Predictive model for survival in patients with gastric cancer

A comparative study of explainable ensemble learning and logistic regression for predicting in-hospital mortality in the emergency department

This study addresses the challenges associated with emergency department (ED) overcrowding and emphasizes the need for efficient risk stratification tools to identify high-risk patients for early intervention. While several scoring systems, often based on logistic regression (LR) models, have been proposed to indicate patient illness severity, this study aims to compare the predictive performance of ensemble learning (EL) models with LR for in-hospital mortality in the ED. A cross-sectional single-center study was conducted at the ED of Imam Reza Hospital in northeast Iran from March 2016 to March 2017. The study included adult patients with one to three levels of emergency severity index. EL models using Bagging, AdaBoost, random forests (RF), Stacking and extreme gradient boosting (XGB) algorithms, along with an LR model, were constructed. The training and validation visits from the ED were randomly divided into 80% and 20%, respectively. After training the proposed models using tenfold cross-validation, their predictive performance was evaluated. Model performance was compared using the Brier score (BS), The area under the receiver operating characteristics curve (AUROC), The area and precision-recall curve (AUCPR), Hosmer-Lemeshow (H-L) goodness-of-fit test, precision, sensitivity, accuracy, F1-score, and Matthews correlation coefficient (MCC). The study included 2025 unique patients admitted to the hospital's ED, with a total percentage of hospital deaths at approximately 19%. In the training group and the validation group, 274 of 1476 (18.6%) and 152 of 728 (20.8%) patients died during hospitalization, respectively. According to the evaluation of the presented framework, EL models, particularly Bagging, predicted in-hospital mortality with the highest AUROC (0.839, CI (0.802-0.875)) and AUCPR = 0.64 comparable in terms of discrimination power with LR (AUROC (0.826, CI (0.787-0.864)) and AUCPR = 0.61). XGB achieved the highest precision (0.83), sensitivity (0.831), accuracy (0.842), F1-score (0.833), and the highest MCC (0.48). Additionally, the most accurate models in the unbalanced dataset belonged to RF with the lowest BS (0.128). Although all studied models overestimate mortality risk and have insufficient calibration (P > 0.05), stacking demonstrated relatively good agreement between predicted and actual mortality. EL models are not superior to LR in predicting in-hospital mortality in the ED. Both EL and LR models can be considered as screening tools to identify patients at risk of mortality.

Comparing In-Hospital Mortality Prediction by Senior Emergency Resident's Judgment and Prognostic Models in the Emergency Department

Background

A comparison of emergency residents' judgments and two derivatives of the Sequential Organ Failure Assessment (SOFA), namely, the mSOFA and the qSOFA, was conducted to determine the accuracy of predicting in-hospital mortality among critically ill patients in the emergency department (ED).

Methods

A prospective cohort research was performed on patients over 18 years of age presented to the ED. We used logistic regression to develop a model for predicting in-hospital mortality by using qSOFA, mSOFA, and residents' judgment scores. We compared the accuracy of prognostic models and residents' judgment in terms of the overall accuracy of the predicted probabilities (Brier score), discrimination (area under the ROC curve), and calibration (calibration graph). Analyses were carried out using R software version R-4.2.0.

Results

In the study, 2,205 patients with median age of 64 (IQR: 50-77) years were included. There were no significant differences between the qSOFA (AUC 0.70; 95% CI: 0.67-0.73) and physician's judgment (AUC 0.68; 0.65-0.71). Despite this, the discrimination of mSOFA (AUC 0.74; 0.71-0.77) was significantly higher than that of the qSOFA and residents' judgments. Additionally, the AUC-PR of mSOFA, qSOFA, and emergency resident's judgments was 0.45 (0.43-0.47), 0.38 (0.36-0.40), and 0.35 (0.33-0.37), respectively. The mSOFA appears stronger in terms of overall performance: 0.13 vs. 0.14 and 0.15. All three models showed good calibration.

Conclusion

The performance of emergency residents' judgment and the qSOFA was the same in predicting in-hospital mortality. However, the mSOFA predicted better-calibrated mortality risk. Large-scale studies should be conducted to determine the utility of these models.

Internal validation and evaluation of the predictive performance of models based on the PRISM-3 (Pediatric Risk of Mortality) and PIM-3 (Pediatric Index of Mortality) scoring systems for predicting mortality in Pediatric Intensive Care Units (PICUs)

PURPOSE

The study was aimed to assess the prognostic power The Pediatric Risk of Mortality-3 (PRISM-3) and the Pediatric Index of Mortality-3 (PIM-3) to predict in-hospital mortality in a sample of patients admitted to the PICUs.

DESIGN AND METHODS

The study was performed to include all children younger than 18 years of age admitted to receive critical care in two hospitals, Mashhad, northeast of Iran from December 2017 to November 2018. The predictive performance was quantified in terms of the overall performance by measuring the Brier Score (BS) and standardized mortality ratio (SMR), discrimination by assessing the AUC, and calibration by applying the Hosmer-Lemeshow test.

RESULTS

A total of 2446 patients with the median age of 4.2 months (56% male) were included in the study. The PICU and in-hospital mortality were 12.4 and 16.14%, respectively. The BS of the PRISM-3 and PIM-3 was 0.088 and 0.093 for PICU mortality and 0.108 and 0.113 for in-hospital mortality. For the entire sample, the SMR of the PRISM-3 and PIM-3 were 1.34 and 1.37 for PICU mortality and 1.73 and 1.78 for in-hospital mortality, respectively. The PRISM-3 demonstrated significantly higher discrimination power in comparison with the PIM-3 (AUC = 0.829 vs 0.745) for in-hospital mortality. (AUC = 0.779 vs 0.739) for in-hospital mortality. The HL test revealed poor calibration for both models in both outcomes.

CONCLUSIONS

The performance measures of PRISM-3 were better than PIM-3 in both PICU and in-hospital mortality. However, further recalibration and modification studies are required to improve the predictive power to a clinically acceptable level before daily clinical use.

PRACTICE IMPLICATIONS

The calibration of the PRISM-3 model is more satisfactory than PIM-3, however both models have fair discrimination power.

Colorectal Cancer in North-Eastern Iran: a retrospective, comparative study of early-onset and late-onset cases based on data from the Iranian hereditary colorectal cancer registry

BACKGROUND

The incidence rate of colorectal cancer (CRC) is increasing among patients below 50 years of age. The reason for this is unclear, but could have to do with the fact that indicative variables, such as tumour location, gender preference and genetic preponderance have not been followed up in a consistent mann er. The current study was primarily conducted to improve the hereditary CRC screening programme by assessing the demographic and clinicopathological characteristics of early-onset CRC compared to late-onset CRC in northeast Iran.

METHODS

This retrospective study, carried out over a three-year follow-up period (2014-2017), included 562 consecutive CRCs diagnosed in three Mashhad city hospital laboratories in north-eastern Iran. We applied comparative analysis of pathological and hereditary features together with information on the presence of mismatch repair (MMR) gene deficiency with respect to recovery versus mortality. Patients with mutations resulting in absence of the MMR gene MLH1 protein product and normal BRAF status were considered to be at high risk of Lynch syndrome (LS). Analyses using R studio software were performed on early-onset CRC (n = 222) and late-onset CRC (n = 340), corresponding to patients ≤50 years of age and patients > 50 years.

RESULTS

From an age-of-onset point of view, the distribution between the genders differed with females showing a higher proportion of early-onset CRC than men (56% vs. 44%), while the late-onset CRC disparity was less pronounced (48% vs. 52%). The mean age of all participants was 55.6 ± 14.8 years, with 40.3 ± 7.3 years for early-onset CRC and 65.1 ± 9.3 years for late-onset CRC. With respect to anatomical tumour location (distal, rectal and proximal), the frequencies were 61, 28 and 11%, respectively, but the variation did not reach statistical significance. However, there was a dramatic difference with regard to the history of CRC in second-degree relatives between two age categories, with much higher numbers of family-related CRCs in the early-onset group. Expression of the MLH1 and PMS2 genes were significantly different between recovered and deceased, while this finding was not observed with regard to the MSH6 and the MSH2 genes. Mortality was significantly higher in those at high risk of LS.

CONCLUSION

The variation of demographic, pathological and genetic characteristics between early-onset and late-onset CRC emphasizes the need for a well-defined algorithm to identify high-risk patients.

Characteristics of gastric precancerous conditions and Helicobacter pylori infection among dyspeptic patients in north-eastern Iran: is endoscopic biopsy and histopathological assessment necessary?

Background

Early detection and appropriate treatment of precancerous, mucosal changes could significantly decrease the prevalence of life-threatening gastric cancer. Biopsy of the normal-appearing mucosa to detect Helicobacter pylori and these conditions is not routinely obtained. This study assesses the prevalence and characteristics of H. pylori infection and precancerous conditions in a group of patients suffering from chronic dyspepsia who were subjected to gastric endoscopy and biopsy mapping.

Methods

This cross-sectional study included dyspeptic patients, not previously treated for H. pylori, undergoing esophagogastroduodenoscopy (EGD) with their gastric endoscopic biopsies obtained for examination for evidence of H. pylori infection and precancerous conditions. Demographic and clinical data on the gender, smoking, opium addiction, alcohol consumption, medication with aspirin, corticosteroids and non-steroidal anti-inflammatory drugs (NSAIDs) and family history of cancer were collected by interviewing the patients and evaluating their health records. The cohort examined consisted of 585 patients with a mean (SD) age of 48.0 (14.46) years, 397 (67.9%) of whom were women.

Results

H. pylori infection was identified in 469 patients (80.2%) with the highest prevalence (84.2%) in those aged 40–60 years. Opium addiction correlated with a higher a H. pylori infection rate, while alcohol consumption was associated with a lower rate by Odds Ratio 1.98 (95% CI 1.11–3.52) and 0.49 (95% CI 0.26–0.92), respectively. The prevalence of intestinal metaplasia, gastric atrophy and gastric dysplasia was 15.2, 12.6 and 7.9%, respectively. Increased age, positive H. pylori infection, endoscopic abnormal findings and opium addiction showed a statistically significant association with all precancerous conditions, while NSAID consumption was negatively associated with precancerous conditions. For 121 patients (20.7% of all), the EGD examination revealed normal gastric mucosa, however, for more than half (68/121, 56.2%) of these patients, the histological evaluation showed H. pylori infection, and also signs of atrophic mucosa, intestinal metaplasia and dysplasia in 1.7, 4.1 and 1.7%, respectively.

Conclusion

EGD with gastric biopsy mapping should be performed even in the presence of normal-appearing mucosa, especially in dyspeptic patients older than 40 years with opium addiction in north-eastern Iran. Owing to the high prevalence of precancerous conditions and H. pylori infection among patients with dyspepsia in parts of Iran, large-scale national screening in this country should be beneficial.

Mortality risk factors in patients with gastric cancer using Bayesian and ordinary Lasso logistic models: a study in the Southeast of Iran

AIM

The aim of this study was to apply two types of statistical models to determine the factors that influence the mortality rate in patients with gastric cancer.

BACKGROUND

In Iran, gastric cancer ranks the first and second most prevalent among men and women, respectively. It is the first cause of death in Iran in both gendersival.

METHODS

In this retrospective study, data were obtained from 339 (216 male) patients diagnosed with gastric cancer in the city of Kerman (South-East of Iran) during 2001-2015. In this study, ordinary and Bayesian Lasso (least absolute shrinkage and selection operator) logistic regression models, with goodness-of-fit indices, were compared and the models' risk factors were also determined.

RESULTS

The mean age of the participants was 62.84 ±14.53 years, and 12.4% of them were younger than 45 years. Also, the mortality rate was 57.7%. Gender, morphology of the tumor, and time of diagnosis were found to be significant factors in the mortality of the patients in both models. This study found that the Bayesian Lasso model had better fitness.

CONCLUSION

The high mortality rate of gastric cancer and its high prevalence at age below 45 years are alarming. Thus, great attention should be paid to prevention, early diagnosis, especially in females, and adenocarcinoma to improve the survival of patients with gastric cancer.

Expression of miR-141 and YAP1 in gastric carcinoma and modulation of cancer cell proliferation and apoptosis

Yes-associated protein 1 (YAP1) plays important roles in facilitating cell proliferation and decreasing apoptosis and is related to gastric cancer. Abnormal down-regulation of miR-141 is associated with gastric cancer pathogenesis, suggesting a potentially tumor suppressor role. Bioinformatics analysis found complementary binding sites between miR-141 and YP1. This study investigated the role of miR-141 in mediating YAP1 expression and biological behavior of gastric cancer cells. Gastric cancer tissues were collected using normal mucosal tissues as the control. qRT-PCR compared expression of miR-141 and YAP1 mRNA, and western blot quantified YAP1 protein expression. Spearman approach analyzed the correlation between miR-141 and YAP1 mRNA in cancer tissues. Dual luciferase reporter gene assay confirmed the targeted regulation between miR-141 and YAP1. Using GES-1 cell as the control, miR-141 and YAP1 expression were measured in gastric cancer cell lines SGC7901 and MGC03. Those cells were transfected with miR-141 mimic in the presence or absence of miR-YAP1 mimic followed by flow cytometry for apoptosis and EdU staining for proliferation. Cancer tissues had decreased miR-141 and higher YAP1 expression, which was associated with TNM stage. YAP1 mRNA and miR-141 were positively correlated (r=-0.623, P<0.001). Dual luciferase assay demonstrated targeted regulation between miR-141 and YAP1. Comparing to GES-1 cells, SGC7901 and MGC803 cells had decreased miR-141 and increased YAP1 expression. Transfection of miR-141 mimic inhibited YAP1 expression or cell proliferation and facilitated apoptosis. However, overexpression of YAP1 decreased the effect of miR-141 mimic on cell proliferation and apoptosis. miR-141 down-regulation and YAP1 up-regulation are correlated with gastric cancer pathogenesis. miR-141 targets and inhibits YAP1 expression, to suppress gastric cancer cell proliferation and induce apoptosis.