Skip to main content
PLOS ONE logoLink to PLOS ONE
. 2020 Dec 10;15(12):e0243063. doi: 10.1371/journal.pone.0243063

Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

Til Bahadur Basnet 1,*, Srijana G C 2, Rajesh Basnet 3, Bidusha Neupane 3
Editor: Samson Gebremedhin4
PMCID: PMC7728256  PMID: 33301496

Abstract

Dietary nutrients have significant effects on the risk of cardiovascular diseases. However, the results were not uniform across different countries. The study aims to determine the relative importance of dietary nutrients associated with coronary artery disease (CAD) among the Nepalese population. A hospital-based matched case-control study was carried out at Shahid Gangalal National Heart Center in Nepal. In the present study, patients with more than seventy percent stenosis in any main coronary artery branch in angiography were defined as cases, while those presenting normal coronary angiography or negative for stressed exercise test were considered controls. Dietary intakes of 612 respondents over the past 12 months were evaluated using a semi-quantitative customized food frequency questionnaire. In conditional regression model, the daily average dietary intake of β-carotene (OR: 0.54; 95%CI: 0.34, 0.87), and vitamin C (OR: 0.96; 95%CI: 0.93, 0.99) were inversely, whereas dietary carbohydrate (OR: 1.16; 95%CI: 1.1, 1.24), total fat/oil (OR: 1.47; 95%CI: 1.27, 1.69), saturated fatty acid (SFA) (OR: 1.2; 95%CI: 1.11, 1.3), cholesterol (OR: 1.01; 95%CI: 1.001, 1.014), and iron intakes (OR: 1.11; 95%CI: 1.03, 1.19) were positively linked with CAD. Moreover, in random forest analysis, the daily average dietary intakes of SFA, vitamin A, total fat/oil, β-carotene, and cholesterol were among the top five nutrients (out of 12 nutrients variables) of relative importance associated with CAD. The nutrients of relative importance imply a reasonable preventive measure in public health nutrients specific intervention to prevent CAD in a resource-poor country like Nepal. The findings are at best suggestive of a possible relationship between these nutrients and the development of CAD, but prospective cohort studies and randomized control trials will need to be performed in the Nepalese population.

Introduction

Coronary artery disease (CAD) is a significant cause of disability and premature death throughout the world. The underlying pathology is atherosclerosis, which develops over many years and is usually advanced by the time symptoms occur, generally in middle age [1]. An estimated 7.4 million people died from CAD in 2015, representing 13% of all global deaths [2]. Primary risk factors are tobacco use, unhealthy diet, physical inactivity, harmful alcohol consumption. These, in turn, show up in people as raised blood pressure, elevated blood glucose, and overweight and obesity risks detrimental to good heart health [3].

A global strategy based on knowledge of the importance of risk factors for cardiovascular disease (CVDs) in different geographic regions and various ethnic groups is needed to prevent diseases effectively [4]. Western people mostly rely on high energy-dense food, substantially not reducing the incidence of obesity and CVDs [5] despite improved medical care and an increase in the cessation of smoking [6]. In low and middle-income countries, fast food, energy-dense food, and diet in high fat are related to an abrupt rise in CAD even in a younger population of high socioeconomic status of an urban area [7].

Dietary habit is considered as one of the potentially modifiable risk factors for CVDs. The quality of dietary carbohydrates plays a significant impact on the development of metabolic diseases and CAD. For instance, refined sugar increases CAD’s risk, while complex carbohydrates lower CAD incidence [8, 9]. Total dietary fat was associated with an increased risk of CVD and all-cause death [10]. After adjustment of some coronary heart disease (CHD) risk factors, higher intakes of polyunsaturated fatty acids (PUFA) and monounsaturated fatty acids (MUFA) were associated with a reduced risk of CHD [11]. Unlike observational studies, randomized control trials suggest that SFAs either do not or only modestly increase the risk for CAD [12, 13]. Evidence supports that industrially-produced trans-fats are linked to increased risk for CVDs [12, 14]. Thus, dietary fat quality contributes to the risk of the leading chronic diseases and is more critical than the quantity of fat/oil in reducing the risk of chronic disease mortality, especially from CVDs.

Dietary fat is rice in energy sources; it also carries fat-soluble vitamins and other nutritious substances, provides essential fatty acids, and aids physiological functions in the body [15]. PUFAs have been of great interest for human health due to their potential anti-inflammatory action that may protect from several chronic-degenerative diseases with inflammatory pathogenesis [16]. In many countries, daily intake of saturated fats exceeds the recommended limit of 10% energy (%E), while intakes of polyunsaturated fats (PUFAs) are often below the recommended range of 6–11%E, and consumption of long-chain ω–3 PUFAs is exceptionally low [17]. The average intake level of fat and carbohydrate varies in different countries, regions, and groups of people across the world. Thus, dietary fat recommendations must consider each country’s dietary fat/oil patterns [17]. However, there are discrepancies in the research findings of the role of vitamin B and antioxidant vitamins for CAD development [1821].

Like in high-income countries, major traditional risk factors: tobacco use, alcohol consumption, unhealthy diet, and physical inactivity were reported in prevalence studies in the Nepalese population [22]. Although people’s food habits vary with different ethnicities and geography, Nepalese commonly consume rice or bread, pulses, and vegetables, with potatoes prepared mostly in vegetable oil as the main meal. Nonetheless, the daily intakes of animal products, fruits, and vegetables are low in Nepalese [23]. However, analytical studies to determine the strength of association between dietary nutrients and CVDs were scarce in the Nepalese population. Therefore, the present study was carried out to examine the association of energy intake, dietary macronutrients, and micronutrients with CAD.

Materials and methods

A matched case-control analytical study was designed to describe the relation of nutrients to CAD. The data of 612 participants were collected from June 4 to September 4, 2018. The face to face interview was accomplished with patients who visited at highly specialized central-level cardiac treatment center, Shahid Gangalal National Heart Center in Nepal, which provides curative services to patients with CVDs. An ethical review board of the Nepal Health Research Council (308/2017-18) approved the present study. Before conducting a survey, permission was taken for collecting clinical data from the respective hospital. Written consent was taken from the respondent before attending the interview.

Study participants

Study cases were selected from admitted patients after suspected myocardial infarction or exercise-induced stress test positive or from those who would electively undergo angiography in the hospital. After angiography, patients with stenosis higher than 70 percent (%) in any main coronary artery branch were defined as study cases. The controls were patients who were either presenting normal coronary angiography or those who were negative for stressed exercise test, also called a treadmill exercise tests (TMT). TMT was carried out for patients who were essentially referred by a physician for the test based on a chief complaint of chest pain and or at least one cardiometabolic risk factor (either hypertension or dyslipidemia or diabetes). Those patients who visited the hospital for an elective check-up or whole body check-up, including TMT test, were also included in the TMT test. A case to control was 1:1; altogether, 306 cases and 306 controls were included in the study. “Sex” and “Age” were matched at the individual level and an interval of five years, respectively. Patients having a report with aortic valve sclerosis on echocardiogram and any abnormality on electrocardiogram were excluded. Severely ill patients like kidney failure, cancer, and heart failure were not included. The participant selection flowchart was presented in Fig 1.

Fig 1. Flowchart diagram for selection of study participants for cases and controls.

Fig 1

OPD: Outpatient department; CAD: Coronary artery disease; ECG: Electrocardiogram, WH: Waist hip.

Data collection technique and tools

Data was collected through face to face interviews and observation, using a semi-structured food frequency questionnaire (FFQ) tool and observation checklist, respectively. The questionnaire set comprised of three-part, namely i. General socio-demographic characteristic ii. Cardio-metabolic and behavioral risk factors and iii. Food frequency questionnaire. Blood pressure, weight and height, waist and hip circumference of cases and controls were measured and recorded using the observation checklist. Data for cases were collected on the second day of angiography after patients became stable. The average time for an interview in FFQ for cases and control was 42±7 minutes and 39±6 minutes, respectively.

Assessment of covariates

A standardized protocol was used to measure the height, weight, and waist and hip circumferences. A wall-mounted stadiometer measured height to the nearest centimeter. We asked respondents to stand upright without shoes, with their back against the wall, heels together, and eyes directed forward. Their weight was measured with a portable electronic weighing scale placed on a firm horizontal surface. Waist and hip circumferences were measured with a non-stretchable standard measuring tape. Waist measurements were obtained over a lightly clothed abdomen at the narrowest point between the costal margin and iliac crest, and hip circumference was measured over light clothing at the level of the widest diameter around the buttocks. Body mass index (BMI) was categorized as normal (<23.0 kg/m2), overweight (23.0 to < 27.5.0 kg/m2), and obese (≥27.5.0 kg/m2) [24]. Abdominal obesity was defined as waist circumference ≥ 90 centimeters in males and ≥ 80 centimeters in females [25]. Dyslipidaemia was defined as hypercholesterolemia or hypertriglyceridemia; if the high-density lipoprotein (HDL) level was below 30 mg/dl, dyslipidemia was considered. Hypertriglyceridemia and hypercholesterolemia were defined as triglyceride (TG) serum and total cholesterol (TC) levels greater than 150 and 200 mg/dl, respectively, or if hypolipidemic treatment was administered [26]. Diabetic individuals were those with fasting blood glucose equal to or greater than 126 mg/dl throughout two tests or those taking diabetes medications [26]. Patients whose blood pressure was greater or equal to 140/90 mmHg or those taking antihypertensive medication according to their medical records were classified as hypertensive [27].

Persons who smoked until within one year of the interview were considered current daily smokers. Never smokers were those who responded with “occasionally” or “not at all” on the questionnaire, and ex-smokers were those who smoked daily before one year of interview. Current alcohol drinkers were categorized as those who engaged in alcohol drinking within the last year. A total of 13.6 g of pure alcohol was considered one standard drink, equivalent to consuming 43 ml of local alcohol (Raksi) and 341 ml of beer, Zaand, or Tongba [28].

Physical activity levels related to work were categorized as vigorous, moderate, or low. Vigorous physical activity was considered any activity that caused a substantial rise in heart and breathing rates, such as digging or plowing fields, lifting heavy weights, etc. Continuous engagement in such activity for at least 10 minutes was considered involvement in vigorous activity. Similarly, moderate physical activity was defined as any activity that caused a moderate increase in heart and breathing rates (examples include domestic chores, gardening, lifting light weights, etc.). Continuously engaging in such activity for at least 30 minutes was considered involvement in moderate activity. Physical activity related to transport was not considered in this study. The recreational activity was also called physical exercise which included two types of activities, vigorous and moderate, based on exertion. The vigorous recreational activity was defined as any recreational activity that significantly increased heart and breathing rates, such as football, fast swimming, and rapid cycling. Ten minutes of such activity was considered involvement in vigorous recreational activity. The moderate recreational activity was defined as any recreational activity that causes a moderate increase in heart and breathing rates; examples include yoga, playing basketball, brisk walking, and regular cycling [29]. During analysis, total physical activity (related to work and recreational) were categorized as “Yes” (includes moderate and vigorous) and “No.”

Dietary assessment

The FFQ was semi-structured, modified, and validated European Prospective Investigation of Cancer FFQ, customized to Nepalese day to day food items for obtaining detailed information regarding dietary nutrients and edible fat and oil intake from study participants. The list of fifty-nine food items (S1 Table), which were frequently consumed by the Nepalese population, was included. For testing internal validity, and intra-class correlation analyses were performed between FFQ1 and FFQ2, criterion validity was measured by Pearson’s correlation of FFQ2 with a "24-h recall diet survey" as a gold standard (S2 Table). An average of at least three days (two weekdays and one weekend) 24-h dietary recall can estimate about mean dietary intake for a day on the population or large-group level [30]. It is an intensive method for assessing dietary intake and is commonly used as a comparison method for validation/calibration studies of structured assessments such as FFQ [31]. However, it does not accurately determine the usual intake over time due to the large intra-individual variation in dietary intakes [30]. As FFQ can provide important information about dietary patterns, it is the most commonly used instrument to assess past dietary intake in epidemiological studies on the relationship between dietary factors and diseases [31].

Intake frequencies for the food items consisted of nine categories ranging from never to more than six times per day. Participants were asked how often they had consumed each food item listed on the FFQ during the past year. After being diagnosed as having any one of CAD's risk factors (obesity/hypertension/diabetes/dyslipidemia), patients who modified their dietary habits and those taking dietary supplements and vitamins were excluded from the study. The quantity of each food consumed by a subject was calculated by multiplying its consumption frequency by the usual amount consumed. Dietary intakes were then calculated using a programmed nutrition calculator based on the value of nutrients per 100 g food consumed per day for each food item with the use of the Nepal food composition table 2017.

A food atlas with color photographs of three portions sized- small, medium, and large- for various food items was developed and displayed to respondents to minimize the recall bias. The food items that did not have natural units or applicable household measures were photographed. Different sizes of glasses or bowls were displayed to estimate the number of liquids. Other items were asked as several specified units (slice, number, spoon, etc.). As people usually consumed seasonal fruits and vegetables, we grouped them into “leafy vegetables” and “other vegetables.” Several vegetables are cooked in combination, including potato, onion, and tomato. Some types of vegetables are available in only one season, while others are consumed more than one season. To address the overestimation of these above problems, we calculated average nutrients per 100 g that were allotting more weight to those vegetable items (cauliflower, mustard leaves, tomatoes), which are consumed more extended periods. Liquid oils are used during food preparation, so it is not easy to estimate the actual amount of oil consumed for an individual. Therefore, we asked separately the average number of days that would be sufficient to cook the foods from one liter of oil or ghee. Then, we calculated the total average amount of oil intake per person per day. Finally, fifty-nine food items were grouped into twenty-five food items with specific food ratios from Nepal’s food composition table and translated into particular dietary nutrients value.

Statistical analyses

Firstly, the Mcnemar test for categorical variables and Wilcoxon sign ranked test for continuous variables were executed to find the association between variables and CAD. After that, a conditional logistic regression model was constructed to test the strength of the association between dietary nutrients and CAD. By stepwise backward deletion process, we developed an energy-adjusted parsimonious model. To adjust the collinearity problem among our data variables, we performed random forest (RF) analysis, explaining the nutrients variability associated with CAD. RF consists of many individual de-correlated decision trees by sampling the random set of original data operating as an ensemble. Each tree gives a classification, and the forest selects the classification having the most votes across all the trees in the forest. RF is also common to perform the prediction task in the medical domain [32, 33]. The receiver operating characteristic (ROC) curve was constructed to assess the logistic regression and RF performance. Data analysis was performed with R packages in version 3.6.2, and two-tailed tests with p-value <0.05 were considered significant.

Results

Proportions of socio-demographic, cardio-metabolic, and behavioral characteristics of respondents between cases and controls in the study are presented in Table 1. The median age was 58 years, which was the same in both case and control groups. Because “Age” was matched at an interval of five years in the study, it was significantly associated with CAD (p-value = 0.001) in bivariate analysis. As CAD incidence is lower in the female population, fewer female CAD cases were admitted to the hospital, resulting in the ratio of male-to-female cases of 3:1. Similarly, diabetes mellitus, dyslipidemia, and general and abdominal obesity were significantly related to CAD (p-value <0.001). Regarding behavioral factors, smoking (p-value < 0.001), alcohol use (p-value = 0.019), and physical activity (p-value < 0.001) were found to be statistically significant linked with the disease.

Table 1. Socio-demographic, cardio-metabolic, and behavioral characteristics of respondents between cases and controls in the study.

Variables Control (%) n = 306 Case (%) n = 306 p-valuea
A. Demographic risk factors
Age 58 (50, 65)b 58 (50, 65) <0.001***
Sex Female 73 (23.9) 73 (23.9) 1.000
B. Cardiovascular Risk factors
Diabetes Yes 40 (13.1) 86 (28.1) <0.001***
Hypertension Yes 143 (46.7) 142 (46.4) 0.938
Dyslipidemia Yes 32 (10.5) 90 (29.4) <0.001***
General obesity Yesc 63 (20.6) 134 (43.8) 0.001***
Abdominal obesity Yesd 160 (52.3) 240 (78.4) <0.001***
C. Behavioral Risk Factors
Alcohol use Yes 66 (21.6) 91 (29.7) 0.019*
Smoking Never 196 (64.1) 113 (36.9) <0.001***
Ex-smoker 70 (22.9) 73 (23.9)
Current smoker 40 (13.1) 120 (39.2)
Physical activity Moderate/ vigorous 241 (78.8) 202 (66) <0.001***

aMcnemar test (categorical variables) and Wilcoxon sign ranked test (continuous variables).

bMedian and interquartile value.

cGeneral obesity: Body mass index ≥ 27.5 kg/m2 (for Asian).

dAbdominal obesity: Waist hip ratio ≥ 0.8 for females and ≥ 0.95 for males (for Asian).

*p ≤ .05

**p≤ .01

***p ≤ .001.

As the data of most of the variables were not normally distributed, median and interquartile values of nutrients intake are presented (Table 2). The median energy intake per day was 2674 (2445, 2909) and 2622 (2373, 2963) in control and case groups showing no statistically significant difference (p-value = 0.679). Total fat/oil, fiber, vitamin C, beta (β)-carotene, vitamin A, MUFA, SFA, and cholesterol intake per day were showing significant association with CAD (p-value < 0.001). In contrast, carbohydrate and PUFA intakes were significantly linked with CAD (p-value = 0.002). Also, a significant association of dietary zinc (p-value = 0.023), iron (p-value = 0.003), thiamine (p-value = 0.013), and riboflavin (p-value = 0.016) with CAD was reported. However, dietary intakes of protein, calcium, phosphorous, and niacin were not significantly associated with the disease.

Table 2. Distribution of nutritional factors associated with coronary artery disease between case and control groups in the study.

Nutrients intake/day Control (n = 306) Case (n = 306) p-valuea
Food energy Kcal 2674 (2445, 2909)b 2622 (2373, 2963) 0.679
Protein g 70 (61, 78) 67 (59, 77) 0.169
Total fat/oil g 56 (47, 64) 61 (52, 72) <0.001***
Carbohydrate g 433 (388, 481) 409 (368, 456) 0.002**
Fiber g 11.2 (9.8, 12.9) 10.1 (8.7, 11.6) <0.001***
Calcium mg 683 (434, 929) 648 (363, 930) 0.244
Phosphorus mg 1431 (1287, 1639) 1407 (1210, 1615) 0.146
Iron mg 21.3 (18.6, 24) 20 (17.4, 23.5) 0.003**
Zinc mg 14.1 (12.2, 16.2) 13.8 (11.7, 15.5) 0.023*
Thiamine mg 1.2 (1, 1.4) 1.2 (0.97, 1.3) 0.013*
Riboflavin mg 1.1 (0.89, 1.3) 1.04 (0.79, 1.3) 0.016*
Niacin mg 13.6 (11.9, 16.6) 13.8 (11.4, 16) 0.671
Vitamin C mg 45.3 (38, 52.9) 39.5 (33, 48.7) <0.001***
β-carotene mcg 2579 (2162, 3352) 2227 (1863, 2698) <0.001***
Vitamin A R.E. 698 (546, 836) 622 (506, 728) <0.001***
PUFA g 18.7 (12.5, 23.5) 19.6 (12.4, 25.7) 0.002**
MUFA g 17.2 (12.4, 23) 19.2 (14, 25.6) 0.001***
SFA g 15.5 (10.6, 19.2) 19 (13.9, 23.6) <0.001***
Cholesterol mg 108 (71,163) 129 (94,181) <0.001***

Kcal: kilocalorie; g: gram; mg: milligram; mcg: microgram; R.E.: retinol equivalent; PUFA: polyunsaturated fatty acid; MUFA: monounsaturated fatty acid; SFA: saturated fatty acid.

aWilcoxon sign ranked test.

bMedian and interquartile value.

*p ≤ .05

**p≤ .01

***p ≤ .001.

Those micronutrients that showed potential associations with CAD (p-value < 0.05) (Table 2) were then tested in the conditional logistic regression analysis (Table 3). In this analysis, we developed a parsimonious energy-adjusted model by stepwise backward deletion. The final model was adjusted with dyslipidemia, diabetes mellitus, smoking, and BMI. In this model, those nutrients inversely related to CAD were β-carotene (OR: 0.54; 95%CI: 0.34, 0.87) and vitamin C (OR: 0.96; 95%CI: 0.93, 0.99) indicating possible protective factors. However, dietary carbohydrate (OR: 1.16; 95%CI: 1.1, 1.24), total fat/oil intake (OR: 1.47; 95%CI: 1.27, 1.69), SFA (OR: 1.2; 95%CI: 1.11, 1.31), cholesterol (OR: 1.01; 95%CI: 1.001, 1.014), and iron intakes (OR: 1.11; 95%CI: 1.03, 1.19) were shown proportionately linked with CAD indicating probable risk factors.

Table 3. A model based on conditional logistic regression analysis showing the effect of nutrients intake on coronary artery disease.

Nutrients intake/day OR (95%CI) p-value
Carbohydrate g 1.16 (1.1, 1.24) <0.001***
Total fat/oil g 1.47 (1.27, 1.69) <0.001***
SFA g 1.2 (1.11, 1.31) <0.001***
Cholesterol g 1.01 (1.001, 1.014) 0.016*
β-carotene mg 0.54 (0.34, 0.87) 0.011*
Vitamin C mg 0.96 (0.93, 99) 0.018*
Iron mg 1.11 (1.03, 1.19) 0.005**

g: gram; mg: milligram; SFA: saturated fatty acid; OR: odds ratio; CI: confidence interval.

*p ≤ .05

**p≤ .01

***p ≤ .001.

The model was adjusted daily energy intake and with cardio-metabolic risk factors (Diabetes mellitus (type II), dyslipidemia and body mass index), and smoking.

We performed random forest analysis to evaluate the important dietary nutrients linked with CAD. In this RF model, we incorporated all the variables in the first step of conditional logistic regression analysis. The top twelve variables were presented in Fig 2; the five topmost important dietary nutrients linked with CAD were SFA, vitamin A RE, total fat/oil, β-carotene, and cholesterol. In this RF analysis, 250 trees and four variables were tried in each split, where the out-of-bag (OOB) estimate of error rate was 16%.

Fig 2. The essential nutritional and traditional variables in random forest regression analysis.

Fig 2

WH ratio: Waist-Hip ratio; g: gram; T2DM: Type II Diabetes mellitus; mg: milligram; mcg: microgram; RE: Retinol equivalent; PUFA: polyunsaturated fatty acid; MUFA: monounsaturated fatty acid; SFA: saturated fatty acid; kcal: kilocalorie.

Fig 3 reveals the area under curve (AUC) that evaluated the logistic regression model and RF model. Although the RF model had a lower AUC (90%) and other performance parameters (Table 4) than the logistic model (AUC—96%), RF adjusted the effect of multi-collinearity so that the interaction between correlates was independent.

Fig 3. Receiver operating curve (ROC) to compare the logistic regression model and in the random forest model.

Fig 3

AUC: area under curve.

Table 4. Comparison of performance for logistic regression and random forest.

Characteristics Logistic regression Random forest
Accuracy 0.902 0.843
Positive predictive rate 0.936 0.84
Negative predictive rate 0.873 0.846
No. of true positive/false negative 264/18 257/49
No. of true negative/false positive 288/42 259/47
Sensitivity 0.863 0.845
Specificity 0.941 0.841
F1 score 0.898 0.843
Out of bag error estimate (%) - 15.69

Discussion

The present hospital-based matched case-control study was designed to determine the association of dietary nutrients with CAD in the Nepalese population. Dietary intakes of carbohydrate, total fat, fiber, riboflavin, thiamine, vitamin C, β-carotene, vitamin A, vitamin C, PUFA, MUFA, SFA, and cholesterol were significantly associated with CAD in bivariate analysis. Furthermore, in multivariable conditional logistic regression analyses, we developed an energy-adjusted parsimonious model by stepwise backward deletion process where we adjusted three cardio-metabolic factors (diabetes, dyslipidemia, and BMI) and smoking. However, even though hypertension is a well-established risk factor, we did not observe a significant association; therefore, we did not include it in the model construction. The reason for the insignificant association of hypertension might be selecting the control groups from the same hospital’s outdoor patients, where more hypertensive patients come for their heart check-up. In the final model, we observed that dietary β-carotene and vitamin C were inversely associated with CAD, whereas higher dietary carbohydrate, total fat and oil, SFA, cholesterol, and iron intake were directly associated with CAD. We also performed random forest analysis to adjust the collinearity problem and then identify the topmost nutritional variables. Random forest analysis revealed that dietary intake of SFA, vitamin A, total fat and oil, β-carotene, and cholesterol were the topmost important nutrients associated with CAD. Even though dietary vitamin A was not significantly associated with CAD in conditional regression analysis, it remained important nutrients related to CAD in the random forest analysis.

The quantity and type of dietary fat/oil and carbohydrate consumption, fiber, protein, and alcohol intakes strongly impact blood lipids and lipoprotein metabolism, thereby developing CVDs [34]. Energy from complex carbohydrates has many benefits compared to refined sugars [34]. For example, a low glycemic index diet could improve blood lipids and blood pressure [35], thus reducing CAD [36]. Short term carbohydrate diet reduces the weight and atherosclerotic plaque in CAD, but the long term effect is still controversial [37]. Besides, a low carbohydrate diet is not associated with coronary artery incidence and progression [38]. The present study showed that an increased intake of dietary carbohydrates had a risk of CAD. However, we were unable to differentiate the dietary carbohydrate into refined and complex carbohydrates. A higher intake of fat without replacing protein and carbohydrates causes metabolic disorders related to CAD [39]. We found that total fat intake was proportionately associated with increased risk of CAD. However, dietary fat types, but not total fat intake, are an important determinant of CVDs [40]. Specifically, intakes of PUFAs and MUFAs are associated with a lower risk of CVDs and death, whereas SFA and trans-fat intakes are linked with a higher risk of CVDs [39]. Consistently, we reported significantly higher odds of CAD with increased SFA intake; PUFA and MUFA intakes were inversely but not significantly associated with CAD. The higher intake of carbohydrates, total fat, and SFA indicated an unhealthy eating pattern among the Nepalese population that might increase CAD prevalence.

Nevertheless, previous literature demonstrated a discrepancy in results among these specific fat intake groups. For example, SFA is proportionately associated with CAD [41], but not in the Kuopio Ischemic Heart Disease Risk Factor Study [42] and meta-analysis [43]. Likewise, in a recent meta-analysis, dietary intake of PUFA was not found significantly associated with CAD [44]. Besides, cholesterol is also independent risk factors of CAD according to lipid theory [45]. Incongruous with this study, we also reported a significant relationship between high dietary cholesterol and CAD’s risk; but, the minimal effect size of the risk was observed. A recent study [46], meta-analysis, and systemic reviews [47] do not conclude the dietary cholesterol as CAD’s risk.

Several epidemiological studies reported that higher dietary fiber is associated with a reduced CAD risk [48]. Mechanistically, dietary fibers could lower atherosclerosis [49] and alter microbiota that modulates the immune system [50]. Besides, high fiber consumption is related to a higher intake of vitamins and minerals [51]. In divergence with the findings mentioned above, we could not observe that a higher fiber intake could lower CAD’s risk. Moreover, the daily fiber intake amount was lower than the daily recommended allowance in both case and control groups, possibly because of specific dietary patterns in the Nepalese population. A prospective cohort study in Japan reported an inverse association of CHD with dietary intake of folic acid, vitamin B6, and vitamin B12 [18]. Recent dose-response meta-analysis shows that a higher intake of folate and vitamin B6 are associated with a lower risk of CAD [19]. Niacin intake has more enormous benefits in lowering LDL and increasing HDL in the blood in dyslipidemia patients; it could reduce the risk of CAD [52]. However, the Umbrella study concludes that nutritional supplements, such as folic acid, vitamin B6, vitamin B12 had no significant effect on mortality or CVDs outcomes [20]. In the present study, we did not observe any significant likelihood of CAD with dietary B vitamins. Vitamin A is associated with CAD severity, and β-carotene level diminish disease severity [21]. The present study revealed that vitamin C, vitamin A, and β-carotene intake were linked with CAD; a significant inverse association was reported with the intake of β-carotene but not with Vitamin A in the logistic model. This finding indicated antioxidant vitamins could be protective factors for the prevention of CAD in the Nepalese people. However, further large cohort or RCTs are required to confirm the present findings. A recent study in the Chinese population reported that β-carotene and vitamin C intake from the diet was inversely associated with deaths from all causes and CVDs in middle-aged or older people [53]. However, an inconsistent association of an antioxidant vitamin with CAD was reported in epidemiological studies [54].

Dietary calcium intake is inversely associated with CVDs [55]. Although a longer-term calcium intake is associated with a reduced risk of atherosclerosis, calcium supplementation may increase the risk of coronary artery calcification [56]. Dietary zinc intake was inversely associated with mortality from CHD in men but not women [57]. In contrast to these findings, our results did not reveal increased dietary calcium and zinc could reduce CAD’s risk. In the present study, we observed a significant result of higher dietary iron intake associated with CAD’s risk. Nonetheless, iron intake was not the topmost factors related to CAD in random forest analysis. The significant association of iron intake in the logistic model might be because of the multi-collinearity problem, which disguised the result. Simultaneously, heme iron intake was positively associated with CHD’s risk in Western populations [58], where red meat is a primary dietary source of iron. In contrast, this relationship was negative in the Japanese, who receive heme iron from fish and shellfish [59]. Several studies have reported that CHD incidence was positively associated with ferritin levels and inversely associated with serum Fe and transferrin saturation [60].

In the present study, the data were only taken from non-fatal CAD, and the sample size (306 cases and 306 control)) was quite small. We excluded the patients with equal or more than 50% and less than 70% stenosis in any one main coronary artery branch. As TMT negative patients and patients with normal coronary angiography were included as a control group, they could have a possibility of microvascular angina. Moreover, the control group was selected from the same hospital with or without having cardiovascular risk factors; there was a possibility of selection bias in the study. Thus, generalization is the drawback of the present study. Moreover, since the study was a case-control study, it might have many inherent biases that influence the causality link between the associated nutrients and the disease. Furthermore, our study observed dietary nutrients’ association based on the food list commonly consumed by the Nepalese population. Another limitation was that we calculated only the values of eighteen nutrients available in Nepal food composition table 2017.

Despite these limitations, we tried to minimize the possible bias, such as recall bias, which was minimized by displaying food atlas for portion size and verifying the information with hospital data and patients’ sick book as possible. Notably, we matched “Sex” individually and “Age” at the interval of five years to limit the confounders’ effect. Moreover, patients who modified their dietary intake habit after being diagnosed as having any one of CAD’s risk factors (obesity/hypertension/diabetes/dyslipidemia) were excluded to avoid possible unequal distribution of dietary nutrients due to predetermined health condition. Furthermore, the distribution of dietary nutrients in the control group was within the range of findings in a previous study conducted among Nepalese [61], which assured our control group represented the base/source population. Our study was unable to link the reverse causality between CAD and the dietary intake, which were likely altered as a result of a cardiovascular event; therefore, we used validated FFQ, which takes the information for recent one year, and also is considered elsewhere for research on nutrition concerning disease, so that we can compare the data with other analyses conveniently. We executed conditional logistic regression for model construction and random forest analysis to select nutrients variables, adjusting the collinearity problem to make the results valid.

Conclusions

Diet plays a crucial role in the development of several non-communicable diseases, including CVDs. Resource-poor countries like Nepal, extracting the dietary nutrients of relative importance, could have rational and promising strategies for CAD prevention through dietary intervention. A combination of multiple factors rather than a single factor is more potent for nutrients intervention. Thus, a dietary intervention approach in CVDs is an effective strategy to reduce the public health burden. We conclude that dietary SFA, vitamin A RE, dietary total fat and oil, β-carotene, and cholesterol are the topmost five essential dietary nutrients associated with CAD development. Consistent with most of the studies, we report dietary SFA, total oil and fat, and cholesterol intakes are proportionately related, whereas β-carotene and vitamin C intakes are inversely related to CAD. Our study suggests a higher dietary intake of β-carotene and vitamin C are possible protective dietary nutrients, while an increased intake of dietary SFA, total fat and oil, and cholesterol are potential risk factors for CAD development. However, prospective cohort and RCTs studies with a large sample size are needed to explore the causal link of these nutrients for the risk of CAD development in the Nepalese population.

Supporting information

S1 Table. List of food items commonly consumed by Nepalese in Nepal.

(DOCX)

S2 Table. Mean daily nutrient intakes estimated by the average of three 24 h dietary recalls (DR) and two food frequency questionnaires (FFQs), and correlations between the two methods.

ICC: Intraclass correlation coefficient; aData are shown as mean ± standard deviation (SD)

(DOCX)

S3 Table. Distribution of nutritional factors associated with coronary artery disease between case and control groups in the study.

kcal: kilocalorie; g: gram; mg: milligram; mcg: microgram; R.E.: retinol equivalent; PUFA: polyunsaturated fatty acid; MUFA: monounsaturated fatty acid; SFA: saturated fatty acid. aPaired t-test. bMean and standard deviation (SD) value. *p ≤ .05; **p≤ .01; ***p ≤ .001.

(DOCX)

S4 Table. Correlation matrix among eighteen dietary nutrients and energy intake.

PUFA: polyunsaturated fatty acid; MUFA: monounsaturated fatty acid; SFA: saturated fatty acid.

(DOCX)

S1 File. Survey questionnaire set and informed consent in the Nepali language.

(PDF)

S2 File. Informed consent in the English language.

(PDF)

S3 File. Survey questionnaire set in the English language.

(PDF)

S4 File. Ethical approval letter from Nepal Health Research Council.

(PDF)

S5 File. Reporting checklist for case-control study based on STROBE guideline.

(PDF)

S6 File. Data set.

(CSV)

S7 File. R code for statistical analyses.

(R)

Acknowledgments

The authors are grateful to Shahid Gangalal National Heart Center in Nepal, where the hospital management assisted with the set-up and data collection. We also acknowledge Professor Aihua Gu and Dr. Xu Cheng (Nanjing Medical University) for directing the entire research work. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication.

Data Availability

All relevant data are within the manuscript and its Supporting Information files.

Funding Statement

The author(s) received no specific funding for this work.

References

  • 1.Harrison TR. The cardiovascular system diseases Principles of Internal Medicine. Vol. 2, 16th ed, McGraw Hill, 2005. ISBN 88-386-2999-4. [Google Scholar]
  • 2.WHO. Cardiovascular diseases fact sheet. World Health Organization; 2017. [retrieved 2020-7-30]; Available from: https://www.who.int/en/news-room/fact-sheets/detail/cardiovascular-diseases-(cvds). [Google Scholar]
  • 3.WHO. Non-communicable Diseases Progress Monitor. Geneva: World Health Organization, 2017. [Google Scholar]
  • 4.Al-Attas O, Al-Daghri N, Alokail M, Abd-Alrahman S, Vinodson B, Sabico S. Metabolic Benefits of Six-month Thiamine Supplementation in Patients With and Without Diabetes Mellitus Type 2. Clin Med Insights Endocrinol Diabetes. 2014;7:1–6. Epub 2014/02/20. 10.4137/CMED.S13573 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Oikonomou E, Psaltopoulou T, Georgiopoulos G, Siasos G, Kokkou E, Antonopoulos A, et al. Western Dietary Pattern Is Associated With Severe Coronary Artery Disease. Angiology. 2018;69(4):339–46. Epub 2017/07/22. 10.1177/0003319717721603 . [DOI] [PubMed] [Google Scholar]
  • 6.Mensah GA, Wei GS, Sorlie PD, Fine LJ, Rosenberg Y, Kaufmann PG, et al. Decline in Cardiovascular Mortality: Possible Causes and Implications. Circulation research. 2017;120(2):366–80. Epub 2017/01/21. 10.1161/CIRCRESAHA.116.309115 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Mayen AL, Marques-Vidal P, Paccaud F, Bovet P, Stringhini S. Socioeconomic determinants of dietary patterns in low- and middle-income countries: a systematic review. The American journal of clinical nutrition. 2014;100(6):1520–31. Epub 2014/11/21. 10.3945/ajcn.114.089029 . [DOI] [PubMed] [Google Scholar]
  • 8.Loewen OK, Ekwaru JP, Ohinmmaa A, Veugelers PJ. Economic Burden of Not Complying with Canadian Food Recommendations in 2018. 2019;11(10). 10.3390/nu11102529 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Jang Y, Lee JH, Kim OY, Park HY, Lee SY. Consumption of whole grain and legume powder reduces insulin demand, lipid peroxidation, and plasma homocysteine concentrations in patients with coronary artery disease: randomized controlled clinical trial. Arteriosclerosis, thrombosis, and vascular biology. 2001;21(12):2065–71. Epub 2001/12/18. 10.1161/hq1201.100258 . [DOI] [PubMed] [Google Scholar]
  • 10.Iyengar SS, Gupta R, Ravi S, Thangam S, Alexander T, Manjunath CN, et al. Premature coronary artery disease in India: coronary artery disease in the young (CADY) registry. Indian Heart J. 2017;69(2):211–6. Epub 2017/05/04. 10.1016/j.ihj.2016.09.009 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Fazeli Moghadam E, Tadevosyan A, Fallahi E, Goodarzi R. Nutritional factors and metabolic variables in relation to the risk of coronary heart disease: A case control study in Armenian adults. Diabetes & metabolic syndrome. 2017;11(1):7–11. Epub 2016/06/25. 10.1016/j.dsx.2016.06.013 . [DOI] [PubMed] [Google Scholar]
  • 12.de Souza RJ, Mente A, Maroleanu A, Cozma AI, Ha V, Kishibe T, et al. Intake of saturated and trans unsaturated fatty acids and risk of all cause mortality, cardiovascular disease, and type 2 diabetes: systematic review and meta-analysis of observational studies. BMJ (Clinical research ed). 2015;351:h3978 Epub 2015/08/14. 10.1136/bmj.h3978 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Hooper L, Summerbell CD, Thompson R, Sills D, Roberts FG, Moore H, et al. Reduced or modified dietary fat for preventing cardiovascular disease. The Cochrane database of systematic reviews. 2011;(7):Cd002137 Epub 2011/07/08. 10.1002/14651858.CD002137.pub2 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Mozaffarian D. Dietary and Policy Priorities for Cardiovascular Disease, Diabetes, and Obesity: A Comprehensive Review. Circulation. 2016;133(2):187–225. Epub 2016/01/10. 10.1161/CIRCULATIONAHA.115.018585 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Brenna JT, Lapillonne A. Background paper on fat and fatty acid requirements during pregnancy and lactation. Ann Nutr Metab. 2009;55(1–3):97–122. Epub 2009/09/16. 10.1159/000228998 . [DOI] [PubMed] [Google Scholar]
  • 16.Marventano S, Kolacz P, Castellano S, Galvano F, Buscemi S, Mistretta A, et al. A review of recent evidence in human studies of n-3 and n-6 PUFA intake on cardiovascular disease, cancer, and depressive disorders: does the ratio really matter? International journal of food sciences and nutrition. 2015;66(6):611–22. Epub 2015/08/27. 10.3109/09637486.2015.1077790 . [DOI] [PubMed] [Google Scholar]
  • 17.Nettleton JA, Villalpando S, Cassani RS, Elmadfa I. Health significance of fat quality in the diet. Ann Nutr Metab. 2013;63(1–2):96–102. 10.1159/000353207 . [DOI] [PubMed] [Google Scholar]
  • 18.Ishihara J, Iso H, Inoue M, Iwasaki M, Okada K, Kita Y, et al. Intake of folate, vitamin B6 and vitamin B12 and the risk of CHD: the Japan Public Health Center-Based Prospective Study Cohort I. Journal of the American College of Nutrition. 2008;27(1):127–36. Epub 2008/05/08. 10.1080/07315724.2008.10719684 . [DOI] [PubMed] [Google Scholar]
  • 19.WHO Global Report: Mortality Attributable to Tobacco. Geneva: World Health Organization, 2012. [Google Scholar]
  • 20.La Torre G, Saulle R, Di Murro F, Siliquini R, Firenze A, Maurici M, et al. Mediterranean diet adherence and synergy with acute myocardial infarction and its determinants: A multicenter case-control study in Italy. PloS one. 2018;13(3):e0193360 Epub 2018/03/16. 10.1371/journal.pone.0193360 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Matos A, Goncalves V, Souza G, Cruz SPD, Cruz S, Ramalho A. Vitamin A nutritional status in patients with coronary artery disease and its correlation with the severity of the disease. Nutr Hosp. 2018;35(5):1215–20. Epub 2018/10/12. 10.20960/nh.1804 . [DOI] [PubMed] [Google Scholar]
  • 22.Koju R, Humagain S, Khanal K. Association of cardiovascular risk factors and coronary artery lesion among coronary artery disease patients. Kathmandu Univ Med J (KUMJ). 2014;12(46):137–40. Epub 2015/01/02. 10.3126/kumj.v12i2.13661 . [DOI] [PubMed] [Google Scholar]
  • 23.Campbell RK, Talegawkar SA, Christian P, Leclerq SC, Khatry SK, Wu LS, et al. Evaluation of a Novel Single-administration Food Frequency Questionnaire for Assessing Seasonally Varied Dietary Patterns among Women in Rural Nepal. Ecol Food Nutr. 2015;54(4):314–27. Epub 2015/02/14. 10.1080/03670244.2014.990635 . [DOI] [PubMed] [Google Scholar]
  • 24.Appropriate body-mass index for Asian populations and its implications for policy and intervention strategies. Lancet (London, England). 2004;363(9403):157–63. Epub 2004/01/17. 10.1016/S0140-6736(03)15268-3 . [DOI] [PubMed] [Google Scholar]
  • 25.Obesity: preventing and managing the global epidemic. Report of a WHO consultation. 2000 0512–3054. [PubMed]
  • 26.Chagas P, Mazocco L, Piccoli J, Ardenghi TM, Badimon L, Caramori PRA, et al. Association of alcohol consumption with coronary artery disease severity. Clinical nutrition (Edinburgh, Scotland). 2017;36(4):1036–9. Epub 2016/07/13. 10.1016/j.clnu.2016.06.017 . [DOI] [PubMed] [Google Scholar]
  • 27.Aidinoff E, Bluvshtein V, Bierman U, Gelernter I, Front L, Catz A. Coronary artery disease and hypertension in a non-selected spinal cord injury patient population. Spinal Cord. 2017;55(3):321–6. Epub 2016/07/20. 10.1038/sc.2016.109 . [DOI] [PubMed] [Google Scholar]
  • 28.Doi-Kanno M, Fukahori H. Predictors of Depression in Patients Diagnosed with Myocardial Infarction after Undergoing Percutaneous Coronary Intervention: A literature review. J Med Dent Sci. 2016;63(2–3):37–43. Epub 2016/10/25. 10.11480/jmds.630301 [DOI] [PubMed] [Google Scholar]
  • 29.WHO. STEPS surveillance manual: The WHO STEP wise approach to chronic disease risk factor surveillance. Geneva: World Health Organization; 2005. [Google Scholar]
  • 30.Murphy SP, Barr SI. Practice paper of the American Dietetic Association: using the Dietary Reference Intakes. Journal of the American Dietetic Association. 2011;111(5):762–70. Epub 2011/04/26. 10.1016/j.jada.2011.03.022 . [DOI] [PubMed] [Google Scholar]
  • 31.Zang J, Luo B, Chang S, Jin S, Shan C, Ma L, et al. Validity and reliability of a food frequency questionnaire for assessing dietary intake among Shanghai residents. 2019;18(1):30 10.1186/s12937-019-0454-2 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Beunza JJ, Puertas E, García-Ovejero E, Villalba G, Condes E, Koleva G, et al. Comparison of machine learning algorithms for clinical event prediction (risk of coronary heart disease). Journal of biomedical informatics. 2019;97:103257 Epub 2019/08/03. 10.1016/j.jbi.2019.103257 . [DOI] [PubMed] [Google Scholar]
  • 33.Zhang X, Dai Z, Lau EHY, Cui C, Lin H, Qi J, et al. Prevalence of bone mineral density loss and potential risk factors for osteopenia and osteoporosis in rheumatic patients in China: logistic regression and random forest analysis. Annals of translational medicine. 2020;8(5):226 Epub 2020/04/21. 10.21037/atm.2020.01.08 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Fan J, Song Y, Wang Y, Hui R, Zhang W. Dietary glycemic index, glycemic load, and risk of coronary heart disease, stroke, and stroke mortality: a systematic review with meta-analysis. PLoS One. 2012;7(12):e52182 Epub 2013/01/04. 10.1371/journal.pone.0052182 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Clar C, Al-Khudairy L, Loveman E, Kelly SA, Hartley L, Flowers N, et al. Low glycaemic index diets for the prevention of cardiovascular disease. Cochrane Database Syst Rev. 2017;7:Cd004467 Epub 2017/08/02. 10.1002/14651858.CD004467.pub3 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Choi Y, Chang Y, Ryu S, Cho J, Kim MK, Ahn Y, et al. Relation of Dietary Glycemic Index and Glycemic Load to Coronary Artery Calcium in Asymptomatic Korean Adults. Am J Cardiol. 2015;116(4):520–6. Epub 2015/06/16. 10.1016/j.amjcard.2015.05.005 . [DOI] [PubMed] [Google Scholar]
  • 37.Hu T, Bazzano LA. The low-carbohydrate diet and cardiovascular risk factors: evidence from epidemiologic studies. Nutr Metab Cardiovasc Dis. 2014;24(4):337–43. Epub 2014/03/13. 10.1016/j.numecd.2013.12.008 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Hu T, Jacobs DR. Low-carbohydrate diets and prevalence, incidence and progression of coronary artery calcium in the Multi-Ethnic Study of Atherosclerosis (MESA). 2019:1–8. 10.1017/s0007114518003513 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Guasch-Ferre M, Babio N, Martinez-Gonzalez MA, Corella D, Ros E, Martin-Pelaez S, et al. Dietary fat intake and risk of cardiovascular disease and all-cause mortality in a population at high risk of cardiovascular disease. 2015;102(6):1563–73. 10.3945/ajcn.115.116046 . [DOI] [PubMed] [Google Scholar]
  • 40.Zock PL, Blom WA, Nettleton JA, Hornstra G. Progressing Insights into the Role of Dietary Fats in the Prevention of Cardiovascular Disease. Current cardiology reports. 2016;18(11):111 Epub 2016/09/22. 10.1007/s11886-016-0793-y [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Zong G, Li Y, Wanders AJ, Alssema M, Zock PL, Willett WC, et al. Intake of individual saturated fatty acids and risk of coronary heart disease in US men and women: two prospective longitudinal cohort studies. BMJ (Clinical research ed). 2016;355:i5796 Epub 2016/11/25. 10.1136/bmj.i5796 www.icmje.org/coi_disclosure.pdf and declare: support from the National Institutes of Health for the submitted work; GZ is supported by a postdoctoral fellowship funded by Unilever R&D, Vlaardingen, Netherlands; AJW, MA, and PLZ are employees of Unilever R&D (Unilever is a producer of food consumer products); FBH has received research support from California Walnut Commission and Metagenics; no other relationships or activities that could appear to have influenced the submitted work. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 42.Virtanen JK, Mursu J, Tuomainen TP, Voutilainen S. Dietary fatty acids and risk of coronary heart disease in men: the Kuopio Ischemic Heart Disease Risk Factor Study. Arterioscler Thromb Vasc Biol. 2014;34(12). 10.1161/ATVBAHA.114.304082 [DOI] [PubMed] [Google Scholar]
  • 43.Farvid MS, Ding M, Pan A, Sun Q, Chiuve SE, Steffen LM, et al. Dietary linoleic acid and risk of coronary heart disease: a systematic review and meta-analysis of prospective cohort studies. Circulation. 2014;130(18):1568–78. Epub 2014/08/28. 10.1161/CIRCULATIONAHA.114.010236 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 44.Chowdhury R, Warnakula S, Kunutsor S, Crowe F, Ward HA, Johnson L, et al. Association of dietary, circulating, and supplement fatty acids with coronary risk: a systematic review and meta-analysis. Annals of internal medicine. 2014;160(6):398–406. Epub 2014/04/12. 10.7326/M13-1788 . [DOI] [PubMed] [Google Scholar]
  • 45.Ruiz-Nunez B, Dijck-Brouwer DA, Muskiet FA. The relation of saturated fatty acids with low-grade inflammation and cardiovascular disease. J Nutr Biochem. 2016;36:1–20. Epub 2016/10/04. 10.1016/j.jnutbio.2015.12.007 . [DOI] [PubMed] [Google Scholar]
  • 46.Virtanen JK, Mursu J, Virtanen HE, Fogelholm M, Salonen JT, Koskinen TT, et al. Associations of egg and cholesterol intakes with carotid intima-media thickness and risk of incident coronary artery disease according to apolipoprotein E phenotype in men: the Kuopio Ischaemic Heart Disease Risk Factor Study. The American journal of clinical nutrition. 2016;103(3):895–901. Epub 2016/02/13. 10.3945/ajcn.115.122317 . [DOI] [PubMed] [Google Scholar]
  • 47.Berger S, Raman G. Dietary cholesterol and cardiovascular disease: a systematic review and meta-analysis. 2015;102(2):276–94. 10.3945/ajcn.114.100305 . [DOI] [PubMed] [Google Scholar]
  • 48.Wu Y, Qian Y, Pan Y, Li P, Yang J, Ye X, et al. Association between dietary fiber intake and risk of coronary heart disease: A meta-analysis. Clin Nutr. 2015;34(4):603–11. Epub 2014/06/16. 10.1016/j.clnu.2014.05.009 . [DOI] [PubMed] [Google Scholar]
  • 49.North CJ, Venter CS, Jerling JC. The effects of dietary fibre on C-reactive protein, an inflammation marker predicting cardiovascular disease. European journal of clinical nutrition. 2009;63(8):921–33. Epub 2009/02/19. 10.1038/ejcn.2009.8 . [DOI] [PubMed] [Google Scholar]
  • 50.Kuo SM. The interplay between fiber and the intestinal microbiome in the inflammatory response. Advances in nutrition (Bethesda, Md). 2013;4(1):16–28. Epub 2013/01/16. 10.3945/an.112.003046 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Kaluza J, Orsini N, Levitan EB, Brzozowska A, Roszkowski W, Wolk A. Dietary calcium and magnesium intake and mortality: a prospective study of men. American journal of epidemiology. 2010;171(7):801–7. Epub 2010/02/23. 10.1093/aje/kwp467 . [DOI] [PubMed] [Google Scholar]
  • 52.Superko HR, Zhao XQ, Hodis HN, Guyton JR. Niacin and heart disease prevention: Engraving its tombstone is a mistake. J Clin Lipidol. 2017;11(6):1309–17. Epub 2017/09/21. 10.1016/j.jacl.2017.08.005 . [DOI] [PubMed] [Google Scholar]
  • 53.Zhao LG, Shu XO, Li HL, Zhang W, Gao J, Sun JW, et al. Dietary antioxidant vitamins intake and mortality: A report from two cohort studies of Chinese adults in Shanghai. J Epidemiol. 2017;27(3):89–97. Epub 2017/02/01. 10.1016/j.je.2016.10.002 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Alissa EM, Bahjri SM, Al-Ama N, Ahmed WH, Starkey B, Ferns GA. Dietary vitamin A may be a cardiovascular risk factor in a Saudi population. Asia Pacific journal of clinical nutrition. 2005;14(2):137–44. Epub 2005/06/02. . [PubMed] [Google Scholar]
  • 55.Kong SH, Kim JH. Dietary calcium intake and risk of cardiovascular disease, stroke, and fracture in a population with low calcium intake. 2017;106(1):27–34. 10.3945/ajcn.116.148171 . [DOI] [PubMed] [Google Scholar]
  • 56.Anderson JJ, Kruszka B, Delaney JA, He K, Burke GL, Alonso A, et al. Calcium Intake From Diet and Supplements and the Risk of Coronary Artery Calcification and its Progression Among Older Adults: 10-Year Follow-up of the Multi-Ethnic Study of Atherosclerosis (MESA). Journal of the American Heart Association. 2016;5(10). Epub 2016/10/13. 10.1161/jaha.116.003815 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 57.Eshak ES, Iso H, Yamagishi K, Maruyama K, Umesawa M, Tamakoshi A. Associations between copper and zinc intakes from diet and mortality from cardiovascular disease in a large population-based prospective cohort study. Journal of Nutritional Biochemistry. 2018;56:126–32. 10.1016/j.jnutbio.2018.02.008 WOS:000435747700014. [DOI] [PubMed] [Google Scholar]
  • 58.de Oliveira Otto MC, Alonso A, Lee DH, Delclos GL, Bertoni AG, Jiang R, et al. Dietary intakes of zinc and heme iron from red meat, but not from other sources, are associated with greater risk of metabolic syndrome and cardiovascular disease. The Journal of nutrition. 2012;142(3):526–33. Epub 2012/01/20. 10.3945/jn.111.149781 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 59.Sun Q, Shi L, Rimm EB, Giovannucci EL, Hu FB, Manson JE, et al. Vitamin D intake and risk of cardiovascular disease in US men and women. The American journal of clinical nutrition. 2011;94(2):534–42. Epub 2011/06/10. 10.3945/ajcn.110.008763 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 60.Hunnicutt J, He K, Xun P. Dietary iron intake and body iron stores are associated with risk of coronary heart disease in a meta-analysis of prospective cohort studies. J Nutr. 2014;144(3):359–66. Epub 2014/01/10. 10.3945/jn.113.185124 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 61.Shrestha A, Koju RP, Beresford SAA, Chan KCG, Connell FA, Karmacharya BM, et al. Reproducibility and relative validity of food group intake in a food frequency questionnaire developed for Nepalese diet. International journal of food sciences and nutrition. 2017;68(5):605–12. Epub 2017/01/18. 10.1080/09637486.2016.1268099 . [DOI] [PubMed] [Google Scholar]

Decision Letter 0

Samson Gebremedhin

27 May 2020

PONE-D-20-07225

Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

PLOS ONE

Dear Dr. BASNET,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

  • The manuscript lacks important methodological details needed for correct interpretation of the study. Please describe in better depth: (i) why your preferred to use “Random forest analysis”, and why both conditional LR and Random Forest Analysis were employed together to answer the same research question? (ii) Why these specific dietary nutrients were selected for analysis (why not others)? (iii) How did you select potential confounders for adjustment? (iv) How was the sample size of 306 cases and 306 controls determined? (v) what was the justification for developing two different multivariable models (model 1 and model 2) to explain an outcome while it is possible to have a single model with a better fit?

  • It is not clear how some of the variables (e.g. physical exercise, smoking, alcohol use) were measured and categories. Can you please add a sub-section (under the methods section) that describes the variables of the study along with the measurement and classifications employed?

  • Can you explain further how you detected very significant statistical difference in the age of the cases and controls after having exactly the same median and IQR values?

  • It seems the authors have already published on risk factors of CHD using the same dataset before (https://pubmed.ncbi.nlm.nih.gov/31588344/). Please describe in the background section how this paper is different from the earlier and why it was not possible to report the findings of the two papers together.

  • Most of the reported ORs only have borderline statistical significance. Based on these findings, would that be possible to given strong practical recommendations? Can you discuss the issue further?

  • As noted by both of the reviewers, please discuss the limitations of study in a better depth. 

Please submit your revised manuscript by Jul 10 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Samson Gebremedhin, PhD

Academic Editor

PLOS ONE

Other section-by-section comments

Abstract

  • Report separately the sample size for cases and controls. It would also be good to provide the concise enrolment criteria for cases and controls.

Background

  • This section is somehow superficial. Can you please add a paragraph that summarizes what is known about the dietary risk factors of CAD?

Methods and materials

  • Line 78-80: what about the 24-hr recall?

  • Line 89-90: can you please describe the "24-h recall diet survey" in a better depth? In the results section, I don’t see any data on the results of this Criterion Validity assessment.

  • Line 112: why did you use Wilcoxon sign ranked test for continuous variables? Was the distribution not normally distributed? Have you tried transformation before resorting to this non-parametric test?

Results

  • Line 129-31: “This might be because of the selection of the control groups from the outdoor patients of the same hospital where more hypertensive patients come for their heart checkup”. This should rather be presented in the “discussion” section

  • Table 1: “Hard” > “vigorous”

  • Table 1: drinking alcohol and smoking: have you tried consider dose of exposure while defining these variables?

  • Line 134-143: is this from the 24-hr recall or the food frequency questionnaire?

  • Table 2: please clearly denote significant differences with “*”

  • Line 145-48: it is good that you have used conditional logistic regression. But what was the variable/s conditioned in the analysis. if “age” was the conditioning variable, then why was it adjusted in the model?

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information.

3. Please amend the manuscript submission data (via Edit Submission) to include authors Ali Asghar Mirjat, Falak Zeb and Wiwik Indayati.

4. Your ethics statement must appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please also ensure that your ethics statement is included in your manuscript, as the ethics section of your online submission will not be published alongside your manuscript.

5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: No

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: No

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: No

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: 1) Innovation perspective the research is not very significant for the researchers globally. Most of the innovations are already available in the literature. As far my knowledge many studies already published these kinds of results. For example, Mahalle et. al. (2016): Association of dietary factors with severity of coronary artery disease. Authors in the manuscript (line no. 257) state “Finally, we found a consistent result with other published studies.”

2) The primary outcome of any case-control study is mainly based on the quality data. If the data is not good quality data then the observations on these data don’t confirm any firm statement. Based on interview questionnaire and the response of the person don’t strongly establish the dietary quantity and quality. If the diet would be provided by any good supply source who would maintain the quantity and quality of the food consumed by the patients, then, the data quality would be much better.

3) There is no external validation of the results. It majorly focused on Nepalese dataset but the research title is generic. External validation (dataset collecting from near countries such as India, Bhutan, Bangladesh) is required for the title otherwise title need to be changed to focus on Nepalese population perspective.

4) The cohort is has been taken from one hospital and therefore, the results may be biased until the data has been taken in standard published process. At least 2 cohorts’ data is required for this study as it is based on face to face interview questions.

5) When we apply model’s then its strength needs to be checked by providing some metrics, such as, model’s stability by providing ROC curve, sensitivity, specificity, accuracy, f-score etc. These are clearly missing here.

6) There are several standard algorithms compared to Random Forest (RF) regression are available. This study chose RF without giving proper justification.

7) Case: control is used 1:1 which is pretty rare in real scenarios. This study has lacks in producing right case and control samples. For example, it doesn’t tell how many patients have participated in the study and how some of them have been excluded from the study with proper logic. By using only Angiography (<70% stenosis) is not enough.

8) In the discussion, some of the statements are contradict with the previous studies. But most of the cases, their rationalities are not explained clearly.

9) Discussion section is not well organized to understand the study as stated in the title.

10) No justification has been given on selecting confounding variables for adjustment.

11) For selecting confounding variables from one result to the next, there are several techniques like forward elimination, backward elimination could be used.

12) There are many statements stated without giving proper references, e.g., line no. 27, 29, 44, etc. and so on.

13) The full questionnaire and data are not exposed to assess the results.

14) Source code of the models and data are available to reproduce the results.

15) Some silly inconsistencies, like, line 144 states p<0.1.

Reviewer #2: Review

Manuscript Number: PONE-D-20-07225

Manuscript Title: Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

Summary of study

This is a retrospective case-control study examining the difference in calorie consumption and intake of 18 nutrients between those with established coronary artery disease (CAD) (n=306) versus a control (n=306). The purpose of the study is to establish associations between the consumption of specific nutrients and CAD in the Nepalese population; associations that the authors believe ought to inform future RCTs/prospective cohort studies and future health policy.

It examined a total of 612 patients from the Shahid Gangalal National Heart Centre, Nepal with case-control matched via age and gender. Patients were recruited to the study following admission to the hospital due to a suspected coronary problem (recent suspected myocardial infarction, an exercise induced positive stress test result, or who elected to have an angiography). Patients were assigned to the ‘case’ group if they showed evidence of severe stenosis (>70%). Control subjects were patients who upon arrival were found to have ‘normal’ angiographic results (authors should specify exactly what this means – the flow chart in Fig 1 gives the impression of 0% stenosis) or who were found to have no ECG abnormalities following an exercise stress test. According to the authors, those with intermediate stenosis (<70% obstruction) were excluded from the study, presumably any patient with evidence of stenosis ranging from 1–69%.

Data on nutrient consumption over the previous 12-months for each participant was derived from an EPIC food frequency questionnaire. Authors calculated average daily calorie consumption and selected 18 nutrients for analysis – total fat, total carbohydrate, total protein, fibre, calcium, phosphorous, iron, zinc, thiamine, riboflavin, niacin, Vitamin C, β-Carotene, Vitamin A, polyunsaturated fatty acids (PUFA), monounsaturated fatty acids (MUFA), saturated fatty acids (SFA), and cholesterol. Data on known risk factors (diabetes; dyslipidaemia; hypertension; obesity based on BMI; obesity based on central obesity via waist–hip ratio), and data on behaviours believed to be associated with CAD (alcohol consumption; smoking status; and physical activity level) were also recorded for each patient.

Using conditional multivariable logistic regression, authors report two statistically significant positive associations after controlling for known risk-factors (model-2): (i) a positive relationship with total fat intake (OR 1.13, 95% CI 1.05–1.21, P≤0.001); (ii) a positive relationship with dietary cholesterol intake (OR 1.06, 95% CI 1–1.12, P=0.02) – note, however, the inclusion of 1 in the confidence interval. The study also found statistically significant differences (inverse associations) between those with CAD and those without in terms of intakes of: (i) total carbohydrate intake (OR 0.93, 95% CI 0.86–0.99, P=0.04); (ii) calcium intake (OR 0.96, 95% CI 0.94–0.99, P=0.003); (iii) zinc intake (OR 0.88, 95% CI 0.79–0.98, P=0.02); (iv) niacin intake (OR 0.8, 95% CI 0.7–0.91, P≤0.001); (v) β-Carotene intake (OR 0.93; 95% CI 0.9–0.97, P=0.001).

Following this, the authors use a random forest regression to adjust for collinearity between the variables, which the authors believe allow them to discern the “five topmost important nutrients…linked with CAD: β-Carotene, fat, cholesterol, vitamin C, and fibre intakes”. However, the authors need to provide substantially more detail in the description of results and methodology used for this than is reported here. As it is, I’m not entirely sure what to make of these results.

They then proceed to offer a superficial comparison of their findings with the existing literature. This requires extensive revision, however, and the authors need to ensure they avoid committing citation bias here in regards to some of their claims. To do this, they need to show a greater understanding of the conflicting results of large RCTs, prospective cohort studies, and recent meta-analyses. Fortunately, for each of the nutrients examined here, there is an extensive literature on their relationship with CAD/CVD – so the authors really need to engage with this literature.

The authors conclude by claiming: “We conclude that dietary β-Carotene, total fat and oil, cholesterol, vitamin C, and fiber in the Nepalese population”.

However, I believe, the following points must be addressed before this study can be published:

1. Ethics

Before publication, the authors need to include more details about ethical approval. PLOS ONE’s policy on this is as follows:

"Human Subject Research (involving human participants and/or tissue)

- Give the name of the institutional review board or ethics committee that approved the study

- Include the approval number and/or a statement indicating approval of this research

- Indicate the form of consent obtained (written/oral) or the reason that consent was not obtained (e.g. the data were analysed anonymously))"

The authors state that this study was approved by the Nepal Health Research Council (NHRC). Is the value given here (308/2017-18) the study registration code? Is this associated with certification of ethical clearance by the NHRC ethics committee? Could the authors please attach the appropriate ethical approval documentation as a supplementary file; a letter from the NHRC stating this clearance was provided will suffice. As the authors state that they have received written informed consent by every study participant, could the authors also go into some detail about whether those participants were informed their data (anonymised) would be available open access?

2. Data availability

The authors must supply all data associated with their analyses. The authors have claimed all relevant data are supplied in the paper or supplementary files, but this is inaccurate. The results of this paper depend on the analysis of distribution data, and this is necessary for replication. PLOS ONE’s policy states – “PLOS journals require authors to make all data necessary to replicate their study’s findings publicly available without restriction at the time of publication”. Accordingly, the relevant data for every study participant on which this papers analysis depends must either be included as supplementary files or stored in an online data repository after patient data has been appropriately anonymised. These data could be provided in spreadsheets – for the 612 patients, this involves providing all data on control/case group membership, age, weight, gender, dyslipidaemia, hypertension, obesity, smoking, alcohol consumption, physical activity, calorie consumption, and all data regarding intake of the 18 examined nutrients. Indeed, in light of the following problems, it is the data collected by the authors here is probably the most important aspect of the study.

3. Problems concerning data analysis

Multiple comparisons:

One major problem is accounting for multiple comparisons in this study. For example, Table 2 lists 19 variables (18 nutrients and total calorie consumption) each of which has been compared with a Wilcoxon rank-sum test – so the quoted significance levels at the very least need to be adjusted for the fact that 19 comparisons have been made. The same issue recurs throughout the analysis. The authors should seek to resolve this issue via appropriate statistical methods. I would also recommend that this study is referred to a statistical editor upon these revisions to ensure that this issue has been appropriately resolved.

Multicollinearity:

Apart from the problem of multiple comparisons here there is also the problem that the data are not fully independent (multicollinearity) – specific micronutrients tend to be associated with other particular nutrients in different food types. Accordingly, it is important not to over interpret associations unless these issues are rigorously excluded. Accordingly, the authors should reflect more on this issue and adjust their methods/interpretations in light of this. One option here would be to extend their discussion of their random forest regression. Indeed, the paper would benefit from extending and deepening the description and results of this analysis, providing results on correlations between nutrient intakes and variance inflation factor. Again, I believe a statistical editor should be consulted.

Other data analysis issues:

In Table 1, the authors claim that the median age of authors is statistically significantly different between the case and control groups. The authors report the median age, interquartile range, and P-value as:

Case: 58 (50–65) | Control: 58 (50–65) | P=0.001

Not only is the median age the same, but so too are the interquartile ranges. Yet, despite this, the age difference is apparently statistically significant? The authors seem to interpret this result as meaningful:

“Because the age was matched in five year intervals in the study, the median age was 58 years, which was the same in both case and control groups, respectively, and still showing strong association (P=0.001).”

The authors claim that age was matched in 5-year intervals, but are we then to interpret these results as suggesting that there is actually a significant difference in age between case-control matched pairs? As CAD is strongly associated with age in previous research, this is important to clarify. To do this, the authors need to report the age distribution data for both groups as a supplementary file.

For the analysis in Table 2, the authors claim “as most of the study data were not normally distributed, median and interquartile range of nutrients are presented”. The authors should, therefore, include in their supplementary material the actual data underpinning their analysis. At the very least, they must include the mean, range, and SD for each nutrient, so the reader can understand exactly what the distribution of these data actually are. Indeed, the data provided in the paper is insufficient to replicate the necessary results reported, despite the authors declaration.

Statistical rhetoric:

The authors highlight a “highly significant” finding (p.9), this language is inappropriate and should be replaced. A result is simply either significant or non-significant and this is determined by whatever threshold of significance the authors deem necessary.

4. Problems of variable selection and measurement

Nutrient selection:

The authors select 18 nutrients to examine here, but why these specific nutrients are analysed is not adequately justified. Accordingly, the authors should make clearer why these items were selected for analysis.

In the supplementary file, a list of common foods consumed is provided. This raises further questions about why the authors chose only to analyse the variables they selected in this paper because other variables appear possible to derive from their data. For example, I see no reason why the amount of sugars in the diet couldn’t be calculated from the listed food items, so why isn’t this examined in the paper? Similarly, their decision to use total carbohydrate intake as a variable without breaking this down into refined and complex carbohydrates appears strange and problematic, particular because the authors acknowledge in the paper that there are important differences between these. Why then didn’t the authors calculate these?

In its current state, this Table of food items is both uninformative and misleading. It also raises further questions about how nutrient intakes were measured. Patients were asked about milk consumption, but the milk category does not clarify whether respondents were asked specifically about the amount of full, semi, or skimmed milk consumed, which would be necessary to understand fat content and fatty acid profiles, or whether this was a single category. Further questions about how the quantities of PUFA, MUFA, and SFA were calculated arise in regards to several of the vague categories, such as “vegetable oils”. Accordingly, the authors should include the specific dietary survey actually provided to patients. Furthermore, supplying the average amount of each food consumed by cases and controls for each item would shed more light on dietary habits. As recent research suggests different whole foods might have different effects on lipid profiles and thereby atherosclerosis, these data are important to report. At the very least the authors need to make available the intakes of each nutrient examined in this study per patient.

Other questions that arise are why were PUFA here considered as a single group and not split further into Omega-3 and Omega-6 variants? Why was the intake of trans-fats not measured? Thus, the authors need to revise the manuscript to give the reader a clearer understanding of the theoretical justification for the selection of the variables. As there is a voluminous literature on the relationship between diet and atherosclerosis/CHD/CVD extending back to the early 20th century, there is a wonderfully rich literature to draw from.

Self-reported nutritional data:

As all the nutritional data are all self-reported, the authors should include a clearly discussion in regards to their reliability given the known problems with this kind of data. I suspect there is a problem here. From Table 2, it appears that total daily nutritional intake was virtually the same in the two groups – despite the significantly higher incidence of obesity in the control group.

5. Referencing

In-text references in this paper appear occasionally only loosely related to the claims they are purported to be associated with. For example, reference number 2 is inserted after the following sentence:

“In Nepal, 30% of total death was related to cardiovascular disease (2).”

Yet, reference 2 is a paper by Rankinen et al. (2015), and nowhere in this paper is this claim made. Another reference chosen at random, reference 20, is used to support the authors claim that:

“Besides cholesterol is also an independent risk factor of CAD according to the lipid theory”

The paper referenced nowhere discussed dietary cholesterol. It is a paper examining, as the title suggests, the “Relationships Between Components of Blood Pressure and Cardiovascular Events in Patients with Stable Coronary Artery Disease and Hypertension”. The only mention of cholesterol in this paper is HDL-C and LDL-C – that is, cholesterol bound in particular classes of lipoproteins carried in the blood.

If the authors make the rest of the revisions outlined, I will examine each of the references of this paper. So my recommendation would be to go through each reference and ensure it is relevant to the claim being made. As discussed, the authors also need to ensure they have adequately represented the state of research in relation to their claims. If the article is resubmitted, I’ll check each

6. Flawed study design

However, there is one problem that may undermine the point of revising this manuscript. The authors have a case-matched control group – but the control group are not healthy individuals, but patients with other health conditions and cardiovascular symptoms. This is clearly evident by the way the authors chose to enrol patients – all patients were being examined because of suspected coronary problems. This makes it impossible to talk of differences between these groups in terms of risk factors.

For example, looking at Table 1, the ‘control’ group has a significantly higher incidence of obesity and central obesity – but it would be obviously wrong to conclude that obesity and central obesity are protective against cardiovascular disease. Here we’re seeing a stratification of phenotypic characteristics between two different patient groups, and from this we can’t conclude anything at all about risk.

This might also explain the extremely strange finding that the number of hypertensives was roughly the same in both the control and case groups - Control: 143 hypertensives (~46.7%) | Case: 142 hypertensives (~46.4%). As hypertension is one of the key known risk factors in the development of CAD/CVD and extensively supported in the literature, this finding requires a lot more reflection. Why were hypertensives so common in the control group? This control group had apparently no evidence of stenosis – so this seems to be quite an important avenue to explore what went on here.

Accordingly, this design is inappropriate for the authors stated intention: “The present case-control study was designed to determine the association of dietary nutrients with CAD in the Nepalese population”.

If this study is to be published, the authors need to somehow explain why this control group can be considered representative of a broader population. Later in the paper the authors do highlight the results may have been biased due to “the selection of the control group from the outdoor patients from the same hospital where more hypertensive patients come for their heart check-up”, but this seems to critically undermine the entire results of this study.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachment

Submitted filename: Review. PONE-D-20-07225.docx

PLoS One. 2020 Dec 10;15(12):e0243063. doi: 10.1371/journal.pone.0243063.r002

Author response to Decision Letter 0


16 Aug 2020

Response Letter

July 30, 2020

To,

Dear Academic editors and Reviewers,

We highly appreciate comments of academic editor and both the reviewers in our manuscript entitled " Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis" (PONE-D-20-07225). We have modified the manuscript; accordingly, there has been a visible improvement in our manuscript after incorporating the comments. The responses to the comments are listed below.

We hope this manuscript will be acceptable for publication in your reputed journal.

Sincerely,

Til Bahadur Basnet

Ph.D. Candidate (Epidemiology and health statistics)

………………………………………..

1. Academic editor comments

• The manuscript lacks important methodological details needed for correct interpretation of the study. Please describe in better depth: (i) why your preferred to use “Random forest analysis”, and why both conditional LR and Random Forest Analysis were employed together to answer the same research question? (ii) Why these specific dietary nutrients were selected for analysis (why not others)? (iii) How did you select potential confounders for adjustment? (iv) How was the sample size of 306 cases and 306 controls determined? (v) what was the justification for developing two different multivariable models (model 1 and model 2) to explain an outcome while it is possible to have a single model with a better fit?

Response: Thank you so much for all the comments, which were very valuable and encouraging. We believe that we have improved the methodological details for correct interpretation of the study addressing the quarries raised.

(i) why your preferred to use “Random forest analysis”, and why both conditional LR and Random Forest Analysis were employed together to answer the same research question?

Random forest (RF) analysis is an algorithm based technique that not only picks up the important variables but also useful technique when the data have normality as well as multicollinearity problem. RF is a useful technique when data have relatively fewer observations because the analysis is based on an ensemble of classification trees in which it split the data into several nodes that maximized the homogeneity in each group, the random forest assembled hundreds more classification trees with a selection of correlates randomly. However, it cannot determine the strength of association. In contrast, conditional LR is the correct method to determine the strength of association in matched case control study. Therefore, we preferred both analyses in our study.

(ii) Why these specific dietary nutrients were selected for analysis (why not others)?

Upon review of the literature, dietary nutrients that we selected were associated with coronary artery disease (CAD) with the discrepancy in results in different populations across the globe. And we calculated nutrient intake based on "Nepal food composition table 2017," which lacks other specific nutrients like biotin, magnesium, selenium, and others related to CAD.

(iii) How did you select potential confounders for adjustment?

Although there are several newer techniques like a-priori change (e.g., 10% or 15%) in the effect estimate criteria, bias-variance tradeoff, directed acyclic graph (DAG), we adopted conventional way of a p-value of cut off in the statistical model. After bivariate analysis (Wilcoxon sign-rank sum test for continuous but non-parametric paired data and McNemar test for dichotomous paired data analysis in matched case-control study ) [1], those variables which showed p-value less than 0.1 ( usually ranges from 0.05 up to 0.2) in bivariate analysis has been considered as potential confounders for adjustments.

(iv) How was the sample size of 306 cases and 306 controls determined?

The sample size was calculated for matched case-control study with group of unequal sample size taking Zα=0.05, Zβ=0.8, prevalence of exposure = 0.19 (prevalence of smoking in the Nepalese population [2]), minimum detectable OR = 1.75. Using the formula developed by Schlesselman, the minimum sample size was 279. After adding a 10% non-response rate, the sample size was 306 in each group.

However, the present work was to construct a model using conditional logistic regression analysis. For multivariable analysis, the number of observations, in general, is ten times the number of predictors was suggested [3]. In this study, 19 nutrients variables and ten socio-demographic and cardio-metabolic risk factors were considered. Indeed, we selected only 23 predictors in the initial step of model construction. In the final model, only 12 variables were considered significantly associated with the outcome variables. Thus, we believe our sample size was considered enough for the present research work.

(v) What was the justification for developing two different multivariable models (model 1 and model 2) to explain an outcome while it is possible to have a single model with a better fit?

Thank you for your suggestion to develop a single model with a better fit. We have constructed a single energy-adjusted parsimonious multivariate model with a better fit by stepwise backward deletion process. And the results from the final model were presented in table 4.

• It is not clear how some of the variables (e.g. physical exercise, smoking, alcohol use) were measured and categories. Can you please add a sub-section (under the methods section) that describes the variables of the study along with the measurement and classifications employed?

We acknowledge your suggestions. So, we included the operational definition of conventional variables (e.g., physical exercise, smoking, alcohol use) as a sub-section under the methods section and described how they were measured and categorized.

• Can you explain further how you detected very significant statistical difference in the age of the cases and controls after having exactly the same median and IQR values?

Our study was matched case-control study, and we exactly matched the “sex," but we matched the “age” at an interval of 5 years. Because of interval matching and Wilcoxon-sign ranked test for matched paired non-parametric data, “age” showed a significant association with outcome.

• It seems the authors have already published on risk factors of CHD using the same dataset before (https://pubmed.ncbi.nlm.nih.gov/31588344/). Please describe in the background section how this paper is different from the earlier and why it was not possible to report the findings of the two papers together.

The paper which we published was the “association of smoking with CAD." If we included the dietary nutrients in that article, that would be lager in word count, which was beyond an essential requirement for the journal. Also, the paper would not be specific and exciting to the reader. Therefore, because of the words limit in the journal and specific detailed description of factors associated, it was not possible to include the dietary factors in the previous manuscript.

• Most of the reported ORs only have borderline statistical significance. Based on these findings, would that be possible to given strong practical recommendations? Can you discuss the issue further?

Unlike conventional risk factors (such as hypertension, diabetes, smoking), there was still a discrepancy in findings of the association of dietary nutrients with CAD in different populations across the world. Furthermore, several studies have reported relatively a higher effect size for conventional risk factors and smaller effect size for nutritional risk factors. We also observed some essential nutrients (beta-carotene, riboflavin, fiber, and vitamin C) that have not met the minimum recommended daily requirements (RDA) both in cases and controls. To confirm the effect of nutrients specific such as antioxidant vitamins on CAD, RCT and large cohort studies are required in the Nepalese population.

• As noted by both of the reviewers, please discuss the limitations of study in a better depth.

Thank you much for scrupulous perusing and valuable comments for making quality paper publishable in PLoS One, a world-famous journal. We included all the feedback provided by both reviewers, including the limitations of the study noted by reviewers.

Other section-by-section comments

Abstract

Report separately the sample size for cases and controls. It would also be good to provide the concise enrolment criteria for cases and controls.

Now, we included the sample size for cases and control in the abstract. Also, we have written the concise enrolment criteria for cases and controls.

Background

• This section is somehow superficial. Can you please add a paragraph that summarizes what is known about the dietary risk factors of CAD?

As per your suggestion, we have included one paragraph briefly describing the dietary risk factors of CAD.

Methods and materials

• Line 78-80: what about the 24-hr recall?

• Line 89-90: can you please describe the "24-h recall diet survey" in a better depth? In the results section, I don’t see any data on the results of this Criterion Validity assessment.

• Line 112: why did you use Wilcoxon sign ranked test for continuous variables? Was the distribution not normally distributed? Have you tried transformation before resorting to this non-parametric test?

We appreciate the comments that assisted a lot in improving our manuscript.

• 24-hr recall has been described in the manuscript.

• Before collecting the information from 306 cases and 306 controls, we carried out a survey among 115 OPD patients in the hospital to determine the validity and reproducibility of FFQ customized to Nepalese food items. Now the result has been incorporated as a supplementary file.

• Because the data were not normally distributed, we determined to apply a non-parametric test. We believe an interpretation of transformed data misleads our result in bivariate analysis. Wilcoxon sign-rank sum test for continuous but non-parametric paired data and McNemar test for dichotomous paired data are the correct tests for the analyses in matched case-control study [1].

Results

• Line 129-31: “This might be because of the selection of the control groups from the outdoor patients of the same hospital where more hypertensive patients come for their heart checkup”. This should rather be presented in the “discussion” section

• Table 1: “Hard” > “vigorous”

• Table 1: drinking alcohol and smoking: have you tried consider dose of exposure while defining these variables?

• Line 134-143: is this from the 24-hr recall or the food frequency questionnaire?

• Table 2: please clearly denote significant differences with “*”

• Line 145-48: it is good that you have used conditional logistic regression. But what was the variable/s conditioned in the analysis. if “age” was the conditioning variable, then why was it adjusted in the model?

Line 129-31: We appreciate the comments and have written it in the discussion section.

• We have changed "hard" into "vigorous."

• Our questionnaire was designed to collect the dose of exposure to alcohol use and smoking. However, because of inconsistency in responses, we resorted to categorical variables.

• The information mentioned in the Line 134-143 was from the food frequency questionnaire. We now described the source of information in the text.

• In Table 2, we now clearly denoted significant differences with “*”.

• Line 145-48: Matching in a case-control study does not control for confounding by the matching factors. A matched design may require controlling for the matching factors in the analysis [4]. In our study, we exactly matched the "sex," but we matched the "age" at an interval of 5 years. Because of interval matching and Wilcoxon-sign ranked test for paired data, “age" showed a significant association with outcome. Therefore, even though "sex" and "age" were conditioning variables in the study, we adjusted “age” in the model. However, it had been removed in step-wise backward deletion process while developing the single parsimonious model as per your suggestion.

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

We have prepared the manuscript according to PLOS ONE's style requirements, including those for file naming.

2. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information.

We are submitting the survey questionnaire in both the original language and English, as Supporting information.

3. Please amend the manuscript submission data (via Edit Submission) to include authors Ali Asghar Mirjat, Falak Zeb and Wiwik Indayati.

Now, we amended the manuscript submission data.

4. Your ethics statement must appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please also ensure that your ethics statement is included in your manuscript, as the ethics section of your online submission will not be published alongside your manuscript.

We appreciated the advice to include the ethical statement. We have written it in the Method section of our manuscript.

5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

We included the captions for supporting information files at the end of the manuscript and updated in-text citations.

Reviewer #1:

1) Innovation perspective the research is not very significant for the researchers globally. Most of the innovations are already available in the literature. As far my knowledge many studies already published these kinds of results. For example, Mahalle et. al. (2016): Association of dietary factors with severity of coronary artery disease. Authors in the manuscript (line no. 257) state “Finally, we found a consistent result with other published studies.”

Thank you so much for the comments. This matched case-control study was carried out to determine the association of dietary nutrients with CAD among Nepalese was the first case-control study. We believe that differences in the dietary habit of the different populations across space and time warrant a broader understanding of the dietary nutrients related to a specific disease.

2) The primary outcome of any case-control study is mainly based on the quality data. If the data is not good quality data then the observations on these data don’t confirm any firm statement. Based on interview questionnaire and the response of the person don’t strongly establish the dietary quantity and quality. If the diet would be provided by any good supply source who would maintain the quantity and quality of the food consumed by the patients, then, the data quality would be much better.

We acknowledge that the quality data are the most for the interpretation of the case-control study. Although a 24h dietary recall survey is considered a standard dietary survey tool, it can only collect the prier 24h diet information. Therefore, we used customized validated FFQ to collect the diet information during the past 12 months, and the average was calculated. Thus, we believe short term supply of quality food in the hospital or home would not have changed our entire data.

3) There is no external validation of the results. It majorly focused on Nepalese dataset but the research title is generic. External validation (dataset collecting from near countries such as India, Bhutan, Bangladesh) is required for the title otherwise title need to be changed to focus on Nepalese population perspective.

We appreciate for your suggestion. We have mentioned the study population in the methods section and external validation in the limitation of the study section.

4) The cohort is has been taken from one hospital and therefore, the results may be biased until the data has been taken in standard published process. At least 2 cohorts’ data is required for this study as it is based on face to face interview questions.

In Nepal, there are only two public hospitals, namely Shahid Gangalal National Heart Center and Monmon Cardiothoracic Treatment Center, which are specially equipped to treat heart-related health problems. We took permission from both hospitals and got ethical approval from the national health research council in Nepal. However, we reported very few cases (~5 cases in a month) from Monmon Cardiothoracic Treatment Center. We determined to carry out in Shahid Gangalal National Heart Center, a national level cardiac referral center in the country.

5) When we apply model’s then its strength needs to be checked by providing some metrics, such as, model’s stability by providing ROC curve, sensitivity, specificity, accuracy, f-score etc. These are clearly missing here.

Thank you for your suggestion. We have included the ROC curve and a comparison table about sensitivity, specificity, accuracy, and f-score of the two regression analysis models.

6) There are several standard algorithms compared to Random Forest (RF) regression are available. This study chose RF without giving proper justification.

We used random forest analysis because our data had a multicollinearity problem. Also, RF analysis is famous in predicting diseases in the medical field [5-7]. In the revised manuscript, we have provided the proper justification in statistical analyses of the "method" section.

7) Case: control is used 1:1 which is pretty rare in real scenarios. This study has lacks in producing right case and control samples. For example, it doesn’t tell how many patients have participated in the study and how some of them have been excluded from the study with proper logic. By using only Angiography (<70% stenosis) is not enough.

Although we have not reported the number of a non-participant in the study, we had collected the dietary information according to our predetermined inclusion and exclusion criteria that we mentioned in the "method" section.

8) In the discussion, some of the statements are contradict with the previous studies. But most of the cases, their rationalities are not explained clearly.

We believe that the discussion section has modified to contrast and support our study findings based on available literature.

9) Discussion section is not well organized to understand the study as stated in the title.

Our title is the relative importance of dietary nutrients related to CAD. We believe that we have discussed all nutrients associated with CAD in the study.

10) No justification has been given on selecting confounding variables for adjustment.

Although there are several newer techniques like a-priori change (e.g., 10% or 15%) in the effect estimate criteria, bias-variance tradeoff, directed acyclic graph, etc., we adopted conventional way of a p-value of cut off in the statistical model. After bivariate analysis (Wilcoxon sign-rank sum test for continuous but non-parametric paired data and McNemar test for dichotomous paired data analysis in matched case-control study ) [1], those variables which showed p-value less than 0.1 ( usually ranges from 0.05 up to 0.2) in bivariate analysis has been considered as potential confounders for adjustments.

11) For selecting confounding variables from one result to the next, there are several techniques like forward elimination, backward elimination could be used.

We used step-wise backward elimination technique while selecting confounding variables from one result to next.

12) There are many statements stated without giving proper references, e.g., line no. 27, 29, 44, etc. and so on.

We added the citation in the statements (line no. 27, 29, 44,) and also where references were missing.

13) The full questionnaire and data are not exposed to assess the results.

We have now submitted the full questionnaire and data as a supplementary file.

14) Source code of the models and data are available to reproduce the results.

We now have submitted the source code of R of the model and data as a supplementary file.

15) Some silly inconsistencies, like, line 144 states p<0.1.

While considering potential confounding factors, we have read that some epidemiological papers were taking variables not only p-value up to <0.2 but also the significant cofounding variables in other literature in the model development process. However, we now determined to resort to 0.05 as per your suggestion.

#Reviewer 2

1. Ethics

Before publication, the authors need to include more details about ethical approval. PLOS ONE’s policy on this is as follows:

"Human Subject Research (involving human participants and/or tissue)

- Give the name of the institutional review board or ethics committee that approved the study

- Include the approval number and/or a statement indicating approval of this research

- Indicate the form of consent obtained (written/oral) or the reason that consent was not obtained (e.g. the data were analysed anonymously))"

The authors state that this study was approved by the Nepal Health Research Council (NHRC). Is the value given here (308/2017-18) the study registration code? Is this associated with certification of ethical clearance by the NHRC ethics committee? Could the authors please attach the appropriate ethical approval documentation as a supplementary file; a letter from the NHRC stating this clearance was provided will suffice. As the authors state that they have received written informed consent by every study participant, could the authors also go into some detail about whether those participants were informed their data (anonymised) would be available open access?

Yes, the value given (308/2017-18) is the study registration code. Of course, this is associated with the certification of ethical clearance by the Nepal Health Research Council (NHRC) ethics committee. According to your suggestion, we are pleased to attach the ethical approval documentation as a supplementary file: a letter from the NHRC stating this clearance. However, we did not inform participants into some detail about their data (anonymised) would be available open access.

2. Data availability

The authors must supply all data associated with their analyses. The authors have claimed all relevant data are supplied in the paper or supplementary files, but this is inaccurate. The results of this paper depend on the analysis of distribution data, and this is necessary for replication. PLOS ONE’s policy states – “PLOS journals require authors to make all data necessary to replicate their study’s findings publicly available without restriction at the time of publication”. Accordingly, the relevant data for every study participant on which this papers analysis depends must either be included as supplementary files or stored in an online data repository after patient data has been appropriately anonymised. These data could be provided in spreadsheets – for the 612 patients, this involves providing all data on control/case group membership, age, weight, gender, dyslipidaemia, hypertension, obesity, smoking, alcohol consumption, physical activity, calorie consumption, and all data regarding intake of the 18 examined nutrients. Indeed, in light of the following problems, it is the data collected by the authors here is probably the most important aspect of the study.

Thank you for your suggestion. We have now submitted all the data in spreadsheets on control/case group membership, including all variables under study.

3. Problems concerning data analysis

Multiple comparisons:

One major problem is accounting for multiple comparisons in this study. For example, Table 2 lists 19 variables (18 nutrients and total calorie consumption) each of which has been compared with a Wilcoxon rank-sum test – so the quoted significance levels at the very least need to be adjusted for the fact that 19 comparisons have been made. The same issue recurs throughout the analysis. The authors should seek to resolve this issue via appropriate statistical methods. I would also recommend that this study is referred to a statistical editor upon these revisions to ensure that this issue has been appropriately resolved.

Our study was about variable selection and model construction. It was not about evaluating the association of each variable and the outcome, and nineteen nutrients were not the categories of a single variable. Each variable was separately tested with a Wilcoxon sign rank test for the selection of potential variables for model construction. Thus, we believe that there were not multiple comparison problems in our data set.

Multicollinearity:

Apart from the problem of multiple comparisons here there is also the problem that the data are not fully independent (multicollinearity) – specific micronutrients tend to be associated with other particular nutrients in different food types. Accordingly, it is important not to over interpret associations unless these issues are rigorously excluded. Accordingly, the authors should reflect more on this issue and adjust their methods/interpretations in light of this. One option here would be to extend their discussion of their random forest regression. Indeed, the paper would benefit from extending and deepening the description and results of this analysis, providing results on correlations between nutrient intakes and variance inflation factor. Again, I believe a statistical editor should be consulted.

Thank you for your valuable suggestion for improving the quality of the manuscript. As per academic editor recommendation, we determined to construct a single model by executing the conditional logistic regression. While making a single parsimony model, we excluded one of the variables that showed a multicollinearity problem deciding based on the square root of vif value >2 as a cutup point. However, excluding one of the variables undermines the importance of that for the risk of disease. Therefore, we performed random forest analysis, including all variables in the model, to get the most important variables associated with CAD.

Other data analysis issues:

In Table 1, the authors claim that the median age of authors is statistically significantly different between the case and control groups. The authors report the median age, interquartile range, and P-value as:

Case: 58 (50–65) | Control: 58 (50–65) | P=0.001

Not only is the median age the same, but so too are the interquartile ranges. Yet, despite this, the age difference is apparently statistically significant? The authors seem to interpret this result as meaningful:

“Because the age was matched in five year intervals in the study, the median age was 58 years, which was the same in both case and control groups, respectively, and still showing strong association (P=0.001).”

The authors claim that age was matched in 5-year intervals, but are we then to interpret these results as suggesting that there is actually a significant difference in age between case-control matched pairs? As CAD is strongly associated with age in previous research, this is important to clarify. To do this, the authors need to report the age distribution data for both groups as a supplementary file.

Our study was a matched case-control study, and we exactly matched the “sex," but we matched the “age” at an interval of 5 years. Because of interval matching and Wilcoxon-sign ranked test for paired data, “age” was showing significant association with outcome. Wilcoxon sign-rank sum test for non-parametric paired data and McNemar test for dichotomous paired data are the correct test for the analysis in the matched case-control study [1]. Matching in a case-control study does not control for confounding by the matching factors. A matched design may require controlling for the matching factors in the analysis [4]. Therefore, even though “sex” and “age” were conditioning variables in the study, we adjusted “age” in the model.

For the analysis in Table 2, the authors claim “as most of the study data were not normally distributed, median and interquartile range of nutrients are presented”. The authors should, therefore, include in their supplementary material the actual data underpinning their analysis. At the very least, they must include the mean, range, and SD for each nutrient, so the reader can understand exactly what the distribution of these data actually are. Indeed, the data provided in the paper is insufficient to replicate the necessary results reported, despite the authors declaration.

We followed the standard statistical norms for the presentation of data. We believe that it looks awkward, putting two averages (median and mean) in a single table representing the average of the same variables. As per your suggestion, we have presented the data in the supplementary table that includes mean, range, and SD (S3 Table).

Statistical rhetoric:

The authors highlight a “highly significant” finding (p.9), this language is inappropriate and should be replaced. A result is simply either significant or non-significant and this is determined by whatever threshold of significance the authors deem necessary.

We appreciate your suggestion. We just changed the language as per your suggestion that “highly significant” to only either significant or non-significant.

4. Problems of variable selection and measurement

Nutrient selection:

The authors select 18 nutrients to examine here, but why these specific nutrients are analysed is not adequately justified. Accordingly, the authors should make clearer why these items were selected for analysis.

We calculated daily nutrient intake from Nepalese, commonly consumed food items based on "Nepal food composition table 2017," which lacks the values of all nutrients per 100 gm food items are available for the food items. Although we found literature where these 18 nutrients were mostly related to CAD, the results were inconsistent in the different populations across the world.

In the supplementary file, a list of common foods consumed is provided. This raises further questions about why the authors chose only to analyse the variables they selected in this paper because other variables appear possible to derive from their data. For example, I see no reason why the amount of sugars in the diet couldn’t be calculated from the listed food items, so why isn’t this examined in the paper? Similarly, their decision to use total carbohydrate intake as a variable without breaking this down into refined and complex carbohydrates appears strange and problematic, particular because the authors acknowledge in the paper that there are important differences between these. Why then didn’t the authors calculate these?

Yes, we acknowledged that we did not breakdown the total carbohydrate into "refined" and "complex." We have now mentioned this issue in the limitation section.

In its current state, this Table of food items is both uninformative and misleading. It also raises further questions about how nutrient intakes were measured. Patients were asked about milk consumption, but the milk category does not clarify whether respondents were asked specifically about the amount of full, semi, or skimmed milk consumed, which would be necessary to understand fat content and fatty acid profiles, or whether this was a single category. Further questions about how the quantities of PUFA, MUFA, and SFA were calculated arise in regards to several of the vague categories, such as “vegetable oils”. Accordingly, the authors should include the specific dietary survey actually provided to patients. Furthermore, supplying the average amount of each food consumed by cases and controls for each item would shed more light on dietary habits. As recent research suggests different whole foods might have different effects on lipid profiles and thereby atherosclerosis, these data are important to report. At the very least the authors need to make available the intakes of each nutrient examined in this study per patient.

Regarding milk category, Nepalese in rural area usually have a practice of making butter: heating milk and allow cooling down and extracting the butter before consumption of milk in a village. In city area, the marketable milk is semi skimmed milk. Therefore, we calculated categories of fat based on semi skimmed milk. Regarding vegetable oil, we included nutrients value separately (soybean oil, mustard oil, sunflower oil). We did not calculate effect of the different whole food on the lipid profile of patients.

Other questions that arise are why were PUFA here considered as a single group and not split further into Omega-3 and Omega-6 variants? Why was the intake of trans-fats not measured? Thus, the authors need to revise the manuscript to give the reader a clearer understanding of the theoretical justification for the selection of the variables. As there is a voluminous literature on the relationship between diet and atherosclerosis/CHD/CVD extending back to the early 20th century, there is a wonderfully rich literature to draw from.

We calculated nutrients based on the "Nepal food composition table 2017," which lacks all nutrients value for the given food items. This limitation, we have now mentioned in the limitation of the study.

Self-reported nutritional data:

As all the nutritional data are all self-reported, the authors should include a clearly discussion in regards to their reliability given the known problems with this kind of data. I suspect there is a problem here. From Table 2, it appears that total daily nutritional intake was virtually the same in the two groups – despite the significantly higher incidence of obesity in the control group.

According to your suggestion, we have discussed the problem related to the self-reported diet survey. We did not report a higher incidence of obesity in the control group. I think the word “Normal” was making confusion. Therefore, we change the word “Normal” to "No." Now, we reported the BMI for Asian ≥27.5 kg/m2 as obesity. So, now the figures in the Table are different from the previous values.

5. Referencing

In-text references in this paper appear occasionally only loosely related to the claims they are purported to be associated with. For example, reference number 2 is inserted after the following sentence:

“In Nepal, 30% of total death was related to cardiovascular disease (2).”

Yet, reference 2 is a paper by Rankinen et al. (2015), and nowhere in this paper is this claim made. Another reference chosen at random, reference 20, is used to support the authors claim that:

“Besides cholesterol is also an independent risk factor of CAD according to the lipid theory”

The paper referenced nowhere discussed dietary cholesterol. It is a paper examining, as the title suggests, the “Relationships Between Components of Blood Pressure and Cardiovascular Events in Patients with Stable Coronary Artery Disease and Hypertension”. The only mention of cholesterol in this paper is HDL-C and LDL-C – that is, cholesterol bound in particular classes of lipoproteins carried in the blood.

If the authors make the rest of the revisions outlined, I will examine each of the references of this paper. So my recommendation would be to go through each reference and ensure it is relevant to the claim being made. As discussed, the authors also need to ensure they have adequately represented the state of research in relation to their claims. If the article is resubmitted, I'll check each.

We are very regretful to inform that while converting from other reference styles (Vancouver) to PLoS one, all reference lists had been mismatched because of some technical problem. Now, we corrected all citation-related issues in the manuscript.

6. Flawed study design

However, there is one problem that may undermine the point of revising this manuscript. The authors have a case-matched control group – but the control group are not healthy individuals, but patients with other health conditions and cardiovascular symptoms. This is clearly evident by the way the authors chose to enrol patients – all patients were being examined because of suspected coronary problems. This makes it impossible to talk of differences between these groups in terms of risk factors.

For example, looking at Table 1, the ‘control’ group has a significantly higher incidence of obesity and central obesity – but it would be obviously wrong to conclude that obesity and central obesity are protective against cardiovascular disease. Here we’re seeing a stratification of phenotypic characteristics between two different patient groups, and from this we can’t conclude anything at all about risk.

In table 1, we did not report a higher prevalence of obesity and central obesity. The percentage we mentioned were about “normal” and also provided in the foot notes. Now, we realized that the word “Normal” is not appropriate and unclear. Therefore, we changed “Normal” to “No”.

This might also explain the extremely strange finding that the number of hypertensives was roughly the same in both the control and case groups - Control: 143 hypertensives (~46.7%) | Case: 142 hypertensives (~46.4%). As hypertension is one of the key known risk factors in the development of CAD/CVD and extensively supported in the literature, this finding requires a lot more reflection. Why were hypertensives so common in the control group? This control group had apparently no evidence of stenosis – so this seems to be quite an important avenue to explore what went on here.

Although hypertension is one of the critical risk factors in the development of CAD/CVD, the same prevalence was reported because the selection of the control groups was from the outdoor patients of the same hospital where more hypertensive patients had come for their hearts checkup. However, we aimed to determine the nutrients factors, not cardiometabolic factors related to CAD. We believe more the matching of the demographic and cardiometabolic factors more precisely can detect the effect size of nutrients to CAD.

Our control group was those patients who were having either stress test negative or normal angiography. Those patients who were recently diagnosed as hypertension apparently did not show stenosis. Mostly the diagnosed patients were taking medicine to control hypertension and dyslipidemia. Notably, we classified them as hypertensive patients.

Accordingly, this design is inappropriate for the authors stated intention: “The present case-control study was designed to determine the association of dietary nutrients with CAD in the Nepalese population”.

If this study is to be published, the authors need to somehow explain why this control group can be considered representative of a broader population. Later in the paper the authors do highlight the results may have been biased due to “the selection of the control group from the outdoor patients from the same hospital where more hypertensive patients come for their heart check-up”, but this seems to critically undermine the entire results of this study.

Our study was focusing on the dietary nutrients related to CAD. Principally, in the case-control study, the matching of the confounding variables, better can predict the risk posed by the intended risk factors (in our study dietary nutrients). We also believe that almost equal distribution of metabolic risk factors in both cases and controls, the mediation effect posed by these metabolic risk factors (obesity, hypertension, and dyslipidemia) were adjusted.

Thank you very much for the critical appraisal of our manuscript, which has helped improve the manuscript quality, making it publishable in a highly famous journal "PLoS One."

References

1. Conway A, Rolley JX, Fulbrook P, Page K, Thompson DR. Improving statistical analysis of matched case-control studies. Research in nursing & health. 2013;36(3):320-4. Epub 2013/02/15. doi: 10.1002/nur.21536. PubMed PMID: 23408517.

2. Aryal K, Neupane S, Mehata S, Vaidya A, Singh S, Paulin F, et al. Non Communicable Diseases Risk Factors: STEPS Survey Nepal 20132014.

3. Altman DG. Practical statistics for medical research. London: Chapman & Hall, 1991.

4. Pearce N. Analysis of matched case-control studies. BMJ (Clinical research ed). 2016;352:i969. Epub 2016/02/27. doi: 10.1136/bmj.i969. PubMed PMID: 26916049; PubMed Central PMCID: PMCPMC4770817 interests and declare the following: none. Provenance and peer review: Not commissioned; externally peer reviewed.

5. Beunza JJ, Puertas E, García-Ovejero E, Villalba G, Condes E, Koleva G, et al. Comparison of machine learning algorithms for clinical event prediction (risk of coronary heart disease). Journal of biomedical informatics. 2019;97:103257. Epub 2019/08/03. doi: 10.1016/j.jbi.2019.103257. PubMed PMID: 31374261.

6. Brisimi TS, Xu T, Wang T, Dai W, Adams WG, Paschalidis IC. Predicting Chronic Disease Hospitalizations from Electronic Health Records: An Interpretable Classification Approach. Proceedings of the IEEE Institute of Electrical and Electronics Engineers. 2018;106(4):690-707. Epub 2019/03/20. doi: 10.1109/jproc.2017.2789319. PubMed PMID: 30886441; PubMed Central PMCID: PMCPmc6419763.

7. Zhang X, Dai Z, Lau EHY, Cui C, Lin H, Qi J, et al. Prevalence of bone mineral density loss and potential risk factors for osteopenia and osteoporosis in rheumatic patients in China: logistic regression and random forest analysis. Annals of translational medicine. 2020;8(5):226. Epub 2020/04/21. doi: 10.21037/atm.2020.01.08. PubMed PMID: 32309373; PubMed Central PMCID: PMCPmc7154412.

Attachment

Submitted filename: ResponseLetter_PloS One.docx

Decision Letter 1

Samson Gebremedhin

22 Sep 2020

PONE-D-20-07225R1

Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

PLOS ONE

Dear Dr. Basnet,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

  • Please accommodate the critical comments raised by the reviewer on the generalizability of the study and risk of selection bias, specially in relation with the nature of the controls. 

  • Please make sure that the major methodological limitations of the study are adequately discussed.

  • Please explain how the values for PUFA and SFA intake considerably changed in the revised version as compared to the original one.

Please submit your revised manuscript by Nov 06 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Samson Gebremedhin, PhD

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: No

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: No

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: First, I must thank the authors for their careful response to the previous round of reviews. Indeed, the changes the authors have made to the manuscript represent an important improvement, particularly the added details related to methodology and the supplementary data and script. However, there are still issues to be addressed:

1. Study design and generalisability

My primary concern remains the conclusions that the authors draw from their analysis. Previously, I highlighted:

“The authors have a case-matched control group – but the control group are not healthy individuals, but patients with other health conditions and cardiovascular symptoms. This is clearly evident by the way the authors chose to enrol patients – all patients were being examined because of suspected coronary problems. This makes it impossible to talk of differences between these groups in terms of risk factors. If this study is to be published, the authors need to somehow explain why this control group can be considered representative of a broader population. Later in the paper the authors do highlight the results may have been biased due to “the selection of the control group from the outdoor patients from the same hospital where more hypertensive patients come for their heart check-up”, but this seems to critically undermine the entire results of this study.”

This remains my position. The authors have not adjusted their conclusions or their interpretation of their study in light of the problems related to their study design. There is no attempt in this study to understand whether the control group is representative of the broader Nepalese population, and there is a major risk of selection bias. This is clearly indicated by the similar number of hypertensive patients in the case and control groups. For example, the major conclusion of this paper remains:

“Thus, a dietary intervention approach in CVDs is an effective strategy to reduce the public health burden. We conclude that dietary SFA, vitamin A.R.E., dietary total fat and oil, β-carotene, and cholesterol are topmost five essential dietary nutrients associated with CAD in the Nepalese population.”

The findings of this paper cannot be extended to make claims about the relationship between the intake of any dietary nutrient in the wider Nepalese population and their risk of CAD. The findings are at best suggestive of a possible relationship between these nutrients and the development of CAD, but prospective cohort studies and RCTs will need to be performed, as the authors do go on to highlight.

Further, it is also clear that the case group here differs drastically from the control group in many important aspects. Compared to the controls, the case group has more than double the number of patients with diabetes, double the number obese (BMI) patients, triple the number of patients suffering from dyslipidaemia, and triple the number who are current smokers. They cases also drink more alcohol and exercise less than the control group. These groups are not comparable – and clearly have very different lifestyles, so it is not clear to me that the authors can draw any conclusions about the respective role of specific nutrients in explaining CAD between the groups.

Accordingly, more needs to be done to modify the conclusions of this paper and highlight the limitations of this study before publication. As there are questions over the generalisability of these findings beyond the study population, my recommendation would be to limit all conclusions to describing the findings of this study in relation to this group alone.

2. Unexplained differences in findings reported between the original and revision.

The authors must explain why some figures in this revised manuscript compared to the original have changed. Specifically, I refer to Table 2. In the original, for Food energy (kcal) per day, the controls are reported as 2560 (2306, 2791) and the cases 2549 (2256, 2897) kcal. However, in the revised manuscript, the controls now are reported as 2674 (2445, 2909) and the cases 2622 (2373, 2963). Despite this change, none of the other macronutrient values have changed, which cannot be true.

Further, I cannot understand how the authors have also changed values for PUFA and SFA intake in this revised version compared to the original – but somehow this has not changed the value for total fat intake?

In this original paper,

Fat g Control 56 (47, 64) | Case 61 (52, 72)

PUFA g Control 18 (11.2, 22.7) | Case 19.6 (11.8, 25.7)

SFA g Control 15.8 (10.8, 20)| Case 16.6 (11, 21.6)

In the revised manuscript,

Total fat/oil g Control 56 (47, 64)| Case 61 (52, 72)

PUFA g Control 18.7 (12.5, 23.5) | Case 19.6 (12.4, 25.7)

SFA g Control 15.5 (10.6, 19.2) | Case 19 (13.9, 23.6)

The authors need to explain why this discrepancy has occurred because it undermines my confidence in the reliability of these data. I am particularly worried about the change in SFA values because the authors now report a significant OR of 1.2 (1.11, 1.31) for SFA intake in the revised manuscript, which was not included in the original.

Another major change is the figures concerning vitamin A,E,R intake between these versions:

In the original:

Vitamin A R.E. Control 739 (578, 885)| Case 657 (535, 790)

In the revised:

Vitamin A R.E. Control 698 (546, 836)| Case 622 (506, 728)

Either there was a major problem with the basic statistical analysis performed for the previous version of this paper, or these data have since been changed.

3. Referencing problems

Some references still do not clearly relate to the statements made by the authors. For example, the authors state:

"An estimated 7.4 million people died from CAD in 2015, representing 13% of all global deaths. In Nepal, 30% of total death was related to cardiovascular disease [2]".

The reference provided for this is “WHO. Cardiovascular diseases fact sheet. WHO. World Health Organization; 2017”. Nowhere in this referenced document are either of these figures provided.

4.Summary

My recommendation, despite the improvements to the paper in many areas, remains to reject this paper. Previously, this was based on the flawed study design that, I believed, undermined the generalisability of these results to the broader Nepalese population. However, the unexplained changes to nutrient intakes in this revised version undermined my confidence in this study.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2020 Dec 10;15(12):e0243063. doi: 10.1371/journal.pone.0243063.r004

Author response to Decision Letter 1


27 Oct 2020

Responses to the academic editor and the reviewer’s comments

Thank you so much for all the comments, which were valuable and encouraging to make quality manuscript publishable in the PLoS One journal. We detail our responses to each of the academic editor and the reviewers’ comments in the order they were raised. We believe that we have improved the methodological details for correct interpretation of the study.

Responses to the academic editor's comments

1. Please accommodate the critical comments raised by the reviewer on the generalizability of the study and risk of selection bias, specially in relation with the nature of the controls.

Response: Bias arises in case-control studies not because the cases and controls differ on characteristics other than exposure but because the selected controls do not accurately reflect exposure prevalence in the study base-geographic scope, socioeconomic, and behavioral characteristics of the source population for these cases. Conceptually, the study base is populated by the people at risk of becoming identified as cases in the study if they got the disease during the time in which cases are identified. However, finding the base population in hospital control is pragmatically difficult as the conceptual definition of the study base is unclear. Moreover, the sampling procedure (unbiased sampling) in such a study is not practical. Therefore, we carried out a matched case-control study to overcome the above problems. We understand that obtaining perfectly coherent case and control groups from the same study base guarantees that there will be no additional selection bias introduced in the case-control sampling beyond whatever selection bias may be inherent in the underlying cohort. The failure to do so, however, does not automatically produce selection bias; it just introduces the possibility.

Our study aimed to determine the association of nutritional factors with coronary artery disease (CAD). The distribution of our interest variables (dietary nutrients) in the control group was within the range of findings in a previous study conducted among Nepalese [1]; thus, we believe our control group represents the base/source population. We excluded the participants who adopted dietary modification after being diagnosed with any cardiometabolic risk factors (hypertension, dyslipidemia, diabetes, obesity). The hospital where we carried out the data collection was a cardiac referral center (Only one national cardiac center in Nepal), and people come for their health check-ups from across the country. Furthermore, cardiometabolic characteristics of our control group were somehow similar to the base (source) population except for hypertension [2]. Thus, we believe the control represents the broader Nepalese population. Although controls were selected from the same hospital with other health conditions, the effect of such conditions was adjusted during statistical analysis. Moreover, in a case-control study, we believe more the characteristics (demographic, cardiometabolic, lifestyle-related factors) of cases and controls are matched except study variable (nutritional factors), more accurately we can determine the strength of association of study variables with the disease (CAD).

2. Please make sure that the major methodological limitations of the study are adequately discussed.

Response: We have revised the major methodological limitations of the study as per reviewer suggestions, which are highlighted in the ‘Revised manuscript with Track Changes.’

3. Please explain how the values for PUFA and SFA intake considerably changed in the revised version as compared to the original one.

Response: We apologize that we did not explain the reason why some figures in the revised manuscript compared to the original has changed in the previous review. We calculated the nutrients of individual observation from the nutrients calculator developed in an excel sheet based on the value from Nepal food composition table 2017 and transferred to the datasheet. We meticulously re-check our nutrients conversion from the food list. While transferring the data, some values were missing in SFA. Therefore value in the SFA has been changed while total fat/oil intake remains the same. The same problems happened to data for food energy per day. Regarding Vitamin A.R.E, the value of Vitamin A.R.E per 100g vegetables was incorrectly placed in the nutrient calculator formula. After correcting this problem, the final value has been changed.

Responses to the reviewr's comments

1. Study design and generalizability My primary concern remains the conclusions that the authors draw from their analysis. Previously, I highlighted:

“The authors have a case-matched control group – but the control group are not healthy individuals, but patients with other health conditions and cardiovascular symptoms. This is clearly evident by the way the authors chose to enrol patients – all patients were being examined because of suspected coronary problems. This makes it impossible to talk of differences between these groups in terms of risk factors. If this study is to be published, the authors need to somehow explain why this control group can be considered representative of a broader population. Later in the paper the authors do highlight the results may have been biased due to “the selection of the control group from the outdoor patients from the same hospital where more hypertensive patients come for their heart check-up”, but this seems to critically undermine the entire results of this study.”

This remains my position. The authors have not adjusted their conclusions or their interpretation of their study in light of the problems related to their study design. There is no attempt in this study to understand whether the control group is representative of the broader Nepalese population, and there is a major risk of selection bias. This is clearly indicated by the similar number of hypertensive patients in the case and control groups. For example, the major conclusion of this paper remains:

Response: Bias arises in case-control studies not because the cases and controls differ on characteristics other than exposure but because the selected controls do not accurately reflect exposure prevalence in the study base-geographic scope, socioeconomic, and behavioral characteristics of the source population for these cases. Conceptually, the study base is populated by the people at risk of becoming identified as cases in the study if they got the disease during the time in which cases are identified. However, finding the base population in hospital control is pragmatically difficult as the conceptual definition of the study base is unclear. Moreover, the sampling procedure (unbiased sampling) in such a study is not practical. Therefore, we carried out a matched case-control study to overcome the above problems. We understand that obtaining perfectly coherent case and control groups from the same study base guarantees that there will be no additional selection bias introduced in the case–control sampling beyond whatever selection bias may be inherent in the underlying cohort. The failure to do so, however, does not automatically produce selection bias; it just introduces the possibility.

Our study aimed to determine the association of nutritional factors with coronary artery disease (CAD). The distribution of our interest variables (dietary nutrients) in the control group was within the range of findings in a previous study conducted among Nepalese [1]; thus, we believe our control group represents the base/source population. We excluded the participants who adopted dietary modification after being diagnosed with any cardiometabolic risk factors (hypertension, dyslipidemia, diabetes, obesity). The hospital where we carried out the data collection was a cardiac referral center (Only one national cardiac center in Nepal), and people come for their health check-ups from across the country. Furthermore, cardiometabolic characteristics of our control group were somehow similar to the base (source) population except for hypertension [2]. Thus, we believe the control represents the broader Nepalese population. Although controls were selected from the same hospital with other health conditions, the effect of such conditions was adjusted during statistical analysis. Moreover, in a case-control study, we believe more the characteristics (demographic, cardiometabolic, lifestyle-related factors) of cases and controls are matched except study variable (nutritional factors), more accurately we can determine the strength of association of study variables with the disease (CAD).

“Thus, a dietary intervention approach in CVDs is an effective strategy to reduce the public health burden. We conclude that dietary SFA, vitamin A.R.E., dietary total fat and oil, β-carotene, and cholesterol are topmost five essential dietary nutrients associated with CAD in the Nepalese population.”

The findings of this paper cannot be extended to make claims about the relationship between the intake of any dietary nutrient in the wider Nepalese population and their risk of CAD. The findings are at best suggestive of a possible relationship between these nutrients and the development of CAD, but prospective cohort studies and RCTs will need to be performed, as the authors do go on to highlight.

Response: Thank you for your constructive feedback. We are pleased to work with the meticulous reviewer and have the opportunity to enhance our knowledge of science. We agreed with your recommendation that a possible relationship between these nutrients and the development of CAD. We have changed our manuscript as per your suggestion and added the statement as

“The findings are at best suggestive of a possible relationship between these nutrients and the development of CAD, but prospective cohort studies and RCTs will need to be performed.”

Further, it is also clear that the case group here differs drastically from the control group in many important aspects. Compared to the controls, the case group has more than double the number of patients with diabetes, double the number obese (BMI) patients, triple the number of patients suffering from dyslipidaemia, and triple the number who are current smokers. They cases also drink more alcohol and exercise less than the control group. These groups are not comparable – and clearly have very different lifestyles, so it is not clear to me that the authors can draw any conclusions about the respective role of specific nutrients in explaining CAD between the groups.

Response: If the comparison was performed only each nutrient with CAD without adjustment with the above-mentioned variables like in 2*2 table, these groups were not comparable. However, our conclusion was based on random forest analysis and multivariable conditional logistic regression, where the effects of these confounding variables were adjusted. Therefore, conclusions about the respective role of specific nutrients in CAD between the groups were justifiable.

Accordingly, more needs to be done to modify the conclusions of this paper and highlight the limitations of this study before publication. As there are questions over the generalisability of these findings beyond the study population, my recommendation would be to limit all conclusions to describing the findings of this study in relation to this group alone.

Response: We agreed with your recommendation to limit all conclusions to describing the findings of this study about this group alone, and have changed our manuscript accordingly. The revised sentences were as:

“Our study suggests higher dietary intake of β-carotene and vitamin C are possible protective dietary nutrients, while an increased intake of dietary SFA, total fat and oil, and cholesterol are potential risk factors for CAD development. However, prospective cohort and RCTs studies with a large sample size are needed to explore the causal link of these nutrients for the risk of CAD development in the Nepalese population.”

2. Unexplained differences in findings reported between the original and revision.

The authors must explain why some figures in this revised manuscript compared to the original have changed. Specifically, I refer to Table 2. In the original, for Food energy (kcal) per day, the controls are reported as 2560 (2306, 2791) and the cases 2549 (2256, 2897) kcal. However, in the revised manuscript, the controls now are reported as 2674 (2445, 2909) and the cases 2622 (2373, 2963). Despite this change, none of the other macronutrient values have changed, which cannot be true.

Further, I cannot understand how the authors have also changed values for PUFA and SFA intake in this revised version compared to the original – but somehow this has not changed the value for total fat intake?

In this original paper,

Fat g Control 56 (47, 64) | Case 61 (52, 72)

PUFA g Control 18 (11.2, 22.7) | Case 19.6 (11.8, 25.7)

SFA g Control 15.8 (10.8, 20)| Case 16.6 (11, 21.6)

In the revised manuscript,

Total fat/oil g Control 56 (47, 64)| Case 61 (52, 72)

PUFA g Control 18.7 (12.5, 23.5) | Case 19.6 (12.4, 25.7)

SFA g Control 15.5 (10.6, 19.2) | Case 19 (13.9, 23.6)

The authors need to explain why this discrepancy has occurred because it undermines my confidence in the reliability of these data. I am particularly worried about the change in SFA values because the authors now report a significant OR of 1.2 (1.11, 1.31) for SFA intake in the revised manuscript, which was not included in the original.

Response: We apologize that we did not explain why some figures in the revised manuscript compared to the original had changed in the previous review. We calculated the nutrients of individual observation from the nutrients calculator developed in an excel sheet based on the value from Nepal food composition table 2017 and transferred to the datasheet. We meticulously re-check our nutrients conversion from the food list. While transferring the data, some values were missing in SFA. Therefore value in the SFA has been changed while total fat/oil intake remains the same. The same problems happened to data for food energy per day.

Another major change is the figures concerning vitamin A,E,R intake between these versions:

In the original:

Vitamin A R.E. Control 739 (578, 885)| Case 657 (535, 790)

In the revised:

Vitamin A R.E. Control 698 (546, 836)| Case 622 (506, 728)

Either there was a major problem with the basic statistical analysis performed for the previous version of this paper, or these data have since been changed.

Response: Regarding Vitamin A.R.E, the value of Vitamin A.R.E per 100g vegetables was incorrectly placed in the nutrient calculator formula. After correcting this problem, the final value has been changed.

3. Referencing problems

Some references still do not clearly relate to the statements made by the authors. For example, the authors state:

"An estimated 7.4 million people died from CAD in 2015, representing 13% of all global deaths. In Nepal, 30% of total death was related to cardiovascular disease [2]".

The reference provided for this is “WHO. Cardiovascular diseases fact sheet. WHO. World Health Organization; 2017”. Nowhere in this referenced document are either of these figures provided.

Response: We have cited it from the WHO webpage and changed to the correct citation for that webpage as [3]. Also we removed the statement, “In Nepal, 30% of total death was related to cardiovascular disease” from that sentence in the manuscript.

4. Summary

My recommendation, despite the improvements to the paper in many areas, remains to reject this paper. Previously, this was based on the flawed study design that, I believed, undermined the generalisability of these results to the broader Nepalese population. However, the unexplained changes to nutrient intakes in this revised version undermined my confidence in this study.

Response: We have addressed the issue raised and revised our manuscript as per reviewer’s suggestions regarding the generalizability of the results. We have meticulously re-checked each nutrient’s value so that current values differ from the original manuscript (first version). We again apologize for the reason for changes that were not mentioned in the previous review. Finally, we have changed the manuscript as per your advice (an expert reviewer) that we believe enough quality for publication in the current journal.

References

1. Shrestha A, Koju RP, Beresford SAA, Chan KCG, Connell FA, Karmacharya BM, et al. Reproducibility and relative validity of food group intake in a food frequency questionnaire developed for Nepalese diet. International journal of food sciences and nutrition. 2017;68(5):605-12. Epub 2017/01/18. doi: 10.1080/09637486.2016.1268099. PubMed PMID: 28092991.

2. NHRC. Nepal Steps Survey 2019-Facts Sheets-Nepal Health Research Council. [retrieved 2020-10-06]; Available from: http://nhrc.gov.np/nepal-steps-survey-2019-fact-sheets/.

3. WHO. Cardiovascular diseases fact sheet. World Health Organization; 2017. [retrieved 2020-7-30]; Available from: https://www.who.int/en/news-room/fact-sheets/detail/cardiovascular-diseases-(cvds).

Attachment

Submitted filename: Response LetterR2.docx

Decision Letter 2

Samson Gebremedhin

4 Nov 2020

PONE-D-20-07225R2

Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

PLOS ONE

Dear Dr. Basnet,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

  • I once again recommend the authors to recheck their analysis on the comparison the two groups based on age. Having the same median and inter-quartile range, how it would be possible to have statistically very significant difference between the two groups? Please check the analysis again.

  • In the abstract section please clearly provide the definitions used for “cases” and “controls”.

  • Please describe how you identified participants who adopted dietary modification after being diagnosed with any cardiometabolic risk factors.

  • Please provide the food frequency questionnaire (FFQ) used in the study as a supporting file with the manuscript.

  • Regarding your request for change of authorship, please describe the contribution of the excluded authors based on the four authorship criteria stated in the PLOS ONE authorship policy.

Please submit your revised manuscript by Dec 19 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Samson Gebremedhin, PhD

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2020 Dec 10;15(12):e0243063. doi: 10.1371/journal.pone.0243063.r006

Author response to Decision Letter 2


12 Nov 2020

Responses to the academic editor’s comments

Thank you so much for all the comments, which were valuable and encouraging to make quality manuscript publishable in the world-famous journal, PLoS One. We have revised the manuscript addressing the quarries raised.

• I once again recommend the authors to recheck their analysis on the comparison the two groups based on age. Having the same median and inter-quartile range, how it would be possible to have statistically very significant difference between the two groups? Please check the analysis again.

Response: Thank you for your suggestion for checking the analysis regarding “Age” variable again. While re-checking, we executed four analyses of the same variable (Age): t-test (parametric and independent data), paired t-test (paired and parametric data), and Wilcoxon Rank-Sum test (independent and non-parametric data), and Wilcoxon Signed-rank test (paired and non-parametric data). The p-values for each analysis were 0.869, 0.0002, 0.893, and 0.00016, respectively. As the editor raised queries that how it would be possible to have a statistically significant difference to the data set having the same median and inter-quartile range, we did not observe statistically significant differences in the third analysis (p=0.893 ). However, the last analysis, the Wilcoxon Signed-rank test, was the appropriate analysis for our data set, which were paired (matched case-control) and non-parametric data. If we exactly matched the “Age” variable individually, it would be expected non-significance statistically. This statistical significance in the present analysis was due to the interval matching of the “Age” variable.

• In the abstract section please clearly provide the definitions used for “cases” and “controls”.

Response: We appreciate your advice to add the definition of “case” and “control” in the abstract section. We added as:

In the present study, patients with more than seventy percent stenosis in any main coronary artery branch in angiography were defined as cases, while those presenting normal coronary angiography or negative for stressed exercise test were considered controls.

• Please describe how you identified participants who adopted dietary modification after being diagnosed with any cardiometabolic risk factors.

Response: We reviewed the patient’s record file of those diagnosed as having coronary artery disease, potentially eligible for “case” in our study. For patients taking anti-diabetic or anti-dyslipidemic or anti-hypertensive medicine for more than one month, we asked them for any modification of their usual diet. If they reported modification of their usual diet, we did not interview and exclude them from the study.

• Please provide the food frequency questionnaire (FFQ) used in the study as a supporting file with the manuscript.

Response: We divided the questionnaire into three parts, namely i. General socio-demographic characteristic ii. Cardio-metabolic and behavioral factors and iii. Food frequency questionnaire (FFQ). The FFQ was a part of the questionnaire set, which was submitted as a supplementary file S3 file.

• Regarding your request for change of authorship, please describe the contribution of the excluded authors based on the four authorship criteria stated in the PLOS ONE authorship policy.

Response: Ali Asghar Mirzat, Falak Zeb, and Wiwik Indayati contributed revising and approving the first version of the manuscript. Mohammed Lamin Sambou supported preliminary data analysis, revision, and approval of the manuscript’s first version.

Decision Letter 3

Samson Gebremedhin

16 Nov 2020

Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

PONE-D-20-07225R3

Dear Dr. Basnet,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Samson Gebremedhin, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Samson Gebremedhin

2 Dec 2020

PONE-D-20-07225R3

Dietary nutrients of relative importance associated with coronary artery disease: Public health implication from random forest analysis

Dear Dr. Basnet:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Samson Gebremedhin

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Table. List of food items commonly consumed by Nepalese in Nepal.

    (DOCX)

    S2 Table. Mean daily nutrient intakes estimated by the average of three 24 h dietary recalls (DR) and two food frequency questionnaires (FFQs), and correlations between the two methods.

    ICC: Intraclass correlation coefficient; aData are shown as mean ± standard deviation (SD)

    (DOCX)

    S3 Table. Distribution of nutritional factors associated with coronary artery disease between case and control groups in the study.

    kcal: kilocalorie; g: gram; mg: milligram; mcg: microgram; R.E.: retinol equivalent; PUFA: polyunsaturated fatty acid; MUFA: monounsaturated fatty acid; SFA: saturated fatty acid. aPaired t-test. bMean and standard deviation (SD) value. *p ≤ .05; **p≤ .01; ***p ≤ .001.

    (DOCX)

    S4 Table. Correlation matrix among eighteen dietary nutrients and energy intake.

    PUFA: polyunsaturated fatty acid; MUFA: monounsaturated fatty acid; SFA: saturated fatty acid.

    (DOCX)

    S1 File. Survey questionnaire set and informed consent in the Nepali language.

    (PDF)

    S2 File. Informed consent in the English language.

    (PDF)

    S3 File. Survey questionnaire set in the English language.

    (PDF)

    S4 File. Ethical approval letter from Nepal Health Research Council.

    (PDF)

    S5 File. Reporting checklist for case-control study based on STROBE guideline.

    (PDF)

    S6 File. Data set.

    (CSV)

    S7 File. R code for statistical analyses.

    (R)

    Attachment

    Submitted filename: Review. PONE-D-20-07225.docx

    Attachment

    Submitted filename: ResponseLetter_PloS One.docx

    Attachment

    Submitted filename: Response LetterR2.docx

    Data Availability Statement

    All relevant data are within the manuscript and its Supporting Information files.


    Articles from PLoS ONE are provided here courtesy of PLOS

    RESOURCES