Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules.

Unique molecular identifiers are random oligonucleotide sequences that remove PCR amplification biases. However, the impact that PCR associated sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We show that PCR errors are a source of inaccuracy in both bulk and single-cell sequencing data, and synthesizing unique molecular identifiers using homotrimeric nucleotide blocks provides an error-correcting solution that allows absolute counting of sequenced molecules.

Study of the Vertical Transmission of COVID-19 by Using the World Health Organisation Protocol in a Tertiary Care Hospital in Eastern India.

BACKGROUND: The World Health Organisation (WHO) has established criteria to diagnose vertical transmission in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to determine the incidence of vertical transmission of SARS-CoV-2 using WHO criteria in a tertiary care centre in eastern India. METHODS: A hospital-based prospective observational study was conducted from June 2021 to February 2022 on women admitted for delivery with a positive nasopharyngeal (NP) swab and a SARS-CoV-2 real-time reverse-transcriptase polymerase chain reaction (RT-PCR) test. Following the delivery, the amniotic fluid (AF) and swab from the placenta were tested for SARS-CoV-2 by the Truenat test. The umbilical cord and maternal blood were analyzed to detect immunoglobulin M (IgM) and immunoglobulin G (IgG). The nasopharyngeal swabs of the newborns were tested for SARS-CoV-2 by RT-PCR. RESULTS: Forty-eight SARS-CoV-2-positive asymptomatic women were included in the study. Twenty-eight (58.3%) were delivered via cesarean section. Preterm delivery occurred in 13 (27.1%) cases. In only one case, vertical transmission was confirmed as the neonate had a positive nasopharyngeal SARS-CoV-2 RT-PCR test and the cord blood was IgM positive (suggesting an immune response in the neonate). The placenta was positive in three cases, and amniotic fluid was positive in two. However, vertical transmission was deemed unlikely in these cases as there was no evidence of immune response or viral persistence according to the WHO criteria. There was one stillbirth, and it tested negative for SARS-CoV-2. CONCLUSION: This study strengthens the evidence of vertical transmission in COVID-19-positive asymptomatic mothers. The data suggest a low transmission rate.

Cognitive Skills and DNA Methylation Are Correlating in Healthy and Novice College Students Practicing Preksha Dhyana Meditation.

The impact of different meditation protocols on human health is explored at the cognitive and cellular levels. Preksha Dhyana meditation has been observed to seemingly affect the cognitive performance, transcriptome, and methylome of healthy and novice participant practitioners. In this study, we performed correlation analyses to investigate the presence of any relationships in the changes in cognitive performance and DNA methylation in a group of college students practicing Preksha Dhyana (N = 34). Nine factors of cognitive performance were assessed at baseline and 8 weeks postintervention timepoints in the participants. Statistically significant improvements were observed in six of the nine assessments, which were predominantly relating to memory and affect. Using Illumina 850 K microarray technology, 470 differentially methylated sites (DMS) were identified between the two timepoints (baseline and 8 weeks), using a threshold of p-value < 0.05 and methylation levels beyond -3% to 3% at every site. Correlation analysis between the changes in performance on each of the nine assessments and every DMS unveiled statistically significant positive and negative relationships at several of these sites. The identified DMS were in proximity of essential genes involved in signaling and other important metabolic processes. Interestingly, we identified a set of sites that can be considered as biomarkers for Preksha meditation improvements at the genome level.

Preksha Dhyana Meditation Effect on the DNA Methylation Signature in College Students.

Introduction: The stress and psychological factors affect the human transcriptomic and epigenomic landscapes. Preksha Dhyana meditation (PM) was found to be effective, in novice healthy college student meditators, at the cognitive skills and transcriptomic levels. Recently published data showed that PM induced alterations at the transcriptome level in healthy and novice college students. Methods: To decipher potential mechanisms underlying the PM effect at the cellular level, array-based methylation analyses in peripheral blood were performed at baseline and 8 weeks postintervention in 34 participants. Results: Overall, 470 CpG sites were nominally differentially methylated (p ≤ 0.05 and change magnitude from ≥3% to ≤ -3%) between baseline and 8 weeks postintervention with 180 sites hypermethylated and 290 sites hypomethylated. Pathway analysis of the genes linked to the differentially methylated sites revealed the enrichment of several molecular and cellular signaling pathways, especially metabolic and brain function signaling pathways. Conclusions: Besides its beneficial effects on cognitive skills and transcriptome alterations, the current data indicate that PM meditation also affects the DNA methylation profile of novice and healthy college students 8 weeks postintervention. Clinical Trial Registration: NCT03779269.

Preksha Dhyana meditation induces alterations at the transcriptome level in novice and healthy college students.

Background: The human transcriptome across a variety of cell types and tissues are affected by stress and other psychological factors. Preksha Dhyana meditation (PM) is effective at improving cognitive skills in novice healthy college student meditators after 8 weeks of intervention, but the molecular and cellular mechanisms involved in these improvements are still largely unknown. Methods: In order to decipher potential mechanisms at the cellular level, transcriptomic profiling analyses, from peripheral blood, were performed at baseline and 8 weeks post-intervention in 18-paired participants (RNASeq). Results: At the transcriptomic level, 494 genes were nominally differentially expressed (p-value ≤ 0.05) between baseline and 8 weeks post-intervention. Our data showed that 136 genes were upregulated, while 358 genes were downregulated. These genes were enriched in several cellular pathways including innate and adaptive immunity, cell signaling, and other metabolic processes. Conclusions: Overall, our findings indicate that PM meditation affects gene expression patterns from whole blood in novice healthy college students. Improvements at the cognitive skills were also mirrored with changes at RNA expression profiling.

Spectrum of toxicity due to pheniramine overuse in a COVID-19 patient. How much do we know?

Pheniramine maleate is an easily accessible, potent antihistaminic compound used for the treatment of various allergic conditions. It acts on histamine one (H1) receptors on the central nervous system (CNS) and the peripheral tissues. It is a safe drug in therapeutic doses. However, overdoses as in suicidal cases, can result in serious, life-threatening drug-toxicity. These include atropine-like antimuscarinic effects like dryness of mucosal membranes, blurring of vision, hallucinations, CNS excitation such as irritability, insomnia, and seizures. Rhabdomyolysis can also occur as a result of its direct toxic effect on muscles, resulting in myoglobinuria, renal failure and electrolyte imbalance. Cardiotoxicity though rare, is also reported. We report a case of pheniramine maleate induced ventricular tachycardia, myoglobinuria with acute kidney injury (AKI) in a 20-year-old man who had consumed 50 tablets. He was incidentally also found to have SARS-CoV2 infection. However, timely intervention and aggressive supportive therapy helped in the recovery of the patient.

Results of Serosurveillance and Forecasting the Third Wave of COVID-19 in an Industrial District in India.

Prevalence of immunoglobulin G (IgG) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in the industrial district of East Singhbhum (Jharkhand, India) from July, August, November, and December 2020 and January 2021 after the first wave and in July 2021 after the second wave of coronavirus disease 2021 (COVID-19) infections may be utilized to find the possibility of a third wave of COVID-19 infections. Based on the trend of the loss of protective IgG antibodies after the first wave and the seropositivity of 75% in the district in July 2021, simple forecasting and proportional estimates of the seropositivity in the next eight months and the estimated maximum number of the cases was done. We also considered the seropositivity without vaccination in July 2021 (63%). Additionally, the trend of the weekly RT-PCR and rapid antigen testing for SARS-CoV-2 may also preemptively predict an imminent wave. Based on the East Singhbhum population and the vaccination coverage with at least one dose till July 2021 (Covishield or Covaxin), it is estimated that a 4-5% monthly vaccination coverage rate of new individuals will not allow the seropositivity to fall below 50% and hold at bay a major wave. Vaccination coverage of 3% or less would allow a continuous drop in acquired immunity in the district and can potentially cause a rise in cases, making the community susceptible to a future surge of infections. A 3-5% vaccination rate of new individuals is unlikely to see a drop in the community seropositivity below 50% and the number of new cases of COVID-19 infections going above 478 to 712 per month at least till March 2022. The assumptions are based on presuming that there will be no new mutant of SARS-CoV-2 that escapes the immunity provided by previous infection or vaccination over the next eight months. However, currently, there is no evidence to speculate on any new variant of concern causing a major wave globally. The B.1.617.2 (delta) variant was first identified in October 2020 and there was a lag of six months to the second surge of COVID-19 infections in East Singhbhum, primarily caused by this variant. Additionally, 3% and above, with a rising weekly trend of reverse transcription-polymerase chain reaction (RT-PCR) positivity for SARS-CoV-2 can provide at least four to eight weeks advance warning before the peak of the wave if an imminent future wave is impending.

Effects of Combining Meditation Techniques on Short-Term Memory, Attention, and Affect in Healthy College Students.

Meditation refers to a family of self-regulation practices that focuses on training attention and awareness to foster psycho-emotional well-being and to develop specific capacities such as calmness, clarity, and concentration. We report a prospective convenience-controlled study in which we analyzed the effect of two components of Preksha Dhyana - buzzing bee sound meditation (Mahapran dhvani) and color meditation (lesya dhyana) on healthy college students. Mahapran and lesya dhyana are two Preksha Dhyana practices that are based on sound and green color, respectively. The study population represents a suitable target as college students experience different stress factors during the school year. This study measures the individual and combined effects of two techniques (one focusing on sound and one focusing on color), on short-term memory, attention, and affect, in novice meditators. We used a battery of cognitive, performance, and compared results with baseline and control values. We found improved cognition, especially attention, short-term memory, and affect in terms of positivity and reduced negativity. Overall, the two techniques produced variable benefits and subjects showed improved scores over baseline for short-term memory, cognitive function, and overall wellbeing. Further studies are required to understand underlying mechanisms for the observed differences between the two techniques and to elucidate mechanisms underlying the more pronounced and global benefits observed with the combined techniques. These results underscore a need to examine individual components of meditation practices in order to individualize treatment approaches for attention disorders in young adults. Clinical Trail Registration:ClinicalTrials.gov Identifier: NCT03779269.

Hepatitis E Genotype 1 Outbreak in Jharkhand, India: A Descriptive Analysis.

INTRODUCTION: A waterborne outbreak of hepatitis E virus occurred in the Jamshedpur city of Jharkhand from March 2018 to October 2018. The aim of the present study is to study the hepatitis E virus outbreak clinically, serologically and etiologically. METHODS: Five hundred and eighty-four clinically and biochemically documented cases were screened for the hepatotropic viral markers (HepatitisA, B, C, and E) by the ELISA. Demographic data such as gender, age, clinical diagnosis, location, outcome and time of admission were extracted from the online hospital management system. Water samples from the affected area were tested for HEV RNA detection. Genotyping of HEV virus was carried out by sequencing and phylogenetic analysis. RESULTS: Hepatitis E genotype 1 was confirmed as the major etiological agent in this outbreak due to the faecal contamination of drinking water supply while establishing illegal water connections. Mixed infection of HEV-HAV (5.31%) or HEV-HBV (0.91%) was also detected in the present series of acute viral hepatitis. CONCLUSION: The study highlights the importance of screening for both enterically transmitted hepatotropic viral markers as well as the parenterally transmitted hepatotropic viral markers during the outbreaks of acute viral hepatitis.

Paracrine signalling by cardiac calcitonin controls atrial fibrogenesis and arrhythmia.

Atrial fibrillation, the most common cardiac arrhythmia, is an important contributor to mortality and morbidity, and particularly to the risk of stroke in humans1. Atrial-tissue fibrosis is a central pathophysiological feature of atrial fibrillation that also hampers its treatment; the underlying molecular mechanisms are poorly understood and warrant investigation given the inadequacy of present therapies2. Here we show that calcitonin, a hormone product of the thyroid gland involved in bone metabolism3, is also produced by atrial cardiomyocytes in substantial quantities and acts as a paracrine signal that affects neighbouring collagen-producing fibroblasts to control their proliferation and secretion of extracellular matrix proteins. Global disruption of calcitonin receptor signalling in mice causes atrial fibrosis and increases susceptibility to atrial fibrillation. In mice in which liver kinase B1 is knocked down specifically in the atria, atrial-specific knockdown of calcitonin promotes atrial fibrosis and increases and prolongs spontaneous episodes of atrial fibrillation, whereas atrial-specific overexpression of calcitonin prevents both atrial fibrosis and fibrillation. Human patients with persistent atrial fibrillation show sixfold lower levels of myocardial calcitonin compared to control individuals with normal heart rhythm, with loss of calcitonin receptors in the fibroblast membrane. Although transcriptome analysis of human atrial fibroblasts reveals little change after exposure to calcitonin, proteomic analysis shows extensive alterations in extracellular matrix proteins and pathways related to fibrogenesis, infection and immune responses, and transcriptional regulation. Strategies to restore disrupted myocardial calcitonin signalling thus may offer therapeutic avenues for patients with atrial fibrillation.

Hb Hope: A Rare Variant of Haemoglobin-Forged a Rise in HbA1c on Immunoturbidimetric Assay.

Glycosylated hemoglobin (HbA1c) determination is a powerful means for assessing the evaluation and management of patients with diabetes mellitus. Hemoglobin (Hb) variants and chemically modified derivatives of Hb can affect the accuracy of measurement of HbA1c done by various analytical methods. We report a patient with a rare variant of Hb (Hb Hope) that caused an abnormally high value of HBA1c when assayed using immunoturbidimetric assay ("Tina-quant" 2nd generation assay) and also elucidate the nature of the variant.

Peer-mediated multimodal intervention program for the treatment of children with ADHD in India: one-year followup.

The objective was to assess the efficacy of a one-year, peer-mediated interventional program consisting of yoga, meditation and play therapy maintained by student volunteers in a school in India. The population consisted of 69 students between the ages of 6 and 11 years, previously identified as having attention deficit hyperactivity disorder (ADHD). A program, known as Climb-Up, was initially embedded in the school twice weekly. Local high school student volunteers were then trained to continue to implement the program weekly over the period of one year. Improvements in ADHD symptoms and academic performance were assessed using Vanderbilt questionnaires completed by both parents and teachers. The performance impairment scores for ADHD students assessed by teachers improved by 6 weeks and were sustained through 12 months in 46 (85%) of the enrolled students. The improvements in their Vanderbilt scores assessed by parents were also seen in 92% (P < 0.0001, Wilcoxon). The Climb-Up program resulted in remarkable improvements in the students' school performances that were sustained throughout the year. These results show promise for a cost-effective program that could easily be implemented in any school.

Study of cytomorphology of solid pseudopapillary tumor of pancreas and its differential diagnosis.

BACKGROUND: Solid pseudopapillary tumor is a rare pancreatic neoplasm with uncertain to low malignant potential. This is an uncommon neoplasm with many pseudonyms, occurring predominantly in young woman under the age of thirty years. AIMS: To study the cytomorphological features of six cases of solid and pseudopapillary epithelial neoplasm of pancreas diagnosed on fine needle aspiration cytology (FNAC) in years 2005 to 2007 and its cyto-histological correlation. MATERIALS AND METHODS: Image-guided FNAs was done in these six patients preoperatively. Alcohol-fixed smears were stained with Papanicolaou stain, cytomorphological findings were evaluated and diagnosis was made. Diagnosis was later confirmed by histology in all cases. RESULTS: All six cases show characteristic cytological features such as hypercellular smears with presence of abundant delicate papillary fragments, dyscohesive cells, monomorphic tumor cells with delicate folded nuclear membranes, and foamy macrophages in the background. CONCLUSIONS: Preoperative correct diagnosis of solid pseudopapillary tumor of pancreas is possible on FNAC and by doing so it helps in management of this surgically curable neoplasm.