Molecular characterization, phylogenetic and variation analyses of SARS-CoV-2 strains in India.

Unlabelled: In the wake of the havoc caused by the COVID-19 pandemic, it is imperative to use the available genomic sequence data to gain insight into the mutational and genomic diversity of SARS-CoV-2. Here we have performed comparative phylogenetic, mutational and genetic diversity analysis on 1962 SARS-CoV-2 genome sequences from seven worst hit Indian states during the third Covid-19 wave, to determine the SARS-CoV-2 strains and mutations in circulation during the third wave and the transmission pattern and disease epidemiology across the states and gain valuable insight into the viral evolution. 6083 Single nucleotide polymorphisms (SNPs) were discovered in the analysis with 93 SNPs common to all states.

Lifestyle, Epstein-Barr virus infection, and other factors could impede nasopharyngeal cancer survivorship: a five-year cross-sectional study in North Eastern India.

Unlabelled: Nasopharyngeal Carcinoma (NPC) is one of the leading cancers in India's north-eastern (NE) region affecting a section of the population each year. A proportion of the NPC cases are observed to recur even after therapy, indicating the involvement of other factors. We aimed to explore the NPC and Epstein-Barr virus (EBV) burden in the NE region and investigate the prognostic factors for the NPC patients' poor survival and recurrence.

BAX -248 G>A and BCL2 -938 C>A Variant Lowers the Survival in Patients with Nasopharyngeal Carcinoma and Could be Associated with Tissue-Specific Malignancies: A Multi-Method Approach.

Background: The association of BAX -248 G>A and BCL2 -938 C>A with different cancers created conflicts.  We studied the correlation and the effect of these polymorphisms in patients with Nasopharyngeal Carcinoma (NPC).  Methods: PCR-RFLP and Sanger sequencing were used to detect polymorphisms.

Joint modelling of longitudinal response and time-to-event data using conditional distributions: a Bayesian perspective.

Over the last 20 or more years a lot of clinical applications and methodological development in the area of joint models of longitudinal and time-to-event outcomes have come up. In these studies, patients are followed until an event, such as death, occurs. In most of the work, using subject-specific random-effects as frailty, the dependency of these two processes has been established.

Identification of airborne pollen allergens from two avenue trees of India.

An attempt has been made to detect airborne pollen of (LS) and S (SC) - two common avenue trees of India as potential sources of aeroallergens and also to identify the major IgE-reactive components present in them. The airborne pollen concentration was assessed using a Burkard sampler. A detailed questionnaire on clinical data of 1490 patients was recorded based on hospital data.

Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers.

Antibiotics are widely used at sub-lethal concentrations as a feed supplement to enhance poultry productivity. To understand antibiotic-induced temporal changes in the structure and function of gut microbiota of chicken, two flocks were maintained for six weeks on a carbohydrate- and protein-rich diet. The feed in the conventional diet (CD) group was supplemented with sub-lethal doses of chlorotetracycline, virginiamycin and amoxicillin, while the organic diet (OD) had no such addition.

Monitoring of airborne fungal spore load in relation to meteorological factors, air pollutants and allergic symptoms in Farakka, an unexplored biozone of eastern India.

Fungi are important components of atmosphere which play a major role in causing respiratory allergy upon inhalation. An airborne fungal spore survey was carried out in two outdoor environments in Farakka-an unexplored township covering the National Thermal Power Station, West Bengal, India for a period of 2 years (October 2013 to September 2015). A Burkard personal volumetric air sampler was used at 15 days interval to collect the total fungal spore load.

Patterns and severity of vincristine-induced peripheral neuropathy in children with acute lymphoblastic leukemia.

Vincristine, a critical component of combination chemotherapy treatment for pediatric acute lymphoblastic leukemia (ALL), can lead to vincristine-induced peripheral neuropathy (VIPN). Longitudinal VIPN assessments were obtained over 12 months from newly diagnosed children with ALL (N = 128) aged 1-18 years who received vincristine at one of four academic children's hospitals. VIPN assessments were obtained using the Total Neuropathy Score-Pediatric Vincristine (TNS©-PV), National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE©), Balis© grading scale, and Pediatric Neuropathic Pain Scale©-Five (PNPS©-5).

Bounded influence function based inference in joint modelling of ordinal partial linear model and accelerated failure time model.

A common objective in longitudinal studies is to characterize the relationship between a longitudinal response process and a time-to-event data. Ordinal nature of the response and possible missing information on covariates add complications to the joint model. In such circumstances, some influential observations often present in the data may upset the analysis.

Simultaneous inferences based on empirical Bayes methods and false discovery rates ineQTL data analysis.

Background: Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with complex human diseases, clinical conditions and traits. Genetic mapping of expression quantitative trait loci (eQTLs) is providing us with novel functional effects of thousands of single nucleotide polymorphisms (SNPs). In a classical quantitative trail loci (QTL) mapping problem multiple tests are done to assess whether one trait is associated with a number of loci.

New aQTL SNPs for the CYP2D6 identified by a novel mediation analysis of genome-wide SNP arrays, gene expression arrays, and CYP2D6 activity.

Background: The genome-wide association studies (GWAS) have been successful during the last few years. A key challenge is that the interpretation of the results is not straightforward, especially for transacting SNPs. Integration of transcriptome data into GWAS may provide clues elucidating the mechanisms by which a genetic variant leads to a disease.

Robust analysis in joint models: an application to a study on muscular dystrophy.

Generalized partial ordinal models occur frequently in biomedical investigations where, along with ordinal longitudinal outcomes, there are time-dependent covariates that act nonparametrically. In these studies, an association between such outcomes and time to an event is of considerable interest to medical practitioners. The primary objective in the present article is to study the robustness of estimators of the parameters of interest in a joint generalized partial ordinal models and a time-to-event model, because in many situations, the estimators in such joint models are sensitive to outliers.

Inferences for joint modelling of repeated ordinal scores and time to event data.

In clinical trials and other follow-up studies, it is natural that a response variable is repeatedly measured during follow-up and the occurrence of some key event is also monitored. There has been a considerable study on the joint modelling these measures together with information on covariates. But most of the studies are related to continuous outcomes.

Genetic association of Toll-like-receptor 4 and tumor necrosis factor-alpha polymorphisms with Plasmodium falciparum blood infection levels.

Dysregulated innate immune responses due to inappropriate signaling by Toll-like receptors (TLRs) and aberrant production of pro-inflammatory cytokines are implicated in the immunopathology and disease outcome in Plasmodium falciparum malaria. This study investigates the relationship between polymorphic variability of candidate genes including TLR-2, -4, -9, tumor necrosis factor-alpha and lymphotoxin-alpha and blood infection level in Indian mild malaria patients. Genotyping was carried out by PCR-RFLP and sequencing.

Mixed models for ordinal data: a pharmacokinetic study on the effectiveness of drug for the reduction of epileptic seizures.

Population pharmacokinetics (PK)/pharmacodynamics analysis is considered as an important component of drug development process in these days. Owing to different standardization techniques in different laboratories, the drug concentrations in blood are reported in intervals in which they lie. For obvious reason the outcomes are then recorded as multiple discrete indicators with natural ordering.