Inferring causal molecular networks: empirical assessment through a community-based effort

Inferring molecular networks is a central challenge in computational biology. However, it has remained unclear whether causal, rather than merely correlational, relationships can be effectively inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge that focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results constitute the most comprehensive assessment of causal network inference in a mammalian setting carried out to date and suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess the causal validity of inferred molecular networks

Inferring causal molecular networks: empirical assessment through a community-based effort

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense

A STUDY ON THE KNOWLEDGE OF TETANUS IMMUNIZATION AMONG INTERNEES IN A GOVERNMENT MEDICAL COLLEGE OF KOLKATA

ABSTRACT The current study was undertaken to assess the knowledge of the internees regarding tetanus immunization in children, pregnant women and adults as per the NIS and the guidelines regarding tetanus immunization in relation to the wound categories depending on the immunisation status of the patients. A pre tested questioner used to access knowledge among 108 internees. 57.4% internees were not aware of the number of doses of tetanus vaccine recommended for children under the age of 16 years and 76.8% internees were not aware of the number of doses of tetanus vaccine recommended for adults over the age of 16 years. More than 90% of the internees considered contaminated wounds, animal bites, burn injuries and wounds greater than 6 hours old to be tetanus prone. 91.7% of internees had considered wounds greater than 6hours old as tetanus prone and 5.6% did not consider this wound to be tetanus prone. On the other hand 97.2% of internees had considered contaminated wounds and animal bite to be tetanus prone and 2.8% did not consider. While 93.5% of internees considered burn injuries to be prone to the development of tetanus, 6.5% of internees thought otherwise. 13% of the internees did not consider human bite to be tetanus prone. 25% of the internees considered every cut injury to be tetanus prone. Better TT awareness of tetanus prophylaxis recommendations is necessary and tetanus prophylaxis recommendations may be more effective if they are better adhered to at the ED and the other departments that are involved in providing tetanus prophylaxis to their patients

Gender differences in notification rates, clinical forms and treatment outcome of tuberculosis patients under the RNTCP

Introduction: An increased notification rate of tuberculosis (TB) in men is seen in the SAARC region. In India, the Revised National Tuberculosis Control Programme (RNTCP) detects nearly three times more male than female TB patients. Gender differences have also been reported in the clinical forms of tuberculous disease and in treatment adherence and cure rates in patients undergoing treatment for tuberculosis. The present study was undertaken to find out the sex differences in the notification rates and treatment outcomes of TB patients registered under the RNTCP in a rural tuberculosis unit (TU) in West Bengal. Materials and Methods: A retrospective record-based study was carried out among a total of 3605 cases registered under the RNTCP between January 1999 and June 2005. Notification rates of TB, clinical forms of TB and disease treatment outcomes recorded in the registers were analyzed based on genders. Outcomes were defined in accordance with the standard RNTCP definitions. The Z-test for proportion (for comparing differences in proportions), Student t-test (for comparing mean), and χ2 test (to see association) were performed for statistical analysis. Results: Among the total of 3605 patients, 2498 (69.3%) were male and 1107 (30.7%) were female with a male female ratio of 2.25:1. In patients less than 20 years of age, the notification rates among males and females were similar. In the other age groups, males were more likely to be notified compared to females and the difference was statistically significant. While new smear positive and retreatment cases were significantly more than in males, among females, new smear negative and new extrapulmonary cases were significantly higher. Among the new smear positive patients 89.4% of females were cured compared to 85.8% of males which was again significant statistically (Z=1.70, P<0.05). Male patients outnumbered females in all the unfavorable outcomes like death, failure, and default although none of the differences were statistically significant (P>0.05). Conclusion: The present study demonstrates a gender difference in the notification rates, clinical presentations and treatment outcomes of patients with tuberculosis. Integrated research is necessary to find the reasons for these differences. Such studies will be helpful in improving the efficacy of the RNTCP

Association of Serum Adiponectin Level with Dyslipidaemia in North Indian Male Population: A Case-control Study

Introduction: Adiponectin is the most abundant adipocytokines secreted from adipose tissues and circulates in considerably high concentration in human plasma. Circulating adiponectin levels are decreased in obese subjects and this decrease has been thought to play a crucial role in the early development of atherosclerosis and cardiovascular diseases. Changes in adiponectin concentration has been reported in dyslipidaemic subjects, but the evidence is controversial and no study has been conducted in north Indian population. Moreover, low molecular adiponectin seems to be linked with a worse lipid profile leading to dyslipidaemic through an association with triglyceride but the exact role of adiponectin in modulating lipid fraction is not well established. Aim: To correlate the level of serum adiponectin with lipid fractions in dyslipidaemic male subjects and also to compare them with apparently healthy individuals. Materials and Methods: This case-control study was conducted from April 2015 to November 2016 in the Biochemistry Department of Rajshree Medical Research Institute, Bareilly, Uttar Pradesh, India. A total of 70 non diabetic dyslipidaemic male subjects between the age group 35 years to 55 years were selected and all the biochemical parameters (adiponectin, fasting plasma glucose, lipid profile) were evaluated and compared with 70 apparently healthy controls. Statistical analysis was performed by licensed version of Statistical Package for Social Sciences (SPSS) 16.0 software. All the data were expressed in “mean±SD”. Student ‘t’ test was also applied to see statistical significance in adiponectin levels between dyslipidaemic subjects and healthy controls. Results: The study shows mean±SD of age in dyslipidaemic group was 43.61±4.85 years and for control group was 43.53±5.53 years. The mean±SD of BMI in dyslipidaemic group 25.72±2.43 was significantly higher than control group 23.42±1.56 with p-value <0.0001. The serum adiponectin concentration was significantly reduced in dyslipidaemic subjects 5.11±2.04 μg/mL as compared to healthy control 6.79±1.37 μg/mL with p-value <0.0001. Serum total cholesterol, triglyceride and Low Density Lipoprotein (LDL)- cholesterol were found to be negatively correlated with serum adiponectin (r= -0.89, -0.76 and -0.74) and positively correlated with High Density Lipoprotein (HDL)-cholesterol (r=0.70). Conclusion: The present study revealed that hypoadiponectinemia is associated with dyslipidaemic in men. The main observation of our present study, however, is that in dyslipidaemic subjects, lower levels of adiponectin were associated with high total cholesterol, triglyceride, LDL-cholesterol and reduced HDL cholesterol, though more extensive, multicentric, prospective research with increase sample size could obtain wider insights

DEVELOPING MODELS TO PREDICT STUNTING AMONG 6-59 MONTHS CHILDREN IN A SLUM OF KOLKATA

Background: India is one among the many countries where child malnutrition is severe and is a major underlying cause of child mortality. &nbsp;48 per cent of under five children in India are stunted and India accounts for more than 3 out of every 10 stunted children in the world. Even after implementation of the national nutritional programmes the magnitude of the problem remains at large, this necessitates a detailed analysis regarding the factors leading to stunting and to identify which group of factors to target first to make a significant effect.Methods: This &nbsp;Community &nbsp;based &nbsp;cross-sectional &nbsp;study was done &nbsp;in &nbsp;the service area of &nbsp;Urban &nbsp;Training &nbsp;Centre &nbsp;in &nbsp;Baghbazar, &nbsp;Kolkata &nbsp;with &nbsp;84 &nbsp;children &nbsp;aged &nbsp;6-59 &nbsp;months. Anthropometric measurements of the study population were done &nbsp;using &nbsp;standard methods and information regarding risk factors were collected from their parents using a pre-designed questionnaire. WHO Anthro for personal computers version3.2.2 (Z score) and SPSS version16.0 was used to analyse the data (multivariate logistic regression and ROC curve). &nbsp;Results: The study indicates a 26.2% prevalence of stunting among the study population. To observe the risk factors for stunting two models were compared by creating ROC curves, a socio demographic factor model which explained 70% of the stunting in the population in comparison to the second model regarding the factors related to birth and feeding practices which explained 65%.&nbsp;Conclusion: The current study further emphasizes the need to implement relevant interventions to combat malnutrition in this region and other similar settings

Comparison between childhood and adult tuberculosis in a rural tuberculosis unit of West Bengal: A retrospective study

Background and Objectives: Tuberculosis (TB) is an important cause of childhood morbidity and mortality with different clinical presentations and outcomes as compared to TB in adults. The present study was designed to compare these differences and to determine if childhood TB was an important predictor of adverse outcome following treatment under the Revised National Tuberculosis Control Program (RNTCP). Materials and Methods: Retrospective record based study of cases registered between January 2008 and December 2011, at the Amdanga TB Unit (TU), West Bengal. Results: Of the total 1,508 cases notified, 3.4% were childhood TB. Differences with adult TB were noted in the number of cases categorized as cat II and III in children (P = 0.012 and 0.000, respectively). New smear positive pulmonary TB was significantly lower (21.6%, P = 0.000), while new extra-pulmonary TB (39.2%, P = 0.000) was significantly higher in children. Smear negative cases comprised 7.8 and 11.4% of the childhood and adult cases of TB, respectively. Retreatment cases were significantly higher in adults (P = 0.012). Among the registered new smear positive cases, the differences in favourable and adverse outcomes did not have a significant statistical difference (P = .100) . Childhood TB was not a significant risk factor for adverse outcome following treatment (adjusted odds ratio [AOR] = 0.80, 95% confidence interval [CI] = 0.28-2.32). Conclusions: The registration of childhood TB under the RNTCP in the TU was low. There were differences in the clinical presentation and treatment outcomes of TB among children and adults. Childhood TB was not a significant predictor of adverse treatment following treatment

Perceived psychological stress among undergraduate medical students: Role of academic factors

Recently, there is a growing concern about stress during undergraduate medical training. The objectives of our study were to assess perceived stress among undergraduate medical students and to find out academic factors as determinants. A cross-sectional, questionnaire-based survey was carried out among undergraduate medical students of R. G. Kar Medical College, India, during July 2011–June 2012. Perceived stress was assessed using the Perceived Stress Scale-14. A 10-item questionnaire was used to assess academic sources of stress and their severity. The overall mean perceived stress score was 29.58 (standard deviation [SD] = 6.60), and 46.3% of the participants were in the group of more stressed (perceived stress score ≥28). The academic stressor factors predicted 78% of variability of perceived stress. A higher level of perceived stress was reported by the students. The students should be taught different stress management techniques to improve their ability to cope with a demanding professional course

Inferring causal molecular networks: empirical assessment through a community-based effort

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense