lattice in CCVs and buds implies how the adaptor structurally modulates coat curvature and coat disassembly.</jats:p

The transition towards a sustainable energy system in Europe: What role can North Africa's solar resources play?

Securing energy supply and speeding up the transition towards a reliable, sustainable, low-carbon energy system are among the major current and future challenges facing Europe. Importing dispatchable solar electricity from North Africa is considered as a potential and attractive option. Nevertheless, as things currently stand, the European Commission focuses mainly on the exploitation of the existing wind power potential in the North Sea, largely ignoring the solar power potential in the Sahara region of North Africa. After discussing the major challenges and issues facing Europe to achieve the assigned ambitious objectives, the paper emphasises the importance of North Africa's solar resources in helping Europe to successfully address the challenge of decarbonising its electricity system, in particular with regards to the security of supply and sustainability. Within these two major challenges, the paper explores the issues of access, barriers and opportunities. The paper highlights why the EU’s energy and climate goals will not be achievable without adequate grid expansion and grid-scale energy storage facilities, as well as other innovative measures to manage demand and ensure a secure energy supply. In this respect, the paper shows how the import of dispatchable electricity from North Africa via specific HVDC links could play a key role in helping the EU achieve its energy targets in a cost effective way without recourse to significant investments in transmission infrastructure and storage facilities. The paper then attempts to identify and analyze the main barriers that continue to inhibit the export of solar electricity from North Africa to Europe. Finally, to make the project more attractive and achievable in the near future, the paper proposes a systematic approach for setting up energy import scenarios. A promising import scenario is presented where energy import via Italy is shown to be a more viable and effective solution than via Spain.Peer reviewe

Autonomic regulation of systemic inflammation in humans: A multi-center, blinded observational cohort study.

OBJECTIVE: Experimental animal models demonstrate that autonomic activity regulates systemic inflammation. By contrast, human studies are limited in number and exclusively use heart rate variability (HRV) as an index of cardiac autonomic regulation. HRV measures are primarily dependent on, and need to be corrected for, heart rate. Thus, independent autonomic measures are required to confirm HRV-based findings. Here, the authors sought to replicate the findings of preceding HRV-based studies by using HRV-independent, exercise-evoked sympathetic and parasympathetic measures of cardiac autonomic regulation to examine the relationship between autonomic function and systemic inflammation. METHODS: Sympathetic function was assessed by measuring heart rate changes during unloaded pedaling prior to onset of exercise, divided into quartiles; an anticipatory heart rate (AHRR) rise during this period is evoked by mental stress in many individuals. Parasympathetic function was assessed by heart rate recovery (HRR) 60s after finishing cardiopulmonary exercise testing, divided into quartiles. Parasympathetic dysfunction was defined by delayed heart rate recovery (HRR) ≤12.beats.min-1, a threshold value associated with higher cardiovascular morbidity/mortality in the general population. Systemic inflammation was primarily assessed by neutrophil-lymphocyte ratio (NLR), where a ratio >4 is prognostic across several inflammatory diseases and correlates strongly with elevated plasma levels of pro-inflammatory cytokines. High-sensitivity C-reactive protein (hsCRP) was also measured. RESULTS: In 1624 subjects (65±14y; 67.9% male), lower HRR (impaired vagal activity) was associated with progressively higher NLR (p=0.004 for trend across quartiles). Delayed HRR, recorded in 646/1624 (39.6%) subjects, was associated with neutrophil-lymphocyte ratio >4 (relative risk: 1.43 (95%CI: 1.18-1.74); P=0.0003). Similar results were found for hsCRP (p=0.045). By contrast, AHRR was not associated with NLR (relative risk: 1.24 (95%CI: 0.94-1.65); P=0.14). CONCLUSIONS: Delayed HRR, a robust measure of parasympathetic dysfunction, is independently associated with leukocyte ratios indicative of systemic inflammation. These results further support a role for parasympathetic modulation of systemic inflammation in humans.British Journal of Anaesthesia/Royal College of Anaesthetists’ Basic Science Career development fellowship [GLA]; UCLH/UCL NIHR Biomedical Research Centre; British Heart Foundation Programme Grant RG/14/4/30736 [GLA]

Severe bronchopulmonary dysplasia improved by noninvasive positive pressure ventilation: a case report

<p>Abstract</p> <p>Introduction</p> <p>This is the first report to describe the feasibility and effectiveness of noninvasive positive pressure ventilation in the secondary treatment of bronchopulmonary dysplasia.</p> <p>Case presentation</p> <p>A former male preterm of Caucasian ethnicity delivered at 29 weeks gestation developed severe bronchopulmonary dysplasia. At the age of six months he was in permanent tachypnea and dyspnea and in need of 100% oxygen with a flow of 2.0 L/minute via a nasal cannula. Intermittent nocturnal noninvasive positive pressure ventilation was then administered for seven hours daily. The ventilator was set at a positive end-expiratory pressure of 6 cmH₂O, with pressure support of 4 cmH₂O, trigger at 1.4 mL/second, and a maximum inspiratory time of 0.7 seconds. Over the course of seven weeks, the patient's maximum daytime fraction of inspired oxygen via nasal cannula decreased from 1.0 to 0.75, his respiratory rate from 64 breaths/minute to 50 breaths/minute and carbon dioxide from 58 mmHg to 44 mmHg.</p> <p>Conclusion</p> <p>Noninvasive positive pressure ventilation may be a novel therapeutic option for established severe bronchopulmonary dysplasia. In the case presented, noninvasive positive pressure ventilation achieved sustained improvement in ventilation and thus prepared our patient for safe home oxygen therapy.</p

The frequency of osteogenic activities and the pattern of intermittence between periods of physical activity and sedentary behaviour affects bone mineral content: the cross-sectional NHANES study

BACKGROUND: Sedentary behaviours, defined as non exercising seated activities, have been shown to have deleterious effects on health. It has been hypothesised that too much sitting time can have a detrimental effect on bone health in youth. The aim of this study is to test this hypothesis by exploring the association between objectively measured volume and patterns of time spent in sedentary behaviours, time spent in specific screen-based sedentary pursuits and bone mineral content (BMC) accrual in youth. METHODS: NHANES 2005–2006 cycle data includes BMC of the femoral and spinal region via dual-energy X-ray absorptiometry (DEXA), assessment of physical activity and sedentary behaviour patterns through accelerometry, self reported time spent in screen based pursuits (watching TV and using a computer), and frequency of vigorous playtime and strengthening activities. Multiple regression analysis, stratified by gender was performed on N = 671 males and N = 677 females aged from 8 to 22 years. RESULTS: Time spent in screen-based sedentary behaviours is negatively associated with femoral BMC (males and females) and spinal BMC (females only) after correction for time spent in moderate and vigorous activity. Regression coefficients indicate that an additional hour per day of screen-based sitting corresponds to a difference of −0.77 g femoral BMC in females [95% CI: -1.31 to −0.22] and of −0.45 g femoral BMC in males [95% CI: -0.83 to −0.06]. This association is attenuated when self-reported engagement in regular (average 5 times per week) strengthening exercise (for males) and vigorous playing (for both males and females) is taken into account. Total sitting time and non screen-based sitting do not appear to have a negative association with BMC, whereas screen based sedentary time does. Patterns of intermittence between periods of sitting and moderate to vigorous activity appears to be positively associated with bone health when activity is clustered in time and inter-spaced with long continuous bouts of sitting. CONCLUSIONS: Some specific sedentary pursuits (screen-based) are negatively associated with bone health in youth. This association is specific to gender and anatomical area. This relationship between screen-based time and bone health is independent of the total amount of physical activity measured objectively, but not independent of self-reported frequency of strengthening and vigorous play activities. The data clearly suggests that the frequency, rather than the volume, of osteogenic activities is important in counteracting the effect of sedentary behaviour on bone health. The pattern of intermittence between sedentary periods and activity also plays a role in bone accrual, with clustered short bouts of activity interspaced with long periods of sedentary behaviours appearing to be more beneficial than activities more evenly spread in time

Metabolomic, transcriptomic and genetic integrative analysis reveals important roles of adenosine diphosphate in haemostasis and platelet activation in non-small-cell lung cancer

Lung cancer is the leading cause of cancer‐related deaths in the world. The most prevalent subtype, accounting for 85% of cases, is non‐small‐cell lung cancer (NSCLC). Lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) are the most common subtypes. Despite recent advances in treatment, the low 5‐year survival rate of NSCLC patients (approximately 13%) reflects the lack of early diagnostic biomarkers and incomplete understanding of the underlying disease mechanisms. We hypothesized that integration of metabolomic, transcriptomic and genetic profiles of tumours and matched normal tissues could help to identify important factors and potential therapeutic targets that contribute to tumorigenesis. We integrated omics profiles in tumours and matched adjacent normal tissues of patients with LUSC (N = 20) and LUAD (N = 17) using multiple system biology approaches. We confirmed the presence of previously described metabolic pathways in NSCLC, particularly those mediating the Warburg effect. In addition, through our combined omics analyses we found that metabolites and genes that contribute to haemostasis, angiogenesis, platelet activation and cell proliferation were predominant in both subtypes of NSCLC. The important roles of adenosine diphosphate in promoting cancer metastasis through platelet activation and angiogenesis suggest this metabolite could be a potential therapeutic target

Collagenous microstructure of the glenoid labrum and biceps anchor.

Submitted versio

Risk Factors, Clinical Features, and Polygenic Risk Scores in Schizophrenia and Schizoaffective Disorder Depressive-Type

There is controversy about the status of schizoaffective disorder depressive-type (SA-D), particularly whether it should be considered a form of schizophrenia or a distinct disorder. We aimed to determine whether individuals with SA-D differ from individuals with schizophrenia in terms of demographic, premorbid, and lifetime clinical characteristics, and genetic liability to schizophrenia, depression, and bipolar disorder. Participants were from the CardiffCOGS sample and met ICD-10 criteria for schizophrenia (n = 713) or SA-D (n = 151). Two samples, Cardiff Affected-sib (n = 354) and Cardiff F-series (n = 524), were used for replication. For all samples, phenotypic data were ascertained through structured interview, review of medical records, and an ICD-10 diagnosis made by trained researchers. Univariable and multivariable logistic regression models were used to compare individuals with schizophrenia and SA-D for demographic and clinical characteristics, and polygenic risk scores (PRS). In the CardiffCOGS, SA-D, compared to schizophrenia, was associated with female sex, childhood abuse, history of alcohol dependence, higher functioning Global Assessment Scale (GAS) score in worst episode of psychosis, lower functioning GAS score in worst episode of depression, and reduced lifetime severity of disorganized symptoms. Individuals with SA-D had higher depression PRS compared to those with schizophrenia. PRS for schizophrenia and bipolar disorder did not significantly differ between SA-D and schizophrenia. Compared to individuals with schizophrenia, individuals with SA-D had higher rates of environmental and genetic risk factors for depression and a similar genetic liability to schizophrenia. These findings are consistent with SA-D being a sub-type of schizophrenia resulting from elevated liability to both schizophrenia and depression