Classification of group A rotavirus VP7 and VP4 genotypes using random forest.

Introduction: Group A rotaviruses are major pathogens in causing severe diarrhea in young children and neonates of many different species of animals worldwide and group A rotavirus sequence data are becoming increasingly available over time. Different methods exist that allow for rotavirus genotyping, but machine learning methods have yet to be explored. Usage of machine learning algorithms such as random forest alongside alignment-based methodology may allow for both efficient and accurate classification of circulating rotavirus genotypes through the dual classification system. Methods: Random forest models were trained on positional features obtained from pairwise and multiple sequence alignment and cross-validated using methods of repeated 10-fold cross-validation thrice and leave one- out cross validation. Models were then validated on unseen data from the testing datasets to observe real-world performance. Results: All models were found to perform strongly in classification of VP7 and VP4 genotypes with high overall accuracy and kappa values during model training (0.975-0.992, 0.970-0.989) and during model testing (0.972-0.996, 0.969-0.996), respectively. Models trained on multiple sequence alignment generally had slightly higher overall accuracy and kappa values than models trained on pairwise sequence alignment method. In contrast, pairwise sequence alignment models were found to be generally faster than multiple sequence alignment models in computational speed when models do not need to be retrained. Models that used repeated 10-fold cross-validation thrice were also found to be much faster in model computational speed than models that used leave-one-out cross validation, with no noticeable difference in overall accuracy and kappa values between the cross-validation methods. Discussion: Overall, random forest models showed strong performance in the classification of both group A rotavirus VP7 and VP4 genotypes. Application of these models as classifiers will allow for rapid and accurate classification of the increasing amounts of rotavirus sequence data that are becoming available.

Novel hazards of waterpipe tobacco and the benefits of stop smoking in men, a prospective cohort study.

Waterpipe smoking is an emerging epidemic and a severe public health problem worldwide. Observational studies on the hazards of a specific new waterpipe tobacco product are timely needed. The objectives were to analyze how dangerous waterpipe tobacco smoking is on the causes of all mortality, including cancer, and how effective smoking cessation is for improving health. We analyzed the hazards of exclusive waterpipe smoking through a prospective cohort study in Northern Vietnam. We obtained exposure data on the smoking status of specific cigarette and waterpipe and smoking cessation histories from each study participant. The outcome includes deaths due to all causes. The cause of death for each case is determined based on medical records. HR (95%CI) was estimated using a Cox proportional-hazards-regression analysis for overall mortality and all cancers. The ever-cigarette smoking group as the reference group, the exclusive waterpipe smoking group had a statistical increase in the risk for overall mortality HR (95% CI): 1.63 (1.32, 2.00), and all cancers HR (95%CI): 1.67 (1.18, 2.38). The risk of death increased statistically in the group of waterpipe smoking over 20 years for overall mortality HR (95%CI): 1.82 (1.45, 2.29), and all cancers HR (95%CI): 1.91 (1.27, 2.88). After stopping smoking, the risk of death decreased steadily. The risk of death was reduced by 41% for overall mortality HR (95%CI): 0.59 (0.39, 0.89), and 74% for death from cancers HR (95%CI): 0.26 (0.08, 0.83) after ten years or longer of cessation. Life expectancy was shortened by more than six years for the group of exclusive waterpipe smokers compared to non-smokers. This study found new novel hazards of exclusive waterpipe tobacco smoking. The findings are scientific evidence for developing strategies, policies, and budget allocations to control this novel tobacco product and promote cessation to improve life expectancy.

Assessment of seasonality of rotavirus PCR detection in swine from Ontario and Quebec between 2016-2020 using submissions to a diagnostic laboratory.

The goal of this study was to determine if seasonality of rotavirus A, B, and C infection is present in Ontario and Quebec swine herds by investigating submissions to a diagnostic laboratory. Samples (N = 1557) within 755 case submissions from Canadian swine herds between 2016 and 2020 were tested for rotaviruses A, B, and C using a real-time polymerase-chain reaction assay and described. Data from Ontario and Quebec were additionally analyzed using boxplots, 6-week rolling averages, time-series decomposition, and negative binomial regression models. Percentage positivity of submissions for rotaviruses A, B, and C were discovered to be highest in nursery/weaner (n = 100, 94.0%, 60.0%, 80.0%) and grower/finisher (n = 13, 84.6%, 46.2%, 61.5%) pigs and lowest in gilt/sow (n = 45, 68.9%, 20.0%, 40.0%) and suckling pigs (n = 102, 67.6%, 10.8%, 38.2%), respectively. The most common combination of rotavirus at the sample level was AC (n = 252, 17%) and ABC (n = 175, 23.2%) at the submission level. Percent positivity for rotavirus A, B, and C across all Canadian provinces included in the study were 69.9%, 32.6%, and 53.1%, respectively. Descriptive analysis suggested little to no evidence of seasonal patterns, although a spike in November was seen in the monthly total submissions and monthly total positive submissions. Statistically, the overall month effect could not be identified as statistically significant (P > 0.05) for any of the evaluated submission counts. Overall, there was no evidence supporting seasonality of rotavirus within Ontario and Quebec swine herds between 2016 and 2020.

Le but de cette étude était de déterminer si la saisonnalité de l'infection à rotavirus A, B et C est présente dans les troupeaux de porcs de l'Ontario et du Québec en examinant les soumissions à un laboratoire de diagnostic. Des échantillons (N = 1557) de 755 cas soumis de troupeaux de porcs canadiens entre 2016 et 2020 ont été testés pour les rotavirus A, B et C à l'aide d'un test de réaction d'amplification en chaîne par polymérase en temps réel et décrits. Les données de l'Ontario et du Québec ont également été analysées à l'aide de diagrammes en boîte, de moyennes mobiles sur 6 semaines, d'une décomposition de séries chronologiques et de modèles de régression binomiale négative. On a découvert que le pourcentage de positivité des soumissions pour les rotavirus A, B et C étaient le plus élevé en pouponnière/sevrage (n = 100, 94,0 %, 60,0 %, 80,0 %) et en croissance/engraissement (n = 13, 84,6 %, 46,2 %, 61,5 %) des porcs et le plus bas chez les cochettes/truies (n = 45, 68,9 %, 20,0 %, 40,0 %) et les porcs à la mamelle (n = 102, 67,6 %, 10,8 %, 38,2 %), respectivement. La combinaison la plus courante de rotavirus au niveau de l'échantillon était AC (n = 252, 17 %) et ABC (n = 175, 23,2 %) au niveau de la soumission. Les pourcentages de positivité pour les rotavirus A, B et C dans toutes les provinces canadiennes incluses dans l'étude étaient de 69,9 %, 32,6 % et 53,1 %, respectivement. L'analyse descriptive a suggéré peu ou pas de preuves de tendances saisonnières, bien qu'un pic en novembre ait été observé dans les soumissions totales mensuelles et les soumissions positives totales mensuelles. Statistiquement, l'effet mensuel global n'a pu être identifié comme statistiquement significatif (P > 0,05) pour aucun des nombres de soumissions évalués. Dans l'ensemble, il n'y avait aucune preuve à l'appui de la saisonnalité du rotavirus dans les troupeaux de porcs de l'Ontario et du Québec entre 2016 et 2020.(Traduit par Docteur Serge Messier).

Case-Control Study of Alcohol Usage and Fruit Intake and Stomach Cancer in the North Viet Nam.

BACKGROUND: The aim was to examine the association between alcohol usage, fruit intake and stomach cancer treated in hospitals in the Hanoi city during 2018-2019. METHODS: A case-control study was performed for 379 newly incidence cases of stomach cancer and matched 1096 hospital controls for sex and age (+/-5). We used the validated semi-quantitative food frequency questionnaire to collect data on the intake of alcohol and fruits and other food groups. The average amount of total fruits intake (grams per week) was estimated. The adjusted Odds ratio and 95% confidence interval (OR (95%CI) were estimated. RESULTS: Intake of alcohol significantly increased the risk of stomach cancer, the mean frequency of intake per year of 345.1 times vs. non-drinkers, OR (95%CI): 1.51 (1.05, 2.17), p_trend=0.026. In contrast, a higher total of fruits intake was associated with a significantly decreased risk of stomach cancer in both sexes, men, and women, (Q5 vs Q1), OR (95%CI): 0.47 (0.30, 0.72), p_trend=0.000, OR (95%CI): 0.45 (0.26, 0.77), p_trend =0.003, OR (95%CI): 0.52 (0.24, 1.12), p_trend=0.026, respectively. CONCLUSIONS: We observed alcohol usage increased the risk of stomach cancers. In contrast, a total of fruits intake was associated with a decreased risk of stomach cancer. 
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A Case-Control Study of Meat Mutagens and Colorectal Cancers in Viet Nam.

OBJECTIVE: The aim was to examine the association between heterocyclic amines 2-amino-1-methyl-6-phenylimidazo pyridine (PhIP) and the risk of colorectal cancer (CRC) in Viet Nam. METHODS: We performed a case-control study for 512 colorectal cancer patients with the histopathological confirmation and 1,096 hospital controls. We collected information on lifestyle, diet, and cooking methods from participants by trained interviewers using the validated questionnaires. We used data of PhIP concentration in cooked beef analyzed by the LC/MS/MS and cooking questionnaire to estimate the daily intake of PhIP. We divided the estimated amount of PhIP (ng/person/day) into three levels of non-intake (the reference), medium, and high to estimate the Odds ratio and 95% confidence interval (OR, 95%CI). RESULTS: The median intake of PhIP (ng/person/day) was 18ng and 102.8ng for medium and high PhIP intake, respectively. There was a significant association between PhIP intake and the risk of colorectal cancer. The adjusted OR (95%C), high intake vs. non-intake, were 4.89 (3.03, 7.89), p_trend.

Waterpipe Tobacco Smoking and Gastric Cancer Risk among Vietnamese Men.

BACKGROUND: The association of waterpipe tobacco (WPT) smoking with gastric cancer (GC) risk was suggested. METHODS: A hospital-based case-control study was conducted to examine the association of WPT with GC risk among Vietnamese men, in Hanoi city, during the period of 2003-2011. Newly-diagnosed GC cases (n = 454) and control patients (n = 628) were matched by age (+/- 5 years) and the year of hospitalization. Information on smoking and alcohol drinking habits and diet including salty food intake and fruits/vegetables consumption were obtained by the interview. Maximum likelihood estimates of odds ratios (ORs) and corresponding 95% confidence intervals (Cis) were obtained using conditional logistic regression models. RESULTS: The group with the highest consumption of citrus fruits showed a significantly low GC risk (OR = 0.6, 95%CI = 0.4-0.8, P for trend = 0.002). However, there was no association of raw vegetable consumption with GC risk. Referring to never smokers, GC risk was significantly higher in current WPT smokers (OR = 1.8, 95%CI = 1.3-2.4), and it was more evident in exclusively WPT smokers (OR = 2.7, 95%CI = 1.2-6.5). GC risk tended to be higher with daily frequency and longer duration of WPT smoking but these trends were not statistically significant (P for trend: 0.144 and 0.154, respectively). GC risk of those who started smoking WPT before the age of 25 was also significantly high (OR = 3.7, 95%CI = 1.2-11.3). Neither cigarette smoking nor alcohol drinking was related to GC risk. CONCLUSION: The present findings revealed that WPT smoking was positively associated with GC risk in Vietnamese men.