Simple and low-cost nucleic acid extraction methods for detection of SARS-CoV2 in self-collected saliva and dry oral swabs.

Background: Ongoing need of alternative strategies for SARS-CoV-2 detection is undeniable. Self-collected samples without viral transport media (VTM), coupled with simple nucleic acid extraction methods for SARS-CoV-2 PCR are beneficial. Objectives: To evaluate results of SARS-CoV-2 PCR using simple nucleic acid extraction methods from self -collected saliva and oral swabs without VTM. Methods: A cross-sectional single-centre study was conducted on 125 participants (101 SARS-CoV-2 positive cases and 24 controls). PCR was performed following five simple nucleic acid extraction methods on self -collect saliva and oral swabs without VTM and results were compared with gold standard PCR. For saliva, kit-based extraction (SKE), Proteinase K and Heat extraction (SPHE), only Heat extraction (SHE) methods and for dry oral swabs, Proteinase K and Heat extraction (DPHE) and only Heat extraction (DHE) was performed. Results: SARS-CoV-2 was detected in self-collected saliva and oral swabs. 93.07% were correctly classified as positive by SKE, 69.31% by SHE, 67.33% by SPHE, 67.33% by DPHE and 55.45% by DHE. Discriminant power of SKE was significantly higher than other methods (p-value < 0.001) with good- fair agreement of alternate extraction methods against gold standard. Conclusion: Combination of self-collected saliva/ oral-swab without VTM and alternative RNA extraction methods offer a simplified, economical substitute strategy for SARS-CoV-2 detection.

Screening for mental illness using GMHAT App of patients with Type 2 diabetes mellitus at a teaching institute hospital in India - A cross sectional study.

People with diabetes will have some coexisting mental illness most of the time and its evaluation and management are essential for the well-being of the person. With this background, the Global Mental Health Assessment Tool (GMHAT) app was used to screen for mental illness among type 2 diabetes mellitus patients attending a tertiary care hospital in Mysore, India. Methods: A cross-sectional study was conducted on 100 patients who were on treatment for type 2 diabetes for at least 6 months from the Out-Patient Department of KR Hospital, Mysore. Interviews were conducted using a structured GMHAT. Data were entered in MS Excel and analysed using SPSS version 21.0. Chi-square, Independent T-test/Mann-Whitney tests were used to investigate associations between the variables. Results: The mean age of the study participants was 48.8 ± 11.6 years. Among the 100 diabetic patients, 39% (n = 39) had mental illness and among the 39 subjects, 21% had depression, 14% had anxiety disorder and 4% suffered from organic disorder. Apart from diabetes, 29, 17, 13, 27, 23 and 20% had hypertension, chronic kidney disease, liver disease, retinopathy, neuropathy and nephropathy, respectively, as comorbid conditions. Conclusion: There is a higher prevalence of mental illness in patients with diabetes mellitus. The prevalence rate increases with an increase in the chronicity of diabetes. The use of the GMHAT app could help in rapid assessment and accurate diagnoses.

Genomic clustering analysis identifies molecular subtypes of thymic epithelial tumors independent of World Health Organization histologic type.

Further characterization of thymic epithelial tumors (TETs) is needed. Genomic information from 102 evaluable TETs from The Cancer Genome Atlas (TCGA) dataset and from the IU-TAB-1 cell line (type AB thymoma) underwent clustering analysis to identify molecular subtypes of TETs. Six novel molecular subtypes (TH1-TH6) of TETs from the TCGA were identified, and there was no association with WHO histologic subtype. The IU-TAB-1 cell line clustered into the TH4 molecular subtype and in vitro testing of candidate therapeutics was performed. The IU-TAB-1 cell line was noted to be resistant to everolimus (mTORC1 inhibitor) and sensitive to nelfinavir (AKT1 inhibitor) across the endpoints measured. Sensitivity to nelfinavir was due to the IU-TAB-1 cell line's gain-of function (GOF) mutation in PIK3CA and amplification of genes observed from array comparative genomic hybridization (aCGH), including AURKA, ERBB2, KIT, PDGFRA and PDGFB, that are known upregulate AKT, while resistance to everolimus was primarily driven by upregulation of downstream signaling of KIT, PDGFRA and PDGFB in the presence of mTORC1 inhibition. We present a novel molecular classification of TETs independent of WHO histologic subtype, which may be used for preclinical validation studies of potential candidate therapeutics of interest for this rare disease.

Computational Biological Modeling Identifies PD-(L)1 Immunotherapy Sensitivity Among Molecular Subgroups of KRAS-Mutated Non-Small-Cell Lung Cancer.

PURPOSE: KRAS-mutated (KRASMUT) non-small-cell lung cancer (NSCLC) is emerging as a heterogeneous disease defined by comutations, which may confer differential benefit to PD-(L)1 immunotherapy. In this study, we leveraged computational biological modeling (CBM) of tumor genomic data to identify PD-(L)1 immunotherapy sensitivity among KRASMUT NSCLC molecular subgroups. MATERIALS AND METHODS: In this multicohort retrospective analysis, the genotype clustering frequency ranked method was used for molecular clustering of tumor genomic data from 776 patients with KRASMUT NSCLC. These genomic data were input into the CBM, in which customized protein networks were characterized for each tumor. The CBM evaluated sensitivity to PD-(L)1 immunotherapy using three metrics: programmed death-ligand 1 expression, dendritic cell infiltration index (nine chemokine markers), and immunosuppressive biomarker expression index (14 markers). RESULTS: Genotype clustering identified eight molecular subgroups and the CBM characterized their shared cancer pathway characteristics: KRASMUT/TP53MUT, KRASMUT/CDKN2A/B/CMUT, KRASMUT/STK11MUT, KRASMUT/KEAP1MUT, KRASMUT/STK11MUT/KEAP1MUT, KRASMUT/PIK3CAMUT, KRAS MUT/ATMMUT, and KRASMUT without comutation. CBM identified PD-(L)1 immunotherapy sensitivity in the KRASMUT/TP53MUT, KRASMUT/PIK3CAMUT, and KRASMUT alone subgroups and resistance in the KEAP1MUT containing subgroups. There was insufficient genomic information to elucidate PD-(L)1 immunotherapy sensitivity by the CBM in the KRASMUT/CDKN2A/B/CMUT, KRASMUT/STK11MUT, and KRASMUT/ATMMUT subgroups. In an exploratory clinical cohort of 34 patients with advanced KRASMUT NSCLC treated with PD-(L)1 immunotherapy, the CBM-assessed overall survival correlated well with actual overall survival (r = 0.80, P < .001). CONCLUSION: CBM identified distinct PD-(L)1 immunotherapy sensitivity among molecular subgroups of KRASMUT NSCLC, in line with previous literature. These data provide proof-of-concept that computational modeling of tumor genomics could be used to expand on hypotheses from clinical observations of patients receiving PD-(L)1 immunotherapy and suggest mechanisms that underlie PD-(L)1 immunotherapy sensitivity.

Local and systemic toxicity of Echis carinatus venom: neutralization by Cassia auriculata L. leaf methanol extract.

Viper bites cause high morbidity and mortality especially in tropical and subtropical regions, affecting a large number of the rural population in these areas. Even though anti-venoms are available, in most cases they fail to tackle viper venom-induced local manifestations that persist even after anti-venom administration. Several studies have been reported the use of plant products and approved drugs along side anti-venom therapy for efficient management of local tissue damage. In this regard, the present study focuses on the protective efficacy of Cassia auriculata L. (Leguminosae) against Echis carinatus venom (ECV) induced toxicity. C. auriculata is a traditional medicinal plant, much valued in alternative medicine for its wide usage in ayurveda, naturopathy, and herbal therapy. Further, it has been used widely by traditional healers for treatment of snake and scorpion bites in the Western Ghats of Karnataka, India. In the present study, C. auriculata leaf methanol extract (CAME) significantly inhibited enzymatic activities of ECV proteases (96 ± 1 %; P = 0.001), PLA2 (45 ± 5 %; P = 0.01) and hyaluronidases (100 %; P = 0.0003) in vitro and hemorrhage, edema and myotoxicity in vivo. Further, CAME effectively reduced the lethal potency of ECV and increased the survival time of mice by ~6 times (17 vs 3 h). These inhibitory potentials of CAME towards hydrolytic enzymes, mortal and morbid symptoms of ECV toxins clearly substantiates the use by traditional healers of C. auriculata as a folk medicinal remedy for snakebite.

Severity of suicidal intent, method and behaviour antecedent to an act of self-harm: a cross sectional study of survivors of self-harm referred to a tertiary hospital in Mysore, south India.

BACKGROUND: Rates of self harm are high in south India, but little is known about the relationship between antecedent behaviour, suicidal intent and method. Aims: To identify clinical, social and behavioural antecedents preceding an act of self-harm. METHODS: 200 participants, consecutively presenting with deliberate self harm to a hospital in south India,were interviewed. Socio-demographic and clinical characteristics were recorded, together with behaviours preceding self-harm. The Pierce Suicidal Intent Scale and Mini International Neuropsychiatric Inventory were administered. RESULTS: Pesticide poisoning was the most common method, especially amongst men, in rural areas, and amongst professionals. No particular antecedent behaviour or activity appears to be associated with higher levels of suicidal intent. Absenteeism from work was the most commonly reported change of behaviour in the month preceding an act of self-harm. Unskilled labourers and professionals had significantly greater suicidal intent (adjusted for age, gender and method) than skilled labourers and the unemployed. There were no differences in suicidal intent between different methods. Rural dwellers had significantly greater suicidal intent compared to urban dwellers, irrespective of the method. Major Depressive Disorder was associated with significantly greater suicidal intent compared with other diagnoses and no diagnosis. CONCLUSIONS: Amongst people who harm themselves in south India, professionals and unskilled labourers, rural residents, and people with current major depressive disorder have higher levels of suicidal intent. Severity of suicidal intent does not appear to influence choice of method of self-harm. Behaviours predictive of self-harm in the west may not be relevant in south India.

A study to find the status of probiotics in New Delhi, India and review of strains of bacteria used as probiotics.

CONTEXT: Probiotics are living microorganisms, principally bacteria, that are safe for human consumption and, when ingested in sufficient quantities, have beneficial effects on human health, beyond basic nutrition. However, in India people are not aware of their benefits and availability. AIMS: To find status of probiotics in India and to assess the awareness regarding probiotics among chemists in New Delhi, India. SETTINGS AND DESIGN: A cross-sectional survey was conducted among 300 chemist shops in different areas of New Delhi, India. MATERIALS AND METHODS: Data were collected through a structured questionnaire, which was responded by the chemist in the course of a telephonic interview. The questionnaire addressed on the availability of probiotic products at their chemist shop. STATISTICAL ANALYSIS USED: The data so gathered were subjected for descriptive analysis using t test. RESULTS: As per availability of probiotic products, total of 25 probiotic products were available at different chemist shops. None of the chemist shop had all the 25 products available. 10% shops had 75% products available and there were 5% such shops which didn't have any of the products available. CONCLUSION: Efforts should be made to increase the awareness among chemists about the probiotic products.

Dental health status among sensory impaired and blind institutionalized children aged 6 to 20 years.

BACKGROUND: This study was planned to assess the dental caries status among disabled children as dental health is an integral part of general body health and this group is deprived of health care needs. MATERIALS & METHODS: A sample of 310 disabled children was gathered including 195- Hearing impaired, 115 - blind. Of which 226 were males and 84 were females. A study questionnaire was prepared to include demographic information and WHO oral health assessment form (1997) to record dental caries status.Data was analysed using student's test and ANOVA test was used at p≤0.05. RESULTS: The overall mean for DMFT scores for males and females was 2.11 (1.753) and 1.75 (1.275) respectively. Similarly overall mean for dft was 0.31 (0.254) for males and 0.27 (0.143) for females. Mean DMFT of blind students was more as compared to hearing impaired ones as 2.16 (2.005) and 1.80 (1.264) respectively. Age factor showed a significant increase in the mean DMFT scores with advancing age at p ≤ 0.001. CONCLUSION: Overall mean scores of caries was very high and it increased with increasing age. Blind children experienced more caries then hearing impaired children in permanent, whereas it was opposite in primary dentition. So there is urgent need of both comprehensive and incremental dental care for this subgroup of population. How to cite the article: Sanjay V, Shetty SM, Shetty RG, Managoli NA, Gugawad SC, Hitesh D. Dental health status among sensory impaired and blind institutionalized children aged 6 to 20 years. J Int Oral Health 2014;6(1):55-8.

No carious cervical lesions: abfraction.

Abfraction or Theory of Abfraction is a theory explaining the non-carious cervical lesions (NCCL). It suggests that they are caused by flexural forces, usually from cyclic loading; the enamel, especially at the cementoenamel junction (CEJ), undergoes this pattern of destruction by separating the enamel rods. Clinical aspect importance of these ineart lesions are at most important to be detected for early intervention and treatment modalities as options during the progression of the disease. How to cite this article: Shetty SM, Shetty RG, Mattigatti S, Managoli NA, Rairam SG, Patil AM. No Carious Cervical Lesions: Abfraction. J Int Oral Health 2013; 5(5):142-5.

Diabetes in rural Pondicherry, India: a population-based study of the incidence and risk factors

Background: For India, the ‘diabetes capital’ of the world, it is essential to knowthe incidence of type 2 diabetes mellitus (T2DM) and its key determinants. Astwo thirds of Indians live in rural areas, a study was undertaken to assess theincidence and risk factors of T2DM in rural Pondicherry, India.Methods: In a population-based cohort study initiated in 2007, a sample of 1223adults > 25 years of age from two villages of Pondicherry were selected using clusterrandom sampling. Data on risk factor exposure were collected using a structuredquestionnaire, anthropometric tests and fasting blood glucose assessment. Duringhouse visits, 1223 of 1403 invited subjects participated. Of these, 71 (5.8%) werefound to have diabetes. In 2010–2011, 85% of the non-diabetics (979/1152) werefollowed up using the same protocol. We calculated the risk of T2DM per annumstandardized by age and sex. Population estimates of the risk factors associatedwith T2DM were analysed using the Generalized Estimating Equation model andthe Population Attributable Risk (PAR) for T2DM calculated.Results: During 2937 person-years (PY) of follow-up, 63 new cases of T2DMoccurred, giving an incidence rate of 21.5/1000 PY. Almost one third (31.7%)of cases occurred in people aged below 40 years. The incidence was doubleamong males (28.7/1000 PY; 95% confidence interval (CI): 21.0–38.7) comparedwith females (14.6/1000 PY; 95% CI: 9.4–21.7). Applying these rates to ruralpopulations, it is estimated that each year 8.7 million people develop T2DM inrural India. Nearly half of the T2DM incidence was attributed to overweight/obesityand alcohol usage.Conclusion: T2DM incidence was 2% per year in adults in rural Pondicherry,India, with the rate increasing twice as fast in men. Increasing age, obesity, alcoholuse and a family history of T2DM independently predicted the development ofdiabetes. As half of T2DM incidence was attributed to overweight/obesity andalcohol use, health promotion interventions focusing on maintaining an optimalweight and decreasing

Diabetes in rural Pondicherry, India: a population-based studyof the incidence and risk factors.

BACKGROUND: For India, the 'diabetes capital' of the world, it is essential to know the incidence of type 2 diabetes mellitus (T2DM) and its key determinants. As two thirds of Indians live in rural areas, a study was undertaken to assess the incidence and risk factors of T2DM in rural Pondicherry, India. METHODS: In a population-based cohort study initiated in 2007, a sample of 1223 adults > 25 years ofage from two villages of Pondicherry were selected using cluster random sampling. Data on risk factor exposure were collected using a structured questionnaire, anthropometric tests and fasting blood glucose assessment. During house visits, 1223 of 1403 invited subjects participated. Of these, 71 (5.8%) were found to have diabetes. In 2010-2011, 85% of the non-diabetics (979/1152) were followed up using the same protocol. We calculated the risk of T2DM per annum standardized by age and sex. Population estimates of the risk factors associated with T2DM were analysed using the Generalized Estimating Equation model and the Population Attributable Risk (PAR) for T2DM calculated. RESULTS: During 2937 person-years (PY) of follow-up, 63 new cases of T2DM occurred, giving an incidence rate of 21.5/1000 PY. Almost one third (31.7%) of cases occurred in people aged below 40 years. The incidence was double among males (28.7/1000 PY; 95% confidence interval (CI): 21.0-38.7) compared with females (14.6/1000 PY; 95% CI: 9.4-21.7). Applying these rates to rural populations, it is estimated that each year 8.7 million people develop T2DM in rural India. Nearly half of the T2DM incidence was attributed to overweight/obesity and alcohol usage. CONCLUSION: T2DM incidence was 2% per year in adults in rural Pondicherry, India, with the rate increasing twice as fast in men. Increasing age, obesity, alcohol use and a family history of T2DM independently predicted the development of diabetes. As half of T2DM incidence was attributed to overweight/obesity and alcohol use, health promotion interventions focusing on maintaining an optimal weight and decreasing alcohol consumption may be effective in reducing the rise in T2DM cases.

Evaluation of oral methotrexate in the treatment of systemic sclerosis.

BACKGROUND: Treatment of scleroderma is difficult and currently no treatment can induce complete remission of the disease. OBJECTIVE: To evaluate weekly oral methotrexate in the treatment of Indian patients with systemic sclerosis. METHODS: Thirty-three patients with systemic sclerosis presenting to the department of dermatology (outpatients) who satisfied the inclusion criteria were enrolled into the study. All cases were admitted into the dermatology ward for detailed evaluation. A detailed history and physical examination, including assessment of disease severity by Rodnan skin scoring, was carried out. Baseline investigations included complete blood counts, blood glucose, serum electrolytes, renal function test, liver function tests, urine examination (albumin, sugar, microscopic examination, 24-h protein), ANA, chest X-ray, Barium swallow, pulmonary function test, electrocardiogram (ECG), HRCT of chest, and 4-mm punch skin biopsy from dorsum of the hand. All the patients were treated with oral methotrexate (15 mg/week) for 6 months, following standard guidelines. RESULTS: The patients included 29 (87.9%) females and four (12.1%) males with a mean age of 31.45 +/- 8.76 years. The mean duration of disease was 5.6 +/- 4.5 years (range 2 months to 15 years). All the patients had binding down of skin, 31 (93.9%) had Raynaud's phenomenon, 31 (93.9%) had pigmentary change, 21 (63.6%) had hand contractures, 17 (51.5%) had fingertip ulcers, 15 (45.5%) had dyspnoea, 14 (42.4%) had restricted mouth opening, 13 (39.4%) had telangiectasia, 11 (33.3%) had fingertip resorption, eight (24.2%) had joint complaints, six (18.2%) had dysphagia, and one (3.03%) had gangrene. On laboratory investigation ANA was positive in 29 (87.9%) patients, dsDNA was raised in only four (12.1%), baseline chest X-ray was abnormal in 18 (54.5%), HRCT was abnormal in 27 (81.8%), abnormal PFT in 32 (96.9%), abnormal ECG in five (15.2%), and barium swallow abnormality in 19 (57.5%) patients. Twenty-five patients completed the 6-month follow up. There was subjective improvement in binding down (80%), Raynaud's phenomenon (96%), fingertip ulceration (88.8%), hyperpigmentation (77.2%) and dyspnoea (45.5%). The objective parameters showed statistically significant improvement in mouth openingm, but improvement of skin score, lung function (chest radiograph, PFT, HRCT), and dysphagia was not significant at the 6-month follow up. In eight patients, treatment was continued for 1 year of methotrexate, which showed statistically significant improvement in skin score. CONCLUSION: It was concluded that methotrexate for 6 months only provides subjective improvement, and further studies after 1 year of treatment with methotrexate are recommended.

Profile of systemic sclerosis in a tertiary care center in North India.

AIM: To study the clinical and immunological profile in patients of systemic sclerosis from North India and compare it with other ethnic groups. METHODS: Patients presenting to us between the years 2001 and 2004 and fulfilling the American Rheumatism Association (ARA) criteria for systemic sclerosis were included. There were 84 females and 16 males with the mean age of 32.5 +/-11.62 years and a mean duration of 6.49 +/- 4.34 years. All patients were admitted to the dermatology ward for detailed history and examination including Rodnan score. Investigations including hemogram, hepatic and renal functions, serum electrolytes, urine for albumin, sugar, microscopy and 24h urinary protein estimation, antinuclear antibody, chest X-ray, barium swallow, pulmonary function test, electrocardiogram and skin biopsy were done. RESULTS: The most common presenting symptoms were skin binding-down (98.5%), Raynaud's phenomenon 92.9%, pigmentary changes 91%, contracture of fingers 64.6%, fingertip ulcer 58.6%, restriction of mouth opening 55.5%, dyspnea 51.1%, joint complaints 36.7% and dysphagia in 35.2%. The mean Rodnan score was 25.81 +/- 10.04 and the mean mouth opening was 24.6 +/- 19.01 mm. The laboratory abnormalities included raised ESR in 87.8%, ANA positive in 89.1%, proteinuria in 6.0%, abnormal chest X-ray in 65.3%, abnormal barium swallow in 70.2% and reduced pulmonary function test in 85.8%. CONCLUSION: The clinical and immunological profile of systemic sclerosis in North India is similar to that of other ethnic groups except that pigmentary changes are commoner and renal involvement is relatively uncommon.