Pericytic Lesions: A Paradigm of Overlapping Features.

Although myopericytoma and glomangiopericytoma are considered the subtypes of the group myopericytomas (MPC), they differ morphologically. Both of the tumors arise from pericytic cells. Scalp MPC are infrequent, but extranasal glomangiopericytomas are extremely rare. Herein, we report a case of a 36-year-old female presenting with slowly growing scalp swelling. Histopathology showed a dermal tumor with features of myopericytoma as well as glomangiopericytoma within the same lesion. Immunohistochemistry and reticulin staining confirmed pericytic origin but could not differentiate between the two tumors. This case report adds to the rarity and morphologic heterogeneity of the group MPC.

Superior haplotypes towards the development of blast and bacterial blight-resistant rice.

Rice blast and bacterial leaf blight, are major disease, significantly threatens rice yield in all rice growing regions under favorable conditions and identification of resistance genes and their superior haplotypes is a potential strategy for effectively managing and controlling this devastating disease. In this study, we conducted a genome-wide association study (GWAS) using a diverse set of 147 rice accessions for blast and bacterial blight diseases in replications. Results revealed 23 (9 for blast and 14 for BLB) significant marker-trait associations (MTAs) that corresponded to 107 and 210 candidate genes for blast and BLB, respectively. The haplo-pheno analysis of the candidate genes led to the identification of eight superior haplotypes for blast, with an average SES score ranging from 0.00 to 1.33, and five superior haplotypes for BLB, with scores ranging from 1.52cm to 4.86cm superior haplotypes. Among these, superior haplotypes LOC_OS12G39700-H4 and LOC_Os06g30440-H33 were identified with the lowest average blast scores of 0.00-0.67, and superior haplotype LOC_Os02g12660-H39 exhibited the lowest average lesion length (1.88 - 2.06cm) for BLB. A total of ten accessions for blast and eight accessions for BLB were identified carrying superior haplotypes were identified. These haplotypes belong to aus and indx subpopulations of five countries (Bangladesh, Brazil, India, Myanmar, and Pakistan). For BLB resistance, eight accessions from six countries (Bangladesh, China, India, Myanmar, Pakistan, and Sri Lanka) and four subpopulations (aus, ind1A, ind2, and ind3) were identified carrying superior haplotypes. Interestingly, four candidate genes, LOC_Os06g21040, LOC_Os04g23960, LOC_Os12g39700, and LOC_Os01g24640 encoding transposon and retrotransposon proteins were among those with superior haplotypes known to play a crucial role in plant defense responses. These identified superior haplotypes have the potential to be combined into a single genetic background through haplotype-based breeding for a broader resistance spectrum against blast and bacterial blight diseases.

Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties.

Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.

SpeedFlower: a comprehensive speed breeding protocol for indica and japonica rice.

To increase rice yields and feed billions of people, it is essential to enhance genetic gains. However, the development of new varieties is hindered by longer generation times and seasonal constraints. To address these limitations, a speed breeding facility has been established and a robust speed breeding protocol, SpeedFlower is developed that allows growing 4-5 generations of indica and/or japonica rice in a year. Our findings reveal that a high red-to-blue (2R > 1B) spectrum ratio, followed by green, yellow and far-red (FR) light, along with a 24-h long day (LD) photoperiod for the initial 15 days of the vegetative phase, facilitated early flowering. This is further enhanced by 10-h short day (SD) photoperiod in the later stage and day and night temperatures of 32/30 °C, along with 65% humidity facilitated early flowering ranging from 52 to 60 days at high light intensity (800 µmol m-2 s-1). Additionally, the use of prematurely harvested seeds and gibberellic acid treatment reduced the maturity duration by 50%. Further, SpeedFlower was validated on a diverse subset of 198 rice accessions from 3K RGP panel encompassing all 12 distinct groups of Oryza sativa L. classes. Our results confirmed that using SpeedFlower one generation can be achieved within 58-71 days resulting in 5.1-6.3 generations per year across the 12 sub-groups. This breakthrough enables us to enhance genetic gain, which could feed half of the world's population dependent on rice.

Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome.

Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.

Multiple neural tube defects: rare developmental anomaly with an elusive embryological explanation.

Neural tube defect is a congenital anomaly resulting from the failure of fusion of the neural folds in the midline which occurs in the third and the fourth week of embryonic development. These defects can occur at any of the three embryological stages-gastrulation, primary neurulation and secondary neurulation. Presence of neural tube defects at multiple (two or more) sites along the craniospinal axis is an extremely rare anomaly and the management depends on clinical as well as imaging findings. These multiple defects are not well explained by the "Zipper closure" theory and can be better explained by the "Multisite closure theory", which will be highlighted in this manuscript. Few of these multiple site anomalies cannot be fully explained even by the multisite closure theory and more research is needed to decipher this entity.

The Efficacy of the Three Types of Plaque Control Methods During Fixed Orthodontic Treatment: A Randomized Controlled Trial.

BACKGROUND: When intraoral orthodontic devices are used, it becomes significantly more difficult to remove plaque effectively. Dentists and orthodontic specialists can come up with more effective preventive strategies while patients are undergoing fixed orthodontic work if they have a deeper understanding of the present scenario. In addition, individuals will become more aware of the importance of good dental hygiene habits as a result of this. OBJECTIVE: To assess and compare the effectiveness of a manual toothbrush, machine-driven toothbrush, and conventional mechanical toothbrush coupled with mouth rinse in removing plaque and maintaining gingival health in patients undergoing fixed orthodontic treatment. METHODS AND MATERIALS: In this research, a total of 222 individuals who met the eligibility and exclusion requirements were randomly selected and offered their written consent. There were a total of 74 participants for each of the three different categories. Category A used a physically driven toothbrush. Category B used a motorized toothbrush. Category C used a physically driven toothbrush together with mouthwash containing 0.2% chlorhexidine gluconate. All study participants were assessed at baseline, one-month follow-up, and two-month follow-up to document the preliminary information, including that of the modified papillary bleeding index (MPBI) by Muhlemann, plaque index (PI) introduced by Silness and Loe, and gingival index (GI) introduced by Loe and Silness. RESULTS: In this study, the mean PI scores at the one-month and two-month follow-ups were minimum in Category C, while it was maximum in Category A at the two-month follow-up. The mean GI scores at the two-month follow-up were minimum in Category C, while it was maximum in Category A at the two-month follow-up. The mean MPBI scores at the two-month follow-up were minimum in Category C, while it was maximum in Category A. It was observed that participants in this trial who only used a typical mechanical brush experienced an increase in PI and GI scores after one and two months of follow-up. At the one-month and two-month follow-ups, it was noted that the values of PI, GI, and MPBI significantly decreased in the study participants using automated toothbrushes as well as in study participants using manual toothbrushes in conjunction with chlorhexidine mouthwash as compared to baseline values. However, when the three categories were compared, it was found that the research participants utilizing both a manual toothbrush and 0.2% chlorhexidine experienced the highest decreases in PI, GI, and MPBI values. CONCLUSION: The reduction in the scores of PI, GI, and MPBI was maximum in orthodontic patients after two months when they apply manual toothbrushing along with 0.2% chlorhexidine.

Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.

Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation among codon usage bias, gene expression, and underlying mechanisms in rice under abiotic and biotic stress conditions. The results indicated that genes with higher expression (up- or downregulated) levels had high GC content (≥60%), a low effective number of codon usage (≤40), and exhibited strong biases towards the codons with C/G at the third nucleotide position, irrespective of stress received. TTC, ATC, and CTC were the most preferred codons, while TAC, CAC, AAC, GAC, and TGC were moderately preferred under any stress (abiotic or biotic) condition. Additionally, downregulated genes are under mutational pressure (R2 ≥ 0.5) while upregulated genes are under natural selection pressure (R2 ≤ 0.5). Based on these results, we also identified the possible target codons that can be used to design an optimized set of genes with specific codons to develop climate-resilient varieties. Conclusively, under stress, rice has a bias towards codon usage which is correlated with GC content, gene expression level, and gene length.

Imaging Findings in Chronic Granulomatous Disease (CGD).

OBJECTIVES: To describe prevalence of various imaging findings in chronic granulomatous disease (CGD) patients; and find imaging biomarkers for differentiating chest infections caused by different micro-organisms. METHODS: A retrospective study was conducted on 15 patients (49 scans) with proven CGD. Scans which had a correlative microbiological diagnosis for organisms were included in the analysis. The scans were reviewed by 3 radiologists on a predefined proforma, under the lung parenchymal, airway, pleural, mediastinal, and extrathoracic abnormalities. Analysis of various imaging parameters on a semiquantitative scale was performed, followed by a correlation of each imaging findings with causative organisms. RESULT: The mean age of presentation was nearly 7 y, with a male preponderance. Definitive proof of causative organisms was obtained in 22 scans. Bacterial infection was found in 7, fungal in 12, tubercular in 2, and viral in 1 scan. Most prevalent thoracic imaging manifestations included lymphadenopathy (commonest), consolidation, nodules, air trapping, and bronchiectasis. Fungal infections showed necrotic conglomerate lymphadenopathy, cavitating nodules, and multilobar consolidation more frequently than bacterial infections (though not statistically significant). Abscesses and lymphadenopathy were the most common extrathoracic manifestations. CONCLUSION: In patients with CGD, multifocal or multilobar consolidation, mass-like consolidation, cavitating nodules, and conglomerate necrotic lymphadenopathy should alert the radiologist to a possible fungal cause.

Intranodal lipiodol injection for the treatment of chyle leak in children - a preliminary experience.

OBJECTIVE: To assess the effectiveness of intranodal lymphangiography using ethiodised oil (Lipiodol; Guerbet Japan, Tokyo, Japan) for the treatment of refractory cases of chylothorax and chylous ascites in the paediatric population. METHODS: Between 2016 and 2020, eight children having chyle leak resistant to conservative management underwent intranodal lymphangiography using lipiodol injection. After ethical approval by the Institutional Review Board, these patients' data were retrospectively analysed. Technical success was defined by opacification of inguinal and retroperitoneal lymphatics while injection on fluoroscopy. Clinical success was defined as progressively decreasing drain output and eventual cessation of output within a week after the procedure. Long-term follow up was done as feasible. RESULTS: Technical success was achieved in all the patients. Complete cessation of drain output was noted within 1 week of procedure in all patients indicating clinical success. One patient had recurrence of chylous leakage after an interval of 1 month and intranodal lymphangiography was repeated for that patient. The child had technical as well as clinical success after the repeat procedure. Hence a total of 9 procedures were performed in 8 patients. CONCLUSION: Intranodal lymphangiography may prove to be a valuable minimally invasive therapeutic tool in cases of refractory chylous leakage in paediatric patients with minimal risk of complications. ADVANCES IN KNOWLEDGE: Intranodal lymphangiography using lipiodol may prove to be a minimally invasive alternative in paediatric patients with refractory lymphatic leaks.

The Bethesda System for Reporting Thyroid Cytopathology: Validating at Tribhuvan University Teaching Hospital

Abstract Introduction Fine needle aspiration cytopathology (FNAC) is widely used for the stratification of thyroid nodules. Objective The objective of the present study is to validate FNAC reporting based on The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) at our institution and to calculate the risk of malignancy in each category. Methods This was a descriptive cross-sectional study conducted jointly at the Department of Ear, Nose and Throat and at the Department of Pathology for a period of 1.5 years (May 2018 to November 2018). All cases presenting with thyroid swelling in the outpatient department were investigated with ultrasonography (USG) of the neck, thyroid function test, and FNAC. All FNAC reporting was done according to TBSRTC. Results A total of 134 thyroidectomies were performed during the study period. The female to male ratio was 5.3:1. The age ranged from 11 to 74 years old. with a mean age of 51 years old. The FNAC has a specificity of 84.9%, a sensitivity of 89.4%, a positive predictive value of 86.4%, a negative predictive value of 88.2%, and an accuracy of 87.3% in detecting thyroid cancer. The implied risk of malignancy (ROM) in Bethesda II, III, IV, V and VI is 11.7%, 25%,40%,76.6% & 96%, respectively. Conclusion The four studied categories had a ROM comparable to other studies, except for the Bethesda III category. Further studies with larger sample sizes and with the use of USG guidance for the aspiration from the thyroid swelling may give better results by reducing the number of false negative and false positive cases.

The Bethesda System for Reporting Thyroid Cytopathology: Validating at Tribhuvan University Teaching Hospital.

Introduction Fine needle aspiration cytopathology (FNAC) is widely used for the stratification of thyroid nodules. Objective The objective of the present study is to validate FNAC reporting based on The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) at our institution and to calculate the risk of malignancy in each category. Methods This was a descriptive cross-sectional study conducted jointly at the Department of Ear, Nose and Throat and at the Department of Pathology for a period of 1.5 years (May 2018 to November 2018). All cases presenting with thyroid swelling in the outpatient department were investigated with ultrasonography (USG) of the neck, thyroid function test, and FNAC. All FNAC reporting was done according to TBSRTC. Results A total of 134 thyroidectomies were performed during the study period. The female to male ratio was 5.3:1. The age ranged from 11 to 74 years old. with a mean age of 51 years old. The FNAC has a specificity of 84.9%, a sensitivity of 89.4%, a positive predictive value of 86.4%, a negative predictive value of 88.2%, and an accuracy of 87.3% in detecting thyroid cancer. The implied risk of malignancy (ROM) in Bethesda II, III, IV, V and VI is 11.7%, 25%,40%,76.6% & 96%, respectively. Conclusion The four studied categories had a ROM comparable to other studies, except for the Bethesda III category. Further studies with larger sample sizes and with the use of USG guidance for the aspiration from the thyroid swelling may give better results by reducing the number of false negative and false positive cases.

Does secondhand smoke exposure increase the risk of acute respiratory infections among children aged 0-59 months in households that use clean cooking fuel? A cross-sectional study based on 601 509 households in India.

This study examines whether exposure to secondhand smoke (SHS) increases the risk of acute respiratory infections (ARI) among children aged 0-59 months. Study utilized nationally representative data from National Family Health Survey (2015-2016), which adopted two-stage stratified random sampling. Four mutually exclusive groups based on the type of cooking fuel usage and SHS exposure were created. Descriptive statistics and multivariate logistics regression analysis were applied. At the national level, 10.5% prevalence of ARI was reported during 2015-2016. About 47.9% (95%CI 47.7-48.2) of households was exposed to SHS and used solid biomass fuel for cooking. Nearly, 20.7% of households with clean fuel usage was exposed to SHS. Regression analysis suggests that the likelihood of ARI among children who were living in households with solid biomass fuel usage and exposed to SHS was 11% (95%CI 1.06-1.17) greater than children living in households with clean fuel usage with no SHS exposure. Moreover, our results further revealed that the odds of ARI among children living in households with clean fuel but exposed to SHS were 19% (95%CI 1.13-1.25) higher than the children living in the household with no SHS exposure and clean fuel use. Children living in households exposed to SHS are at higher risk of ARI.

QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea.

To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

Transcutaneous Mediastinal Ultrasonography for Lymphadenopathy in Children: A Pictorial Essay of Technique and Imaging Findings.

Ultrasonography (US) forms the mainstay of imaging in children; however, in the chest, its use has traditionally been limited to evaluation of pleural pathology. US techniques such as endobronchial and endoscopic ultrasound, which are commonly used for detection of mediastinal lymphadenopathy are invasive, aerosol generating, and often require sedation. Transcutaneous mediastinal sonography (TMUS) offers a useful alternative, which is easier to perform and overcomes these limitations. In this review, we summarize the technique, as well as imaging appearances of lymph nodes on TMUS. We also list common problems faced by operators and suggest troubleshooting methods for these.

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits.

KEY MESSAGE: Integrating genomics technologies and breeding methods to tweak core parameters of the breeder's equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers' fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder's equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder's equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.

Cryptococcus neoformans in a child with CSF rhinorrhoea: A cytopathological diagnosis.

Cryptococcosis is caused by Cryptococcus neoformans and is fatal in children. The fungus is known to enter respiratory tract by inhalation and localizes in lungs in immunocompetent host. Patients with immunocompromised state facilitate dissemination of disease. However, disseminated cases have been described in immunocompetent HIV-negative individuals. CSF rhinorrhoea as a predisposing cause of cryptococcal meningitis has been rarely reported. We hereby describe C. neoformans directly spreading to the meninges in 1 year child due to CSF rhinorrhoea and the fungus was detected on fluid cytology.

Mapping the triple burden of smoking, smokeless tobacco and alcohol consumption among adults in 28,521 communities across 640 districts of India: A sex-stratified multilevel cross-sectional study.

National estimates on tobacco and alcohol consumption are insufficient to guide policy at the sub-national level. This study assessed the sex-stratified prevalence of different types of smoking and smokeless tobacco and alcohol consumption among adults aged 15-49 using the National Family Health Survey (2015-16) at sub-national administrative units. Three-level logistic regression models were applied to quantify the variation at district- and community-level in smoking and consumption of smokeless tobacco and alcohol. A higher prevalence of smoking, smokeless tobacco and alcohol consumption was observed among men. The study found that the considerable unexplained variations in two different forms of tobacco and alcohol consumption among men attributed to between-population differences at district-level and community-level. The between-population differences were even larger at the district- and community-level in tobacco and alcohol consumption among women. Continious assessment of tobacco and alcohol consumption at lower administrative units and the development of evidence-based localised cessation interventions must be integrated with health policy to reduce disease burden and preventable deaths.