scholarly journals KMplot.com: a survival analysis tool tailored for medical research (Preprint)

2021 ◽  
Author(s):  
András Lánczky ◽  
Balázs Győrffy
Keyword(s):  
Survival Analysis ◽  
Medical Research ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Multiple Hypothesis Testing ◽  
Analysis Tool ◽  
Web Based ◽  
False Discovery ◽  
Using Data ◽  
Basic Medical

UNSTRUCTURED Survival analysis is a cornerstone of medical research enabling the assessment of clinical outcome for disease progression and treatment efficiency. Despite its central importance, neither commonly used spreadsheet software can handle it nor is there a web server for its computation. Here we introduce a web-based tool capable to perform uni- and multivariate Cox proportional hazards survival analysis using data generated by genomic, transcriptomic, proteomic, or metabolomics studies. We implemented different methods to establish cutoff values for trichotomization or for the dichotomization of continuous data. False discovery rate is computed to correct for multiple hypothesis testing. Multivariate analysis option enables comparing omics data with clinical variables. The registration-free web-service is available at https://kmplot.com/custom_data. The tool fills a gap and will be an invaluable help for basic medical and clinical research.

scholarly journals Adapting the Default Weighted Survival Analysis Modelling Approach to Model IFRS 9 LGD

Risks ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 103
Author(s):  
Morne Joubert ◽  
Tanja Verster ◽  
Helgard Raubenheimer ◽  
Willem D. Schutte
Keyword(s):  
Survival Analysis ◽  
Financial Reporting ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Survival Curve ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Reporting Standard ◽  
International Financial Reporting Standard ◽  
Ifrs 9

Survival analysis is one of the techniques that could be used to predict loss given default (LGD) for regulatory capital (Basel) purposes. When using survival analysis to model LGD, a proposed methodology is the default weighted survival analysis (DWSA) method. This paper is aimed at adapting the DWSA method (used to model Basel LGD) to estimate the LGD for International Financial Reporting Standard (IFRS) 9 impairment requirements. The DWSA methodology allows for over recoveries, default weighting and negative cashflows. For IFRS 9, this methodology should be adapted, as the estimated LGD is a function of in the expected credit losses (ECL). Our proposed IFRS 9 LGD methodology makes use of survival analysis to estimate the LGD. The Cox proportional hazards model allows for a baseline survival curve to be adjusted to produce survival curves for different segments of the portfolio. The forward-looking LGD values are adjusted for different macro-economic scenarios and the ECL is calculated for each scenario. These ECL values are probability weighted to produce a final ECL estimate. We illustrate our proposed IFRS 9 LGD methodology and ECL estimation on a dataset from a retail portfolio of a South African bank.

scholarly journals Dementia Adjudication Triggers Associated With Increased Mortality for Older Australians: Evidence From ASPREE

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 161-161
Author(s):  
Jane Banaszak-Holl ◽  
Xiaoping Lin ◽  
Jing Xie ◽  
Stephanie Ward ◽  
Henry Brodaty ◽  
...  
Keyword(s):  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
The Elderly ◽  
Cox Proportional Hazards ◽  
Service Planning ◽  
Cox Proportional Hazards Model ◽  
Cognitive Test ◽  
Risk Of Death ◽  
Hazards Model ◽  
Using Data

Abstract Research Aims: This study seeks to understand whether those with dementia experience higher risk of death, using data from the ASPREE (ASPirin in Reducing Events in the Elderly) clinical trial study. Methods: ASPREE was a primary intervention trial of low-dose aspirin among healthy older people. The Australian cohort included 16,703 dementia-free participants aged 70 years and over at enrolment. Participants were triggered for dementia adjudication if cognitive test results were poorer than expected, self-reporting dementia diagnosis or memory problems, or dementia medications were detected. Incidental dementia was adjudicated by an international adjudication committee using the Diagnostic and Statistical Manual for Mental Disorders (DSM-IV) criteria and results of a neuropsychological battery and functional measures with medical record substantiation. Statistical analyses used a cox proportional hazards model. Results: As previously reported, 1052 participants (5.5%) died during a median of 4.7 years of follow-up and 964 participants had a dementia trigger, of whom, 575 (60%) were adjucated as having dementia. Preliminary analyses has shown that the mortality rate was higher among participants with a dementia trigger, regardless of dementia adjudication outcome, than those without (15% vs 5%, Χ2 = 205, p <.001). Conclusion: This study will provide important analyses of differences in the hazard ratio for mortality and causes of death among people with and without cognitive impairment and has important implications on service planning.

scholarly journals Evaluation of Changes on World Stock Exchanges in Connection with the SARS-CoV-2 Pandemic. Survival Analysis Methods

Risks ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 121
Author(s):  
Beata Bieszk-Stolorz ◽  
Krzysztof Dmytrów
Keyword(s):  
Survival Analysis ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Stock Exchange ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Stock Exchanges ◽  
Analysis Methods ◽  
Hazards Model ◽  
Kaplan Meier

The aim of our research was to compare the intensity of decline and then increase in the value of basic stock indices during the SARS-CoV-2 coronavirus pandemic in 2020. The survival analysis methods used to assess the risk of decline and chance of rise of the indices were: Kaplan–Meier estimator, logit model, and the Cox proportional hazards model. We observed the highest intensity of decline in the European stock exchanges, followed by the American and Asian plus Australian ones (after the fourth and eighth week since the peak). The highest risk of decline was in America, then in Europe, followed by Asia and Australia. The lowest risk was in Africa. The intensity of increase was the highest in the fourth and eleventh week since the minimal value had been reached. The highest odds of increase were in the American stock exchanges, followed by the European and Asian (including Australia and Oceania), and the lowest in the African ones. The odds and intensity of increase in the stock exchange indices varied from continent to continent. The increase was faster than the initial decline.

scholarly journals Risk and Timing of Cardiovascular Disease After Androgen-Deprivation Therapy in Men With Prostate Cancer

2015 ◽  
Vol 33 (11) ◽  
pp. 1243-1251 ◽  
Author(s):  
Sean O'Farrell ◽  
Hans Garmo ◽  
Lars Holmberg ◽  
Jan Adolfsson ◽  
Pär Stattin ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cardiovascular Disease ◽  
Androgen Deprivation Therapy ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Androgen Deprivation ◽  
Gnrh Agonists ◽  
Cvd Risk ◽  
Comparison Cohort ◽  
Using Data

Purpose Findings on the association between risk of cardiovascular disease (CVD) and the duration and type of androgen-deprivation therapy (ADT) in men with prostate cancer (PCa) are inconsistent. Methods By using data on filled drug prescriptions in Swedish national health care registers, we investigated the risk of CVD in a cohort of 41,362 men with PCa on ADT compared with an age-matched, PCa-free comparison cohort (n = 187,785) by use of multivariable Cox proportional hazards regression models. Results From 2006 to 2012, 10,656 men were on antiandrogens (AA), 26,959 were on gonadotropin-releasing hormone (GnRH) agonists, and 3,747 underwent surgical orchiectomy. CVD risk was increased in men on GnRH agonists compared with the comparison cohort (hazard ratio [HR] of incident CVD, 1.21; 95% CI, 1.18 to 1.25; and orchiectomy: HR, 1.16; 95% CI, 1.08 to 1.25). Men with PCa on AA were at decreased risk (HR of incident CVD, 0.87; 95% CI, 0.82 to 0.91). CVD risk was highest during the first 6 months of ADT in men who experienced two or more cardiovascular events before therapy, with an HR of CVD during the first 6 months of GnRH agonist therapy of 1.91 (95% CI, 1.66 to 2.20), an HR of CVD with AA of 1.60 (95% CI, 1.24 to 2.06), and an HR of CVD with orchiectomy of 1.79 (95% CI, 1.16 to 2.76) versus the comparison cohort. Conclusion Our results support that there should be a solid indication for ADT in men with PCa so that benefit outweighs potential harm; this is of particular importance among men with a recent history of CVD.

scholarly journals Confounding by indication of the safety of de-escalation in community-acquired pneumonia: a simulation study embedded in a prospective cohort

2019 ◽  
Author(s):  
Inger van Heijl ◽  
Valentijn A. Schweitzer ◽  
C.H. Edwin Boel ◽  
Jan Jelrik Oosterheert ◽  
Susanne M. Huijts ◽  
...  
Keyword(s):  
Propensity Scores ◽  
Proportional Hazards ◽  
Community Acquired Pneumonia ◽  
Cox Proportional Hazards ◽  
Hazard Ratio ◽  
Adjusted Hazard Ratio ◽  
Confounding By Indication ◽  
Potential Impact ◽  
Using Data ◽  
Clinical Stability

BackgroundObservational studies have demonstrated that de-escalation of antimicrobial therapy is independently associated with lower mortality. This most probably results from confounding by indication. Reaching clinical stability is associated with the decision to de-escalate and with survival. However, studies rarely adjust for this confounder. We quantified the potential confounding effect of clinical stability on the estimated impact of de-escalation on mortality in patients with community-acquired pneumonia.MethodsData were used from the Community-Acquired Pneumonia immunization Trial in Adults (CAPiTA). The primary outcome was 30-day mortality. We performed Cox proportional-hazards regression with de-escalation as time-dependent variable and adjusted for baseline characteristics using propensity scores. The potential impact of unmeasured confounding was quantified through simulating a variable representing clinical stability on day three, using data on prevalence and associations with mortality from the literature.ResultsOf 1,536 included patients, 257 (16.7%) were de-escalated, 123 (8.0%) were escalated and in 1156 (75.3%) the antibiotic spectrum remained unchanged. The adjusted hazard ratio of de-escalation for 30-day mortality (compared to patients with unchanged coverage), without adjustment for clinical stability, was 0.36 (95%CI: 0.18-0.73). If 90% to 100% of de-escalated patients were clinically stable on day three, the fully adjusted hazard ratio would be 0.53 (95%CI: 0.26-1.08) to 0.90 (95%CI: 0.42-1.91), respectively. The simulated confounder was substantially stronger than any of the baseline confounders in our dataset.ConclusionsWith plausible, literature-based assumptions, clinical stability is a very strong confounder for the effects of de-escalation. Quantification of effects of de-escalation on patient outcomes without proper adjustment for clinical stability results in strong negative bias. As a result, the safety of de-escalation remains to be determined.

scholarly journals Risk of depressive disorders after tobacco smoking cessation: a retrospective cohort study in Fukuoka, Japan

BMJ Open ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. e025124 ◽  
Author(s):  
Takako Fujita ◽  
Akira Babazono ◽  
Yumi Harano ◽  
Peng Jiang
Keyword(s):  
Smoking Cessation ◽  
Cohort Study ◽  
Survival Analysis ◽  
Retrospective Cohort ◽  
Depressive Disorders ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Proportional Hazards Models ◽  
Cox Proportional Hazards Models ◽  
Significant Difference

ObjectiveWe sought to examine the effect of smoking cessation on subsequent development of depressive disorders.DesignThis was a retrospective cohort study.MethodsWe used administrative claim and health check data from fiscal years 2010 to 2014, obtained from the largest health insurance association in Fukuoka, Japan. Study participants were between 30 and 69 years old. The end-point outcome was incidence of depressive disorders. Survival analysis and Cox proportional hazards models were conducted. The evaluated potential confounders were sex, age, standard monthly income and psychiatric medical history.ResultsThe final number of participants was 87 255, with 7841 in the smoking cessation group and 79 414 in the smoking group. The result of survival analysis showed no significant difference in depressive disorders between the two groups. The results of Cox proportional hazards models showed no significant difference by multivariate analysis between participants, including users of smoking cessation medication (HR 1.04, 95% Cl 0.89 to 1.22) and excluding medication use (HR 0.97, 95% Cl 0.82 to 1.15).ConclusionsThe present study showed that there were no significant differences with respect to having depressive disorders between smoking cessation and smoking groups. We also showed that smoking cessation was not related to incidence of depressive disorders among participants, including and excluding users of smoking cessation medication, after adjusting for potential confounders. Although the results have some limitations because of the nature of the study design, our findings will provide helpful information to smokers, health professionals and policy makers for improving smoking cessation.

scholarly journals Refusal of Cancer-Directed Surgery Strongly Impairs Survival of Patients with Localized Hepatocellular Carcinoma

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Jue Wang ◽  
Fen Wei Wang
Keyword(s):  
Hepatocellular Carcinoma ◽  
Logistic Regression ◽  
African American ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
High Rate ◽  
Advanced Stage ◽  
Tumor Characteristics ◽  
Using Data ◽  
Program Characteristics

Background: This study investigated the frequency of patients with HCC who refused cancer-directed surgery and the characteristics and outcomes of these patients.Patients and Methods: A retrospective study was performed using data from the Surveillance, Epidemiology, and End Results (SEER) Program. Characteristics of patients who refused CDS were compared with those who accepted surgery using logistic regression. The effect of refusing CDS on mortality was evaluated by Cox proportional hazards analysis.Results: Among 4373 surgical candidates, 142 patients (3.2%) refused the recommended CDS. The patients who refused CDS were frequently older, African American, widowed or divorced, and had advanced-stage tumors. In a logistic regression analysis, older age, African American, and being divorced or widowed were independently associated with refusal of CDS. After adjusting for other patient and tumor characteristics, the patients who refused CDS had a 2.5-fold (95% confidence interval, 2.339–3.189) higher risk of dying from HCC in comparison with patients who had CDS. Conclusions: The high rate of refusal may contribute in part to the disparity in utilization of CDS. Of greatest concern is that the patients who declined CDS had an impaired survival. This information might be helpful for patients to make a better-informed decision.

scholarly journals Mid-Life Patterns and the Residential Mobility of Older Men

2004 ◽  
Vol 23 (1) ◽  
pp. 73-89
Author(s):  
Lynda M. Hayward
Keyword(s):  
Proportional Hazards ◽  
Baby Boom ◽  
Economic Status ◽  
Family Relations ◽  
Later Life ◽  
The Elderly ◽  
Cox Proportional Hazards ◽  
Life Course Perspective ◽  
Future Research ◽  
Using Data

ABSTRACTThere are numerous ways to better integrate the elderly into communities, many of which are contingent upon whether they will remain in their pre-retirement homes or make a move. Using a life course perspective, this paper establishes that residential history, social and family relations, socio-economic status, and health trajectories measured at mid-life can be associated with moves in later life, either directly, or indirectly through their effect on the mid-life residential trajectory. These relationships are examined with multivariate Cox proportional hazards and Poisson regression models, using data from the Ontario Longitudinal Study of Aging. These findings suggest directions for future research, to aid the development of public policy for the large baby-boom cohorts that are just entering mid-life.

The association between lymphopenia and serious infection risk in rheumatoid arthritis

Rheumatology ◽  
2019 ◽  
Vol 59 (4) ◽  
pp. 762-766
Author(s):  
Sujith Subesinghe ◽  
Alexander Kleymann ◽  
Andrew Ian Rutherford ◽  
Katie Bechman ◽  
Sam Norton ◽  
...  
Keyword(s):  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Mixed Effect ◽  
Proportional Hazards Regression ◽  
Effect Model ◽  
Serious Infection ◽  
Patients At Risk ◽  
Using Data ◽  
The Relationship

Abstract Objectives To investigate the relationship between occurrence of serious infection (SI) and lymphocyte counts in patients with RA using data from a single centre. Methods We used routinely captured data from a single tertiary rheumatology centre to explore the relationship between lymphopenia and SI risk. Adult RA patients were included over a 5-year follow-up period. Admissions due to confirmed SI were considered. SI rate with 95% confidence intervals was calculated. The association between SI with baseline lymphocyte counts, time-averaged lymphocyte counts throughout all follow-up, and a nadir lymphocyte count was assessed using Cox proportional hazards regression. The relationship between lymphopenia over time and SI was analysed using a mixed-effect model of lymphocyte counts prior to SI. Results This analysis included 1095 patients with 205 SIs during 2016 person-years of follow-up. The SI rate was 4.61/100 patient-years (95% CI: 3.76, 5.65). Compared with patients with nadir lymphocyte counts >1.5 × 109 cells/l, nadir lymphopenia <1 × 109 cells/l was significantly associated with higher SI risk (HR 3.28; 95% CI: 1.59, 6.76), increasing to HR 8.08 (95% CI: 3.74, 17.44) in patients with lymphopenia <0.5 × 109 cells/l. Lymphocyte counts were observed to be reduced in the 30-day period prior to SI. Conclusion Lymphocyte counts below <1.0 × 109 cells/l were associated with higher SI risk in RA patients; the strongest association between lymphopenia and SI was observed when lymphocyte counts were below <0.5 × 109 cells/l. Lymphopenia may be used as a measure to stratify patients at risk of SI.

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