| 1. |
- Romagnoni, A, et al.
(author)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Journal article (peer-reviewed)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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| 2. |
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| 3. |
- Fazel, Seena, et al.
(author)
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Risk of death by suicide following self-harm presentations to healthcare : development and validation of a multivariable clinical prediction rule (OxSATS)
- 2023
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In: BMJ Mental Health. - : BMJ Publishing Group Ltd. - 2755-9734. ; 26:1
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Journal article (peer-reviewed)abstract
- BACKGROUND: Assessment of suicide risk in individuals who have self-harmed is common in emergency departments, but is often based on tools developed for other purposes. OBJECTIVE: We developed and validated a predictive model for suicide following self-harm.METHODS: We used data from Swedish population-based registers. A cohort of 53 172 individuals aged 10+ years, with healthcare episodes of self-harm, was split into development (37 523 individuals, of whom 391 died from suicide within 12 months) and validation (15 649 individuals, 178 suicides within 12 months) samples. We fitted a multivariable accelerated failure time model for the association between risk factors and time to suicide. The final model contains 11 factors: age, sex, and variables related to substance misuse, mental health and treatment, and history of self-harm. Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis guidelines were followed for the design and reporting of this work.FINDINGS: An 11-item risk model to predict suicide was developed using sociodemographic and clinical risk factors, and showed good discrimination (c-index 0.77, 95% CI 0.75 to 0.78) and calibration in external validation. For risk of suicide within 12 months, using a 1% cut-off, sensitivity was 82% (75% to 87%) and specificity was 54% (53% to 55%). A web-based risk calculator is available (Oxford Suicide Assessment Tool for Self-harm or OxSATS).CONCLUSIONS: OxSATS accurately predicts 12-month risk of suicide. Further validations and linkage to effective interventions are required to examine clinical utility.CLINICAL IMPLICATIONS: Using a clinical prediction score may assist clinical decision-making and resource allocation.
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| 4. |
- Hardell, Lennart, et al.
(author)
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Secret ties to industry and conflicting interests in cancer research
- 2007
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In: American Journal of Industrial Medicine. - : Wiley-Liss Inc.. - 0271-3586 .- 1097-0274. ; 50:3, s. 227-233
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Research review (peer-reviewed)abstract
- Background: Recently it was reported that a Swedish professor in environmental health has for decades worked as a consultant for Philip Morris without reporting his employment to his academic employer or declaring conflicts of interest in his research. The potential for distorting the epidemiological assessments of hazard and risk through paid consultants, pretending to be independent, is not exclusive to the tobacco industry.Methods: Documentation is drawn from peer reviewed publications, websites, documents from the Environmental Protection Agency, University reports, Wellcome Library Special Collections and the Washington Post.Results: Some consulting firms employ university researchers for industry work thereby disguising industry links in the income of large departments. If the industry affiliation is concealed by the scientist, biases from conflicting interests in risk assessments cannot be evaluated and dealt with properly. Furthermore, there is reason to suspect that editors and journal staff may suppress publication of scientific results that are adverse to industry owing to internal conflict of interest between editorial integrity and business needs.Conclusions: Examples of these problems from Sweden, UK, and USA are presented. The shortfalls cited in this article illustrate the need for improved transparency, regulations that will help curb abuses as well as instruments for control and enforcement against abuses.
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| 5. |
- Humes, D. J., et al.
(author)
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Duration and magnitude of postoperative risk of venous thromboembolism after planned inguinal hernia repair in men : a population-based cohort study
- 2018
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In: Hernia. - : Springer. - 1265-4906 .- 1248-9204. ; 22:3, s. 447-453
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Journal article (peer-reviewed)abstract
- Purpose: Little is known regarding the magnitude and timing of the risk of VTE following inguinal hernia surgery. We aimed to determine the absolute and relative rates of venous thromboembolism (VTE) following planned inguinal hernia repair.Methods: We analysed male adults with a first inguinal hernia repair with no prior record of VTE from the Clinical Practice Research Datalink, linked to the Hospital Episode Statistics (2001-2011). Crude rates and adjusted hazard ratios (HR) of the first VTE were calculated using Cox regression analysis to compare specific time periods following the surgery compared to the general population.Results: We identified 28,782 men who underwent an inguinal hernia repair with 53 (0.18%) having a first VTE in the 90 days following surgery. The overall rate of VTE in the first 90 days following surgery was 7.61 per 1000 person years (pyrs) (95% CI 5.82-9.96). Increasing age, a body mass index > 30 kg/m(2) and an in-patient procedure were associated with an increased risk of VTE, when compared to the general population. The risk of VTE was highest in the 1st month following the surgery with a 2.3- (aHR 2.33; 95% CI 1.09-4.99) and 3.5- (aHR 3.47; 95% CI 2.07-5.83) fold increased risk compared to the general population for both day case and planned in-patient procedures, respectively.Conclusions: Reassuringly, the absolute rates of VTE following inguinal hernia repair are low. Patients should be informed that their peak risk of VTE is during the 1st month following the surgery. Further studies on the optimum duration of thromboprophylaxis following surgery are required in high-risk patients undergoing hernia repair.
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| 6. |
- Humes, D. J., et al.
(author)
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Risk of symptomatic venous thromboembolism following emergency appendicectomy in adults
- 2016
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In: British Journal of Surgery. - West, Sussex, United Kingdom : John Wiley & Sons. - 0007-1323 .- 1365-2168. ; 103:4, s. 443-450
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Journal article (peer-reviewed)abstract
- Background: Appendicectomy is the commonest intra-abdominal emergency surgical procedure, and little is known regarding the magnitude and timing of the risk of venous thromboembolism (VTE) after surgery. This study aimed to determine absolute and relative rates of symptomatic VTE following emergency appendicectomy.Methods: A cohort study was undertaken using linked primary (Clinical Practice Research Datalink) and secondary (Hospital Episode Statistics) care data of patients who had undergone emergency appendicectomy from 2001 to 2011. Crude rates and adjusted incidence rate ratios (IRRs) for VTE were calculated using Poisson regression, compared with baseline risk in the year before appendicectomy.Results: A total of 13 441 patients were identified, of whom 56 (0·4 per cent) had a VTE in the first year after surgery. The absolute rate of VTE was highest during the in-hospital period, with a rate of 91·29 per 1000 person-years, which was greatest in those with a length of stay of 7 days or more (267·12 per 1000 person-years). This risk remained high after discharge, with a 19·1- and 6·6-fold increased risk of VTE in the first and second months respectively after discharge, compared with the year before appendicectomy (adjusted IRR: month 1, 19·09 (95 per cent c.i. 9·56 to 38·12); month 2, 6·56 (2·62 to 16·44)).Conclusion: The risk of symptomatic VTE following appendicectomy is relatively high during the in-hospital admission and remains increased after discharge. Trials of extended thromboprophylaxis are warranted in patients at particularly high risk.
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| 7. |
- Karpyak, Victor M., et al.
(author)
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Association of the PDYN gene with alcohol dependence and the propensity to drink in negative emotional states
- 2013
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In: International Journal of Neuropsychopharmacology. - : Oxford University Press. - 1461-1457 .- 1469-5111. ; 16:5, s. 975-985
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Journal article (peer-reviewed)abstract
- Synthetic κ-opioid receptor (KOR) agonists induce dysphoric and pro-depressive effects and variations in the KOR (OPRK1) and prodynorphin (PDYN) genes have been shown to be associated with alcohol dependence. We genotyped 23 single nucleotide polymorphisms (SNPs) in the PDYN and OPRK1 genes in 816 alcohol-dependent subjects and investigated their association with: (1) negative craving measured by a subscale of the Inventory of Drug Taking Situations; (2) a self-reported history of depression; (3) the intensity of depressive symptoms measured by the Beck Depression Inventory-II. In addition, 13 of the 23 PDYN and OPRK1 SNPs, which were previously genotyped in a set of 1248 controls, were used to evaluate association with alcohol dependence. SNP and haplotype tests of association were performed. Analysis of a haplotype spanning the PDYN gene (rs6045784, rs910080, rs2235751, rs2281285) revealed significant association with alcohol dependence (p = 0.00079) and with negative craving (p = 0.0499). A candidate haplotype containing the PDYN rs2281285-rs1997794 SNPs that was previously associated with alcohol dependence was also associated with negative craving (p = 0.024) and alcohol dependence (p = 0.0008) in this study. A trend for association between depression severity and PDYN variation was detected. No associations of OPRK1 gene variation with alcohol dependence or other studied phenotypes were found. These findings support the hypothesis that sequence variation in the PDYN gene contributes to both alcohol dependence and the induction of negative craving in alcohol-dependent subjects.
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| 8. |
- Koelmel, Jeremy P., et al.
(author)
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An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry
- 2022
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In: Exposome. - : Oxford University Press. - 2635-2265 .- 2635-2265. ; 2:1
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Journal article (peer-reviewed)abstract
- Omics-based technologies have enabled comprehensive characterization of our exposure to environmental chemicals (chemical exposome) as well as assessment of the corresponding biological responses at the molecular level (eg, metabolome, lipidome, proteome, and genome). By systematically measuring personal exposures and linking these stimuli to biological perturbations, researchers can determine specific chemical exposures of concern, identify mechanisms and biomarkers of toxicity, and design interventions to reduce exposures. However, further advancement of metabolomics and exposomics approaches is limited by a lack of standardization and approaches for assigning confidence to chemical annotations. While a wealth of chemical data is generated by gas chromatography high-resolution mass spectrometry (GC-HRMS), incorporating GC-HRMS data into an annotation framework and communicating confidence in these assignments is challenging. It is essential to be able to compare chemical data for exposomics studies across platforms to build upon prior knowledge and advance the technology. Here, we discuss the major pieces of evidence provided by common GC-HRMS workflows, including retention time and retention index, electron ionization, positive chemical ionization, electron capture negative ionization, and atmospheric pressure chemical ionization spectral matching, molecular ion, accurate mass, isotopic patterns, database occurrence, and occurrence in blanks. We then provide a qualitative framework for incorporating these various lines of evidence for communicating confidence in GC-HRMS data by adapting the Schymanski scoring schema developed for reporting confidence levels by liquid chromatography HRMS (LC-HRMS). Validation of our framework is presented using standards spiked in plasma, and confident annotations in outdoor and indoor air samples, showing a false-positive rate of 12% for suspect screening for chemical identifications assigned as Level 2 (when structurally similar isomers are not considered false positives). This framework is easily adaptable to various workflows and provides a concise means to communicate confidence in annotations. Further validation, refinements, and adoption of this framework will ideally lead to harmonization across the field, helping to improve the quality and interpretability of compound annotations obtained in GC-HRMS.
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| 10. |
- Rask, Eva, 1958-, et al.
(author)
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Tissue-specific dysregulation of cortisol metabolism in human obesity
- 2001
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In: Journal of Clinical Endocrinology and Metabolism. - : Williams & Wilkins Co.. - 0021-972X .- 1945-7197. ; 86:3, s. 1418-1421
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Journal article (peer-reviewed)abstract
- Cortisol has been implicated as a pathophysiological mediator in idiopathic obesity, but circulating cortisol concentrations are not consistently elevated. The tissue-specific responses to cortisol may be influenced as much by local pre-receptor metabolism as by circulating concentrations. For example, in liver and adipose tissue cortisol is regenerated from inactive cortisone by 11 beta -hydroxysteroid dehydrogenase type 1 (11 beta -HSD1). In obese Zucker rats 11 beta -HSD1 activity is reduced in liver but enhanced in adipose tissue. This study addressed whether the same tissue-specific disruption of cortisol metabolism occurs in human obesity. 34 men were recruited from the MONICA population study in Northern Sweden to represent a wide range of body composition and insulin sensitivity. Plasma cortisol was measured at 0830h and 1230h, after overnight low-dose dexamethasone suppression, after intravenous corticotropin releasing hormone (CRH), and after oral cortisone administration. Urinary cortisol metabolites were measured in a 24 h sample. A subcutaneous fat biopsy was obtained from le participants to measure cortisol metabolism in vitro. Higher body mass index was associated with increased total cortisol metabolite excretion (r=0.47, p<0.01), but lower plasma cortisol at 1230 h and after dexamethasone, and no difference in response to CRH. Obese men excreted a greater proportion of glucocorticoid as metabolites of cortisone rather than cortisol (r=0.43, p<0.02), and converted less cortisone to cortisol after oral administration (r=-0.49, p<0.01), suggesting impaired hepatic 11-HSD1 activity. By contrast, in vitro 11 beta -HSD1 activity in subcutaneous adipose tissue was markedly enhanced in obese men (r=0.66, p<0.01). We conclude that in obesity, reactivation of cortisone to cortisol by 11-HSD1 in liver is impaired, so that plasma cortisol levels tend to fall, and there may be a compensatory increase in cortisol secretion mediated by a normally functioning hypothalamic-pituitary-adrenal axis. However, changes in 11 beta -HSD1 are tissue-specific: strikingly enhanced reactivation of cortisone to cortisol in subcutaneous adipose tissue may exacerbate obesity; and it may be beneficial to inhibit this enzyme in adipose tissue in obese patients.
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