Mitosis domain generalization in histopathology images -- The MIDOG challenge

The density of mitotic figures within tumor tissue is known to be highly correlated with tumor proliferation and thus is an important marker in tumor grading. Recognition of mitotic figures by pathologists is known to be subject to a strong inter-rater bias, which limits the prognostic value. State-of-the-art deep learning methods can support the expert in this assessment but are known to strongly deteriorate when applied in a different clinical environment than was used for training. One decisive component in the underlying domain shift has been identified as the variability caused by using different whole slide scanners. The goal of the MICCAI MIDOG 2021 challenge has been to propose and evaluate methods that counter this domain shift and derive scanner-agnostic mitosis detection algorithms. The challenge used a training set of 200 cases, split across four scanning systems. As a test set, an additional 100 cases split across four scanning systems, including two previously unseen scanners, were given. The best approaches performed on an expert level, with the winning algorithm yielding an F_1 score of 0.748 (CI95: 0.704-0.781). In this paper, we evaluate and compare the approaches that were submitted to the challenge and identify methodological factors contributing to better performance.Comment: 19 pages, 9 figures, summary paper of the 2021 MICCAI MIDOG challeng

Is Opium a Real Risk Factor for Esophageal Cancer or Just a Methodological Artifact? Hospital and Neighborhood Controls in Case-Control Studies

Background: Control selection is a major challenge in epidemiologic case-control studies. The aim of our study was to evaluate using hospital versus neighborhood control groups in studying risk factors of esophageal squamous cell carcinoma (ESCC). Methodology/Principal Findings: We compared the results of two different case-control studies of ESCC conducted in the same region by a single research group. Case definition and enrollment were the same in the two studies, but control selection differed. In the first study, we selected two age- and sex-matched controls from inpatient subjects in hospitals, while for the second we selected two age- and sex-matched controls from each subject's neighborhood of residence. We used the test of heterogeneity to compare the results of the two studies. We found no significant differences in exposure data for tobacco-related variables such as cigarette smoking, chewing Nass (a tobacco product) and hookah (water pipe) usage, but the frequency of opium usage was significantly different between hospital and neighborhood controls. Consequently, the inference drawn for the association between ESCC and tobacco use did not differ between the studies, but it did for opium use. In the study using neighborhood controls, opium use was associated with a significantly increased risk of ESCC (adjusted OR 1.77, 95% CI 1.17–2.68), while in the study using hospital controls, this was not the case (OR 1.09, 95% CI 0.63–1.87). Comparing the prevalence of opium consumption in the two control groups and a cohort enrolled from the same geographic area suggested that the neighborhood controls were more representative of the study base population for this exposure. Conclusions/Significance: Hospital and neighborhood controls did not lead us to the same conclusion for a major hypothesized risk factor for ESCC in this population. Our results show that control group selection is critical in drawing appropriate conclusions in observational studies

Verbal Autopsy: Reliability and Validity Estimates for Causes of Death in the Golestan Cohort Study in Iran

BACKGROUND: Verbal autopsy (VA) is one method to obtain valid estimates of causes of death in the absence of valid medical records. We tested the reliability and validity of a VA questionnaire developed for a cohort study in Golestan Province in northeastern Iran. METHOD: A modified version of the WHO adult verbal autopsy was used to assess the cause of death in the first 219 Golestan Cohort Study (GCS) subjects who died. The GCS cause of death was determined by two internists who independently reviewed all available medical records. Two other internists ("reviewers") independently reviewed only the VA answers and classified the cause of death into one of nine general categories; they repeated this evaluation one month later. The reliability of the VA was measured by calculating intra-reviewer and inter-reviewer kappa statistics. The validity of the VA was measured using the GCS cause of death as the gold standard. RESULTS: VA showed both good validity (sensitivity, specificity, PPV, and NPV all above 0.81) and reliability (kappa>0.75) in determining the general cause of death independent of sex and place of residence. The overall multi-rater agreement across four reviews was 0.84 (95%CI: 0.78-0.89). The results for identifying specific cancer deaths were also promising, especially for upper GI cancers (kappa = 0.95). The multi-rater agreement in cancer subgroup was 0.93 (95%CI: 0.85-0.99). CONCLUSIONS: VA seems to have good reliability and validity for determining the cause of death in a large-scale adult follow up study in a predominantly rural area of a middle-income country

The role of Toll-Like Receptor Gene Polymorphisms in Tuberculosis Susceptibility: A Systematic Review and Meta-Analysis

Introduction: Susceptibility to tuberculosis (TB) infection varies in individuals and is linked to genetic variations in the toll-like receptors (TLRs) genes. The current study employed a systematic literature review and meta-analysis to describe the most prevalent single nucleotide polymorphisms (SNPs) from various TLRs and to assess the association between these polymorphisms and tuberculosis susceptibility. Methods: The PubMed, Google Scholar, Scopus, and ISI Web of Knowledge databases were searched for all articles published before May 25, 2015, that contained the target keywords. Following the application of the inclusion and exclusion criteria, a total of 37 relevant articles were identified that examined the association between the TLRs gene polymorphism and susceptibility to tuberculosis.Result: A meta-analyses approach to the research determined that there is a statistically significant association between TLR1 rs4833095, TLR6 rs5743810, and TLR8 rs3788935 in the allelic model and also TLR1 rs4833095, TLR1 rs5743018, TLR2 rs5743708, TLR6 rs5743810, and TLR8 rs3761624 in the co-dominant model with increased or decreased susceptibility to tuberculosis. No associations were observed between the other TLRs polymorphisms and tuberculosis risk.Discussion: Several studies have found that host genetic factors, such as SNPs in TLRs gene, may increase an individual’s susceptibility to tuberculosis. Therefore, the identification of these SNPs is important to investigate immune responses to TB.Conclusion: The present study concluded that there is an association between some polymorphisms of TLRs and tuberculosis risk. Thus, for a better understanding about the role of SNPs to TB susceptibility, additional studies on alternative TLRs SNPs are needed

Activity-travel analysis of women in a patriarchal society with strong gender norms

In this paper, we investigate activity-travel pattern of Iranian women, where typical patriarchal views and specific social and cultural norms may alter the patterns from those in western societies. We pay special attention to the role of marital and employment status of them on their activity-travel patterns. To this extent, we develop a joint mode and daily activity pattern (DAP) discrete choice model, which is a mixed nested Logit. The upper tier of the proposed model embodies women’s DAP choices, and the lower tier belongs to the mode choices. We try to show how different factors in a traditional society like Iran affect or restrict women's type and structure of activity- travel patterns

The clinical manifestation and outcome of COVID-19 in patients with a history of ischemic heart disease; a retrospective case-control study

Abstract Introduction Coronary artery disease (CAD) is considered an independent risk factor for COVID-19. However, no study has specifically examined the clinical manifestations and outcomes of COVID-19 in patients with ischemic heart disease (IHD). Methods In a retrospective case-control study between 20 March 2020 to 20 May 2020, the medical record of 1611 patients with laboratory-confirmed SARS-CoV-2 infection was reviewed. IHD was defined as a history of an abnormal coronary angiography, coronary angioplasty, coronary artery bypass graft (CABG), or chronic stable angina. Demographic data, past medical history, drug history, symptoms, vital signs, laboratory findings, outcome, and death were investigated from medical records. Results 1518 Patients (882 men (58.1%)) with a mean age of 59.3 ± 15.5 years were included in the study. Patients with IHD (n = 300) were significantly less likely to have fever (OR: 0.170, 95% CI: 0.34–0.81, P  0.05). After adjusting for demographic characteristics, comorbidities and vital signs, the risk factors for mortality of these patients were older age (OR: 1.04 and 1.07) and cancer (OR: 1.03, and 1.11) in both groups. In addition, in the patients without IHD, diabetes mellitus (OR: 1.50), CKD (OR: 1.21) and chronic respiratory diseases (OR: 1.48) have increased the odds of mortality. In addition, the use of anticoagulants (OR: 2.77) and calcium channel blockers (OR: 2.00) has increased the odds of mortality in two groups. Conclusion In comparison with non-IHD, the symptoms of SARS-CoV-2 infection such as fever, chills and diarrhea were less common among patients with a history of IHD. Also, older age, and comorbidities (including cancer, diabetes mellitus, CKD and chronic obstructive respiratory diseases) have been associated with a higher risk of mortality in patients with IHD. In addition, the use of anticoagulants and calcium channel blockers has increased the chance of death in two groups without and with IHD