Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences.

MOTIVATION: Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), which has a strain- or lineage-based clonal population structure. The evolution of drug-resistance in the MTBC poses a threat to successful treatment and eradication of TB. Machine learning approaches are being increasingly adopted to predict drug-resistance and characterize underlying mutations from whole genome sequences. However, such approaches may not generalize well in clinical practice due to confounding from the population structure of the MTBC. RESULTS: To investigate how population structure affects machine learning prediction, we compared three different approaches to reduce lineage dependency in random forest (RF) models, including stratification, feature selection, and feature weighted models. All RF models achieved moderate-high performance (area under the ROC curve range: 0.60-0.98). First-line drugs had higher performance than second-line drugs, but it varied depending on the lineages in the training dataset. Lineage-specific models generally had higher sensitivity than global models which may be underpinned by strain-specific drug-resistance mutations or sampling effects. The application of feature weights and feature selection approaches reduced lineage dependency in the model and had comparable performance to unweighted RF models. AVAILABILITY AND IMPLEMENTATION: https://github.com/NinaMercedes/RF_lineages.

Acuminatums E and F, two new cyclic lipopeptides from Fusarium lateritium HU0053 and their antifungal activity.

Two new cyclic lipopeptides, acuminatums E (1) and F (2), together with four known cyclic lipopeptides, acuminatums A-D (3-6) were isolated from the corn culture of endophytic Fusarium lateritium HU0053. Their structures were elucidated by spectroscopic and advanced Marfey's amino acid analysis. All compounds were found to exhibit antifungal activities against Penicillium digitatum. Acuminatum F (2), a new cyclic lipopeptide containing an unusual 3, 4-dihydroxy-phenylalanine unit exhibited the strongest antifungal activities with inhibition zone of 6.5 mm at the dose of 6.25 µg. Therefore, acuminatum F might be a potential environmental-friendly preservative for citrus fruits.

Multi-Level Transformer-Based Social Relation Recognition.

Social relationships refer to the connections that exist between people and indicate how people interact in society. The effective recognition of social relationships is conducive to further understanding human behavioral patterns and thus can be vital for more complex social intelligent systems, such as interactive robots and health self-management systems. The existing works about social relation recognition (SRR) focus on extracting features on different scales but lack a comprehensive mechanism to orchestrate various features which show different degrees of importance. In this paper, we propose a new SRR framework, namely Multi-level Transformer-Based Social Relation Recognition (MT-SRR), for better orchestrating features on different scales. Specifically, a vision transformer (ViT) is firstly employed as a feature extraction module for its advantage in exploiting global features. An intra-relation transformer (Intra-TRM) is then introduced to dynamically fuse the extracted features to generate more rational social relation representations. Next, an inter-relation transformer (Inter-TRM) is adopted to further enhance the social relation representations by attentionally utilizing the logical constraints among relationships. In addition, a new margin related to inter-class similarity and a sample number are added to alleviate the challenges of a data imbalance. Extensive experiments demonstrate that MT-SRR can better fuse features on different scales as well as ameliorate the bad effect caused by a data imbalance. The results on the benchmark datasets show that our proposed model outperforms the state-of-the-art methods with significant improvement.

Longitudinal clinical trajectory analysis of individuals before and after diagnosis of Type 2 Diabetes Mellitus (T2DM) indicates that vascular problems start early.

INTRODUCTION: Type 2 diabetes mellitus (T2DM) frequently associates with increasing multi-morbidity/treatment complexity. Some headway has been made to identify genetic and non-genetic risk factors for T2DM. However, longitudinal clinical histories of individuals both before and after diagnosis of T2DM are likely to provide additional insight into both diabetes aetiology/further complex trajectory of multi-morbidity. METHODS: This study utilised diabetes patients/controls enrolled in the DARE (Diabetes Alliance for Research in England) study where pre- and post-T2DM diagnosis longitudinal data was available for trajectory analysis. Longitudinal data of 281 individuals (T2DM n = 237 vs matched non-T2DM controls n = 44) were extracted, checked for errors and logical inconsistencies and then subjected to Trajectory Analysis over a period of up to 70 years based on calculations of the proportions of most prominent clinical conditions for each year. RESULTS: For individuals who eventually had a diagnosis of T2DM made, a number of clinical phenotypes were seen to increase consistently in the years leading up to diagnosis of T2DM. Of these documented phenotypes, the most striking were diagnosed hypertension (more than in the control group) and asthma. This trajectory over time was much less dramatic in the matched control group. Immediately prior to T2DM diagnosis, a greater indication of ischaemic heart disease proportions was observed. Post-T2DM diagnosis, the proportions of T2DM patients exhibiting hypertension and infection continued to climb rapidly before plateauing. Ischaemic heart disease continued to increase in this group as well as retinopathy, impaired renal function and heart failure. CONCLUSION: These observations provide an intriguing and novel insight into the onset and natural progression of T2DM. They suggest an early phase of potentially related disease activity well before any clinical diagnosis of diabetes is made. Further studies on a larger cohort of DARE patients are underway to explore the utility of establishing predictive risk scores.

Explainable statistical learning in public health for policy development: the case of real-world suicide data.

BACKGROUND: In recent years, the availability of publicly available data related to public health has significantly increased. These data have substantial potential to develop public health policy; however, this requires meaningful and insightful analysis. Our aim is to demonstrate how data analysis techniques can be used to address the issues of data reduction, prediction and explanation using online available public health data, in order to provide a sound basis for informing public health policy. METHODS: Observational suicide prevention data were analysed from an existing online United Kingdom national public health database. Multi-collinearity analysis and principal-component analysis were used to reduce correlated data, followed by regression analyses for prediction and explanation of suicide. RESULTS: Multi-collinearity analysis was effective in reducing the indicator set of predictors by 30% and principal component analysis further reduced the set by 86%. Regression for prediction identified four significant indicator predictors of suicide behaviour (emergency hospital admissions for intentional self-harm, children leaving care, statutory homelessness and self-reported well-being/low happiness) and two main component predictors (relatedness dysfunction, and behavioural problems and mental illness). Regression for explanation identified significant moderation of a well-being predictor (low happiness) of suicide behaviour by a social factor (living alone), thereby supporting existing theory and providing insight beyond the results of regression for prediction. Two independent predictors capturing relatedness needs in social care service delivery were also identified. CONCLUSIONS: We demonstrate the effectiveness of regression techniques in the analysis of online public health data. Regression analysis for prediction and explanation can both be appropriate for public health data analysis for a better understanding of public health outcomes. It is therefore essential to clarify the aim of the analysis (prediction accuracy or theory development) as a basis for choosing the most appropriate model. We apply these techniques to the analysis of suicide data; however, we argue that the analysis presented in this study should be applied to datasets across public health in order to improve the quality of health policy recommendations.

Utility of colon leakage score in left-sided colorectal surgery.

BACKGROUND: The aim of the study was to evaluate the clinical utility of the colon leakage score (CLS) in predicting the risk of anastomotic leakage (AL) after left-sided colorectal surgery. MATERIALS AND METHODS: This investigation was designed as a retrospective study of 304 patients who underwent left-sided colorectal surgery. The patients were classified into two groups as those who developed AL and those who did not develop AL, and the CLSs of the two groups were compared. The predictive value and the cutoff value of the CLS were assessed by receiver operating characteristic and logistic regression analysis. RESULTS: A significant difference was noted in the mean CLSs of the groups with and without AL (P < 0.001). The values of the area under the receiver operating characteristic curve (0.965; confidence interval, 0.913-1.00) and the odds ratio (2.9; confidence interval, 1.59-4.83; P < 0.001) indicated that CLS was a good predictor of AL. A CLS of 11 was found to be the best cutoff value, with a sensitivity and specificity of 84.6% and 87.2%, respectively. CONCLUSIONS: Our findings indicate that CLS can effectively predict the risk of AL after left-sided colorectal surgery and that a CLS of 11 can be used as a cutoff value for the risk level.

The Role of Maternal Gestational Diabetes in Inducing Fetal Endothelial Dysfunction.

Gestational diabetes mellitus (GDM) is known to be associated with fetal endothelial dysfunction, however, the mechanisms are not fully understood. This study examines the effect of maternal diabetes on fetal endothelial function and gene expression under physiological glucose conditions (5 mM). Human umbilical vein endothelial cell (HUVEC) isolated from diabetic mothers (d.HUVEC) grew more slowly than HUVEC isolated from healthy mothers (c.HUVEC) and had delayed doubling time despite increased levels of total vascular endothelial growth factor (VEGF) expression and protein production as determined by real-time PCR and ELISA respectively. Using western blot, the levels of antiproliferative VEGF165b isoform were increased in d.HUVEC relative to c.HUVEC. Successful VEGF165b knockdown by small interfering RNA (siRNA) resulted in increased proliferation of d.HUVEC measured by MTT, compared with negative siRNA control, to similar levels measured in c.HUVEC. In addition, d.HUVEC generated excess levels of ROS as revealed by 2',7' Dichlorodihydrofluorescein Diacetate (DCFH-DA) and Nitrotetrazolium blue (NBT). Using microarray, 102 genes were differentially overexpressed between d.HUVEC versus c.HUVEC (>1.5-fold change; P < 0.05). Functional clustering analysis of these differentially expressed genes revealed participation in inflammatory responses (including adhesion) which may be related to pathological outcomes. Of these genes, ICAM-1 was validated as upregulated, confirming microarray results. Additional confirmatory immunofluorescence staining revealed increased protein expression of ICAM-1 compared with c.HUVEC which was reduced by vitamin C treatment (100 µM). Thus, maternal diabetes induces persistent alterations in fetal endothelial function and gene expression following glucose normalization and antioxidant treatment could help reverse endothelium dysfunction.

[Chemical constituents from Canarium pimela fruits].

OBJECTIVE: To investigate the chemical constituents from Canarium pimela fruits. METHODS: Compounds were obtained after separation and purification by silica gel and Sephadex LH-20. The structures were identified on the basis of physico-chemical properties and spectrum data. RESULTS: Eight compounds were isolated from Canarium pimela fruits. The structures were identified as amentoflavone (1), kaempferol-3-O-ß-D-galactopyranoside (2), shikimic acid (3), quercetin (4), kaempferol (5), 3,3'-di-O-methylellagic acid (6), 3,3',4-tri-O-methylellagic acid (7) and stigmasterol (8). CONCLUSION: Compounds 1-8 are isolated from Canarium pimela fruits for the first time.

Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, has a significant impact on global health worldwide. The development of multi-drug resistant strains that are resistant to the first-line drugs isoniazid and rifampicin threatens public health security. Rifampicin and isoniazid resistance are largely underpinned by mutations in rpoB and katG respectively and are associated with fitness costs. Compensatory mutations are considered to alleviate these fitness costs and have been observed in rpoC/rpoA (rifampicin) and oxyR'-ahpC (isoniazid). We developed a framework (CompMut-TB) to detect compensatory mutations from whole genome sequences from a large dataset comprised of 18,396 M. tuberculosis samples. We performed association analysis (Fisher's exact tests) to identify pairs of mutations that are associated with drug-resistance, followed by mediation analysis to identify complementary or full mediators of drug-resistance. The analyses revealed several potential mutations in rpoC (N = 47), rpoA (N = 4), and oxyR'-ahpC (N = 7) that were considered either 'highly likely' or 'likely' to confer compensatory effects on drug-resistance, including mutations that have previously been reported and validated. Overall, we have developed the CompMut-TB framework which can assist with identifying compensatory mutations which is important for more precise genome-based profiling of drug-resistant TB strains and to further understanding of the evolutionary mechanisms that underpin drug-resistance.

Differential cytotoxicity to human cells in vitro of tire wear particles emitted from typical road friction patterns: The dominant role of environmental persistent free radicals.

Tire wear particles (TWPs) have been recognized as one of the major sources of microplastics (MPs), however, effects of initial properties and photochemical behavior of TWPs on cytotoxicity to human cells in vitro have not been reported. Therefore, here, three TWPs generated from typical wear of tires and pavements (i.e., rolling friction (R-TWPs) and sliding friction (S-TWPs)) and cryogenically milled tire tread (C-TWPs), respectively, and their photoaging counterparts were used to study the reasons for their differential cytotoxicity to 16HBE cells in vitro. Results showed in addition to changes of surface structure and morphology, different preparation methods could also induce formation of different concentration levels of environmental persistent free radicals (EPFRs) (from 1.24 to 3.06 × 1017 spins/g with g-factors ranging 2.00307-2.00310) on surfaces of TWPs, which contained 7.3%-65.8% of reactive EPFRs (r-EPFRs). Meanwhile, photoaging for 90 d could strengthen formation of EPFRs (from 4.03 to 4.61 × 1017 spins/g) with containing 74.7%-78.1% r-EPFRs on surfaces of TWPs and improve their g-factor indexes (ranging 2.00309-2.00313). At 100 µg mL-1 level, compared to C-TWPs, both R-TWPs and S-TWPs (whether photoaging or not) carried higher intensity EPFRs could significantly inhibit 16HBE cells proliferation activity, cause more cells oxidative stress and induce more cell apoptosis/necrosis and secretion of inflammatory factor (P < 0.05). However, regardless of how TWPs were prepared, photoaged or not, exposure at a concentration of 1 µg mL-1 appeared to be non-acute cytotoxic. Correlation analysis suggested dominant toxicity of TWPs was attributed to the formation of r-EPFRs on their surfaces, which could promote accumulation of excess reactive oxygen species in cells and the massive deposition of intracellular particles. This study provides direct evidence of TWPs cytotoxicity, and underlining the need for a better understanding of the influences of initial properties and photochemical characteristics on risk assessment of TWPs released into the environment.

COVID-19 Vaccination and Diabetes Mellitus: How Much Has It Made a Difference to Outcomes Following Confirmed COVID-19 Infection?

INTRODUCTION: Since early 2020 the whole world has been challenged by the SARS-CoV-2 virus (COVID-19), its successive variants and the associated pandemic caused. We have previously shown that for people living with type 2 diabetes (T2DM), the risk of being admitted to hospital or dying following a COVID-19 infection progressively decreased through the first months of 2021. In this subsequent analysis we have examined how the UK COVID-19 vaccination programme impacted differentially on COVID-19 outcomes in people with T1DM or T2DM compared to appropriate controls. METHODS: T1DM and T2DM affected individuals were compared with their matched controls on 3:1 ratio basis. A 28-day hospital admission or mortality was used as the binary outcome variable with diabetes status and vaccination for COVID-19 as the main exposure variables. RESULTS: A higher proportion of T1DM individuals vs their controls was found to be vaccinated at the point of their first recorded positive COVID-19 test when compared to T2DM individuals vs their controls. Regarding the 28-day hospital admission rate, there was a greater and increasing protective effect of subsequent vaccination dosage (one, two or three) in mitigating the effects of COVID-19 infection versus no vaccination in T1DM than in T2DM individuals when compared with matched controls. Similar effects were observed in T2DM for death. Across both diabetes and non-diabetes individuals, those at greater socio-economic disadvantage were more likely to test positive for COVID-19 in the early phase of the pandemic. For T2DM individuals socio-economic disadvantage was associated with a greater likelihood of hospital admission and death, independent of vaccination status. Age and male sex were also independently associated with 28-day hospital admission in T2DM and to 28-day mortality, independent of vaccination status. African ethnicity was also an additional factor for hospital admission in people with T2DM. CONCLUSION: A beneficial effect of COVID-19 vaccination was seen in mitigating the harmful effects of COVID-19 infection; this was manifest in reduced hospital admission rate in T1DM individuals with a lesser effect in T2DM when compared with matched controls, regarding both hospital admission and mortality. Socio-economic disadvantage influenced likelihood of COVID-19 confirmed infection and the likelihood of hospital admission/death independent of the number of vaccinations given in T2DM.

Effect of natural gums on pasting, rheological, structural and hydrolysis properties of kudzu starch.

Hydrocolloids have been widely used to adjust properties of natural starches, but related research on kudzu starch is still rare. In this study, we investigated the effects of gum arabic (AG), sodium alginate (SA), locust bean gum (LG), and guar gum (GG) on kudzu starch from the perspective of its particle size, pasting, texture, rheology, dehydration rate, thermal properties, microstructure, and sensitivity to amyloglucosidase. Results showed that GG significantly increased the particle size of starch. Addition of AG led to lower peak-, final- and holding-viscosity. SA increased the retention viscosity of kudzu starch, while LG and GG increased its peak viscosity. Addition of hydrocolloids increased the hardness, chewiness, and cohesiveness of starch-hydrocolloid complexes, and reduced the dehydration rate of complex gels. Dynamic rheological data showed that the energy storage modulus (G') was significantly higher than the loss modulus (G″). The magnitude of modulus increased with frequency, and elastic properties were better than viscous properties. Thermal analysis showed that hydrocolloids increased the starting temperature (To), and the final temperature (Tc). With addition of each of these four hydrocolloids, a more regular and porous thick-wall dense structure was formed, which effectively lowered kudzu starch's sensitivity to amyloglucosidase. It indicated that the binding of hydrocolloid to starch may slow down glucose release into blood during digestion. These results will help understand effects of natural hydrocolloid on kudzu starch, as well as expanding its application in food industry.

A Longitudinal Clinical Trajectory Analysis Examining the Accumulation of Co-morbidity in People with Type 2 Diabetes (T2D) Compared with Non-T2D Individuals.

BACKGROUND: Type 2 diabetes mellitus (T2D) is commonly associated with an increasing complexity of multimorbidity. While some progress has been made in identifying genetic and non-genetic risk factors for T2D, understanding the longitudinal clinical history of individuals before/after T2D diagnosis may provide additional insights. METHODS: In this study, we utilised longitudinal data from the DARE (Diabetes Alliance for Research in England) study to examine the trajectory of clinical conditions in individuals with and without T2D. Data from 1932 individuals (T2D n = 1196 vs. matched non-T2D controls n = 736) were extracted and subjected to trajectory analysis over a period of up to 50 years (25 years pre-diagnosis/25 years post-diagnosis). We also analysed the cumulative proportion of people with diagnosed coronary artery disease (CAD) in their general practice (GP) record with an analysis of lower respiratory tract infection (RTI) as a comparator group. RESULTS: The mean age of diagnosis of T2D was 52.6 (95% confidence interval 52.0-53.4) years. In the years leading up to T2D diagnosis, individuals who eventually received a T2D diagnosis consistently exhibited a considerable increase in several clinical phenotypes. Additionally, immediately prior to T2D diagnosis, a significantly greater prevalence of hypertension (35%)/RTI (34%)/heart conditions (17%)/eye, nose, throat infection (19%) and asthma (12%) were observed. The corresponding trajectory of each of these conditions was much less dramatic in the matched controls. Post-T2D diagnosis, proportions of T2D individuals exhibiting hypertension/chronic kidney disease/retinopathy/infections climbed rapidly before plateauing. At the last follow-up by quintile of disadvantage, the proportion (%) of people with diagnosed CAD was 6.4% for quintile 1 (least disadvantaged) and 11% for quintile 5 (F = 3.4, p = 0.01 for the difference between quintiles). CONCLUSION: These findings provide novel insights into the onset/natural progression of T2D, suggesting an early phase of inflammation-related disease activity before any clinical diagnosis of T2D is made. Measures that reduce social inequality have the potential in the longer term to reduce the social gradient in health outcomes reported here.

Activation of Sphingomyelin Phosphodiesterase 3 in Liver Regeneration Impedes the Progression of Colorectal Cancer Liver Metastasis Via Exosome-Bound Intercellular Transfer of Ceramides.

BACKGROUND & AIMS: The machinery that prevents colorectal cancer liver metastasis (CRLM) in the context of liver regeneration (LR) remains elusive. Ceramide (CER) is a potent anti-cancer lipid involved in intercellular interaction. Here, we investigated the role of CER metabolism in mediating the interaction between hepatocytes and metastatic colorectal cancer (CRC) cells to regulate CRLM in the context of LR. METHODS: Mice were intrasplenically injected with CRC cells. LR was induced by 2/3 partial hepatectomy (PH) to mimic the CRLM in the context of LR. The alteration of corresponding CER-metabolizing genes was examined. The biological roles of CER metabolism in vitro and in vivo were examined by performing a series of functional experiments. RESULTS: Induction of LR augmented apoptosis but promoted matrix metalloproteinase 2 (MMP2) expression and epithelial-mesenchymal transition (EMT) to increase the invasiveness of metastatic CRC cells, resulting in aggressive CRLM. Up-regulation of sphingomyelin phosphodiesterase 3 (SMPD3) was determined in the regenerating hepatocytes after LR induction and persisted in the CRLM-adjacent hepatocytes after CRLM formation. Hepatic Smpd3 knockdown was found to further promote CRLM in the context of LR by abolishing mitochondrial apoptosis and augmenting the invasiveness in metastatic CRC cells by up-regulating MMP2 and EMT through promoting the nuclear translocation of ß-catenin. Mechanistically, we found that hepatic SMPD3 controlled the generation of exosomal CER in the regenerating hepatocytes and the CRLM-adjacent hepatocytes. The SMPD3-produced exosomal CER critically conducted the intercellular transfer of CER from the hepatocytes to metastatic CRC cells and impeded CRLM by inducing mitochondrial apoptosis and restricting the invasiveness in metastatic CRC cells. The administration of nanoliposomal CER was found to suppress CRLM in the context of LR substantially. CONCLUSIONS: SMPD3-produced exosomal CER constitutes a critical anti-CRLM mechanism in LR to impede CRLM, offering the promise of using CER as a therapeutic agent to prevent the recurrence of CRLM after PH.

Antifungal Mechanism of MTE-1, a Novel Oligosaccharide Ester, against Ustilaginoidea virens.

Ustilaginoidea virens is a pathogenic fungus that causes false smut disease in rice during the flowering stage through stamen filaments. Currently, there is a need to develop safe and effective antifungal agents for the control of this disease. In our preliminary experiments, we found that MTE-1, a new trisaccharide ester, exhibits significant inhibitory activity against U. virens. Hence, the effects and inhibitory mechanism of MTE-1 in U. virens were investigated. Results showed that the MTE-1 inhibited the hyphae growth of U. virens with an IC50 of 5.67 µg/mL. Similarly, MTE-1 disrupted the endomembrane system in U. virens, especially the plasma membrane, mitochondria, and lipidosome. Moreover, transcriptome and proteome analysis indicated that MTE-1 inhibited the growth of U. virens by inhibiting the synthesis of lipids, altering the primary metabolic pathways including carbohydrates and amino acid metabolism, and affecting the intracellular redox dyshomeostasis, thus leading to the disorder of active oxygen metabolism. These findings lay the foundation for the future application of MTE-1-derived agents in the management of antifungal diseases.

Effects of tire wear particles with and without photoaging on anaerobic biofilm sulfide production in sewers and related mechanisms.

Tire wear particles (TWPs) are considered to be one of the major sources of microplastics (MPs) in sewers; however, little has been reported on the surface properties and photochemical behavior of TWPs, especially in terms of their environmental persistent radicals, leachate type, and response after photoaging. It is also unknown how TWPs influence the production of common pollutants (e.g., sulfides) in anaerobic biofilms in sewers. In our study, the effects of cryogenically milled tire treads (C-TWPs) and their corresponding photoaging products (photoaging-TWPs, A-TWPs) on anaerobic biofilm sulfide production in sewers and related mechanisms were studied. The results showed that the two TWPs at a low concentration (0.1 mg L-1) exerted no significant (p > 0.05) effects on sulfide yield, whereas exposure to a high concentration of TWPs (100 mg L-1) inversely affected sulfide yield, with A-TWPs exerting a significant inhibitory effect on sulfide yield in the sewers (p < 0.01). The main reason was that A-TWPs carried higher concentrations of reactive environmental persistent radicals on their surfaces after photoaging than C-TWPs, which could induce the formation of oxygen radicals. In addition, A-TWPs were more uniformly distributed in the wastewater system and could penetrate the biofilm to damage bacterial cells, and their ability to leach polycyclic aromatic hydrocarbons and heavy metals such as zinc additives enhanced their toxic effects. In contrast, C-TWPs contributed significantly to sulfide production (p < 0.01), primarily because of their low biotoxicity, ability to leach a considerable amount of sulfide, and stimulatory effect on anaerobic biofilm surface sulfate-reducing bacteria. Our study complements the toxicity studies of the TWPs particles themselves and provides insight on a new influencing factor for determining the changes in sulfide generation and control measures in sewers.

The Risk Factors Potentially Influencing Hospital Admission in People with Diabetes, Following SARS-CoV-2 Infection: A Population-Level Analysis.

INTRODUCTION: Since early 2020 the whole world has been challenged by the SARS-CoV-2 virus and the associated global pandemic (Covid-19). People with diabetes are particularly at high risk of becoming seriously unwell after contracting this virus. METHODS: This population-based study included people living in the Greater Manchester conurbation who had a recorded diagnosis of type 1 diabetes mellitus (T1DM) or type 2 diabetes mellitus (T2DM) and subsequent Covid-19 infection. Each individual with T1DM (n = 862) or T2DM (n = 13,225) was matched with three Covid-19-infected non-diabetes controls. RESULTS: For individuals with T1DM, hospital admission rate in the first 28 days after a positive Covid-19 test was 10% vs 4.7% in age/gender-matched controls [relative risk (RR) 2.1]. For individuals with T2DM, hospital admission rate after a positive Covid-19 test was 16.3% vs 11.6% in age/gender-matched controls (RR 1.4). The average Townsend score was higher in T2DM (1.8) vs matched controls (0.4), with a higher proportion of people with T2DM observed in the top two quintiles of greatest disadvantage (p < 0.001). For Covid-19-infected individuals with T1DM, factors influencing admission likelihood included age, body mass index (BMI), hypertension, HbA1c, low HDL-cholesterol, lower estimated glomerular filtration rate (eGFR), chronic obstructive pulmonary disease (COPD) and being of African/mixed ethnicity. In Covid-19-infected individuals with T2DM, factors related to a higher admission rate included age, Townsend index, comorbidity with COPD/asthma and severe mental illness (SMI), lower eGFR. Metformin prescription lowered the likelihood. For multivariate analysis in combined individuals with T2DM/controls, factors relating to higher likelihood of admission were having T2DM/age/male gender/diagnosed COPD/diagnosed hypertension/social deprivation (higher Townsend index) and non-white ethnicity (all groups). CONCLUSION: In a UK population we have confirmed a significantly higher likelihood of admission in people with diabetes following Covid-19 infection. A number of factors mediate that increased likelihood of hospital admission. For T2DM, the majority of factors related to increased admission rate are common to the general population but more prevalent in T2DM. There was a protective effect of metformin in people with T2DM.

Mortality in People with Type 2 Diabetes Following SARS-CoV-2 Infection: A Population Level Analysis of Potential Risk Factors.

INTRODUCTION: Research is ongoing to increase our understanding of how much a previous diagnosis of type 2 diabetes mellitus (T2DM) affects someone's risk of becoming seriously unwell following a COVID-19 infection. In this study we set out to determine the relative likelihood of death following COVID-19 infection in people with T2DM when compared to those without T2DM. This was conducted as an urban population study and based in the UK. METHODS: Analysis of electronic health record data was performed relating to people living in the Greater Manchester conurbation (population 2.82 million) who had a recorded diagnosis of T2DM and subsequent COVID-19 confirmed infection. Each individual with T2DM (n = 13,807) was matched with three COVID-19-infected non-diabetes controls (n = 39,583). Data were extracted from the Greater Manchester Care Record (GMCR) database for the period 1 January 2020 to 30 June 2021. Social disadvantage was assessed through Townsend scores. Death rates were compared in people with T2DM to their respective non-diabetes controls; potential predictive factors influencing the relative likelihood of admission were ascertained using univariable and multivariable logistic regression. RESULTS: For individuals with T2DM, their mortality rate after a COVID-19 positive test was 7.7% vs 6.0% in matched controls; the relative risk (RR) of death was 1.28. From univariate analysis performed within the group of individuals with T2DM, the likelihood of death following a COVID-19 recorded infection was lower in people taking metformin, a sodium-glucose cotransporter 2 inhibitor (SGLT2i) or a glucagon-like peptide 1 (GLP-1) agonist. Estimated glomerular filtration rate (eGFR) and hypertension were associated with increased mortality and had odds ratios of 0.96 (95% confidence interval 0.96-0.97) and 1.92 (95% confidence interval 1.68-2.20), respectively. Likelihood of death following a COVID-19 infection was also higher in those people with a diagnosis of chronic obstructive pulmonary disease (COPD) or severe enduring mental illness but not with asthma, and in people taking aspirin/clopidogrel/insulin. Smoking in people with T2DM significantly increased mortality rate (odds ratio of 1.46; 95% confidence interval 1.29-1.65). In a combined analysis of patients with T2DM and controls, multiple regression modelling indicated that the factors independently relating to a higher likelihood of death (accounting for 26% of variance) were T2DM, age, male gender and social deprivation (higher Townsend score). CONCLUSION: Following confirmed infection with COVID-19 a number of factors are associated with mortality in individuals with T2DM. Prescription of metformin, SGLT2is or GLP-1 agonists and non-smoking status appeared to be associated with a reduced the risk of death for people with T2DM. Age, male sex and social disadvantage are associated with an increased risk of death.

Data-Enabled Digestive Medicine: A New Big Data Analytics Platform.

This paper presents a big data analystics platform for clinical research and practice in the Gastroenterology Department of Xiangya Hospital at Central South University in China. This platform features a comprehensive and systematic support of big data in digestive medicine including geneneral health management, clinical gastroenterology practice, and related genomics research, which is proven to be helpful in real world clinical practices. A typical use case of integrated analysis based on electronic medical records and colonoscopy data was presented and discussed, the analaystic report on risk factors of colorectal diseases shows a reasonable recommendation about the age when people should start to screen the colorectal cancer, which could be very useful to individual and group health management for the general population in China.