BER genes expression in oral and pre-oral cancer: Combinatorial approach to propose potential biomarker.

OBJECTIVE: DNA repair genes and their variants have been found to alter the risk of oral cancer. METHOD: The level of expression of XRCC3, NBS1, and OGG1 genes among 20 cases of oral cancer, 6 pre-oral cancer, and 50 healthy control subjects was measured with RT-PCR. All the subjects were also genotyped for XRCC3 rs861539 C>T, NBS1 rs1805794 C>G, and OGG1 rs1052133 C>G polymorphisms by the PCR-RFLP method; their genotypes were correlated with their level of expression. Further, a localized fold structure analysis of the mRNA sequence surrounding the studied SNPs was performed with RNAfold. RESULTS: Results showed increased expression of XRCC3, NBS1, and OGG1 transcripts among oral cancer (4.49 fold, 3.45 fold, and 3.27 fold) as well as pre-oral cancer (3.04 fold, 5.32 fold, and 1.74 fold) as compared to control subjects. The transcript level of OGG1 was found to be significantly increased (6.68 fold, p-value 0.009) with the GG genotype compared to the CC genotype. The C>T polymorphism of XRCC3 and the C>G polymorphism of OGG1 result in an apparent change in its mRNA secondary structure. Folding energy with the C allele for XRCC3 C>T polymorphism was lower than that of the T allele (MFE C vs T: -50.20 kcal/mol vs -48.70 kcal/mol). In the case of OGG1 C>G polymorphism MFE for the C allele was higher (-23.30 kcal/mole) than with the G allele (-24.80 kcal/mol). CONCLUSION: Our results showed elevated levels of XRCC3, NBS1, and OGG1 both in oral cancer and pre-oral cancer conditions, which indicates their role as prospective biomarkers of oral cancer and pre-cancerous lesions. SNPs in these genes alter their level of expression, possibly by altering the secondary structure of their transcript. However, due to the small sample size our study can only provide a suggestive conclusion and warned future study with large sample size to verify our findings.

Understanding the Landscape of Bronchoscopy in Lung Cancer: Insights From Lesion Location, Gender, and Diagnostic Efficacy.

INTRODUCTION: Lung cancer constitutes a critical global health concern. According to the International Agency for Research on Cancer's (IARC) GLOBOCAN 2020 estimates, lung cancer is the leading cause of death in cancer patients. In areas where tuberculosis is prevalent, misdiagnosis and mistreatment frequently result from overlap, creating significant difficulties that delay diagnosis and treatment. Amid this complication, bronchoscopic techniques emerge as critical diagnostic tools, though their efficacy varies between studies. METHOD: Our retrospective study, conducted from July 2021 to December 2022 at the Department of Respiratory Medicine, Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, examined 156 participants with malignancies. Our focus encompassed diverse lesions within the bronchial landscape, revealing intriguing findings. RESULTS: Bronchoscopic examinations unravelled prevalent abnormalities: 52 (33.3%) manifested as intraluminal growth, 48 (31.6%) as mucosal irregularities, and a less frequent (16, 10.3%) as an intraluminal bulge. Transbronchial needle aspiration stood out with a 10/11 (91%) positivity rate, biopsy came in second at 38/46 (83%), and bronchoalveolar lavage showed a 44/152 (29%) positivity rate. It was interesting to see how the lesions were spread out among the different types of histology. For example, squamous cell carcinoma showed 17/37 (46%) intraluminal growth, while adenocarcinoma showed 22/60 (36.7%) intraluminal growth and 4/60 (6.7%) intraluminal bulge. Moreover, a significant absence of abnormalities was observed in various lesions, underlining the intricacies of characterising bronchial lesions. CONCLUSION: Our study shows that direct tissue sampling is better and that new bronchoscopic technologies are important for diagnosing lesions that were hard to get to in the past. However, limitations in patient selection biases and the single-centre focus caution against generalised interpretations. Our research illuminates the pivotal role of bronchoscopic methods in diagnosing lung lesions, emphasising the necessity for continued advancements to enhance diagnostic accuracy and treatment efficacy in lung cancer subtypes.

iSCORE-PD: an isogenic stem cell collection to research Parkinson's Disease.

Parkinson's disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer the uniique potential to advance our understanding of PD etiology by providing disease-relevant cell-types carrying patient mutations along with isogenic control cells. To facilitate this experimental approach, we generated a collection of 55 cell lines genetically engineered to harbor mutations in genes associated with monogenic PD (SNCA A53T, SNCA A30P, PRKN Ex3del, PINK1 Q129X, DJ1/PARK7 Ex1-5del, LRRK2 G2019S, ATP13A2 FS, FBXO7 R498X/FS, DNAJC6 c.801 A>G+FS, SYNJ1 R258Q/FS, VPS13C A444P, VPS13C W395C, GBA1 IVS2+1). All mutations were generated in a fully characterized and sequenced female human embryonic stem cell (hESC) line (WIBR3; NIH approval number NIHhESC-10-0079) using CRISPR/Cas9 or prime editing-based approaches. We implemented rigorous quality controls, including high density genotyping to detect structural variants and confirm the genomic integrity of each cell line. This systematic approach ensures the high quality of our stem cell collection, highlights differences between conventional CRISPR/Cas9 and prime editing and provides a roadmap for how to generate gene-edited hPSCs collections at scale in an academic setting. We expect that our isogenic stem cell collection will become an accessible platform for the study of PD, which can be used by investigators to understand the molecular pathophysiology of PD in a human cellular setting.

A Giant Scrotal Neurofibroma in a Child Masquerading as Filariasis: Uncommon Presentation of a Common Disease.

Neurofibroma of the scrotum is a very uncommon benign neoplasm, specifically when it affects teenagers and is not associated with neurofibromatosis type I. To the best of our knowledge, only a couple of cases of neurofibroma in children have been documented. Here, we report a case study of a 17-year-old boy who had a giant scrotal lump for ten years masquerading clinically as filariasis. A provisional diagnosis of benign nerve sheath neoplasm was made based on cytology findings. The lump was surgically removed from the patient, and a histopathological and immunohistochemistry examination established the diagnosis of neurofibroma. The combined clinical, preoperative cytological, histological, and immunohistochemistry findings were not presented in the literature in any of the formerly documented cases of scrotal neurofibroma. The current case expands the spectrum of differential diagnoses for scrotal tumours that clinicians have previously observed.

Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells.

Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability and sensitize cancer cells to inhibition by the poly(ADP-ribose) polymerase (PARP). Here we show that human pluripotent stem cells (hPSCs) with one copy of BRCA2 deleted can be used to annotate variants of this gene and to test their sensitivities to PARP inhibition. By using Cas9 to edit the functional BRCA2 allele in the locally haploid hPSCs and in fibroblasts differentiated from them, we characterized essential regions in the gene to identify permissive and loss-of-function mutations. We also used Cas9 to directly test the function of individual amino acids, including amino acids encoded by clinical BRCA2 variants of uncertain significance, and identified alleles that are sensitive to PARP inhibitors used as a standard of care in BRCA2-deficient cancers. Locally haploid human pluripotent stem cells can facilitate detailed structure-function analyses of genes and the rapid functional evaluation of clinically observed mutations.

Ovarian aspergilloma in an immunocompetent patient masquerading as ovarian neoplasm.

Aspergillus is a ubiquitous fungus that can cause a variety of clinical syndromes. It can lead to a spectrum of clinical presentations depending upon the severity of the disease, degree of immune compromisation, nature and intensity of inflammatory host response. Ovarian aspergilloma is extremely unusual, only a few case reports have been described in the literature. Here, we report a case of ovarian aspergilloma which was masquerading as ovarian neoplasm on clinical examination and radiology. To the best of our knowledge, this is the first case report of isolated ovarian aspergillosis in an immunocompetent patient.

Comparison of LED-Based Transillumination Device with Traditional Vein Viewing Methods for Difficult Intravenous Cannulation in Indian Children: A Nonrandomized Controlled Trial.

OBJECTIVES: To compare the utility of transillumination device with traditional vein viewing in situations with difficult peripheral venous access in pediatric patients. METHODS: This was a nonrandomized, controlled trial. All the children aged between 3 to 36 mo admitted in tertiary care referral hospital, who satisfied difficult intravenous access (DIVA) score of equal to or more than 4 were included in the study. The children were assigned to transillumination device group (intervention) and traditional vein viewing group (traditional). The proportion of successful cannulation in the first attempt and median number attempts required to successfully cannulate in each group were estimated. RESULTS: A total of 509 children were included in the study. The proportion of single attempt cannulation was significantly higher in the intervention group as compared to traditional group (p value = 0.001). The median number of attempts to successfully cannulate was found to be significantly less in the interventional group (median 1 vs. 2; p value = 0.001). On bivariate analysis, use of transillumination device was found to have a 2.64 times higher likelihood to successfully cannulate in the first attempt. CONCLUSION: The use of transillumination device significantly improves the first attempt success rate and number of attempts for successful cannulation.

Highly efficient generation of isogenic pluripotent stem cell models using prime editing.

The recent development of prime editing (PE) genome engineering technologies has the potential to significantly simplify the generation of human pluripotent stem cell (hPSC)-based disease models. PE is a multicomponent editing system that uses a Cas9-nickase fused to a reverse transcriptase (nCas9-RT) and an extended PE guide RNA (pegRNA). Once reverse transcribed, the pegRNA extension functions as a repair template to introduce precise designer mutations at the target site. Here, we systematically compared the editing efficiencies of PE to conventional gene editing methods in hPSCs. This analysis revealed that PE is overall more efficient and precise than homology-directed repair of site-specific nuclease-induced double-strand breaks. Specifically, PE is more effective in generating heterozygous editing events to create autosomal dominant disease-associated mutations. By stably integrating the nCas9-RT into hPSCs we achieved editing efficiencies equal to those reported for cancer cells, suggesting that the expression of the PE components, rather than cell-intrinsic features, limit PE in hPSCs. To improve the efficiency of PE in hPSCs, we optimized the delivery modalities for the PE components. Delivery of the nCas9-RT as mRNA combined with synthetically generated, chemically-modified pegRNAs and nicking guide RNAs improved editing efficiencies up to 13-fold compared with transfecting the PE components as plasmids or ribonucleoprotein particles. Finally, we demonstrated that this mRNA-based delivery approach can be used repeatedly to yield editing efficiencies exceeding 60% and to correct or introduce familial mutations causing Parkinson's disease in hPSCs.

From muscles to nerves, our body is formed of many kinds of cells which can each respond slightly differently to the same harmful genetic changes. Understanding the exact relationship between mutations and cell-type specific function is essential to better grasp how conditions such as Parkinson's disease or amyotrophic lateral sclerosis progress and can be treated. Stem cells could be an important tool in that effort, as they can be directed to mature into many cell types in the laboratory. Yet it remains difficult to precisely introduce disease-relevant mutations in these cells. To remove this obstacle, Li et al. focused on prime editing, a cutting-edge 'search and replace' approach which can introduce new genetic information into a specific DNA sequence. However, it was unclear whether this technique could be used to efficiently create stem cell models of human diseases. A first set of experiments showed that prime editing is superior to conventional approaches when generating mutated genes in stem cells. Li et al. then further improved the efficiency and precision of the method by tweaking how prime editing components are delivered into the cells. The refined approach could be harnessed to quickly generate large numbers of stem cells carrying mutations associated with Parkinson's disease; crucially, prime editing could then also be used to revert a mutated gene back to its healthy form. The improved prime editing approach developed by Li et al. removes a major hurdle for scientists hoping to use stem cells to study genetic diseases. This could potentially help to unlock progress in how we understand and ultimately treat these conditions.

16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development.

Microdeletions and microduplications of the 16p11.2 chromosomal locus are associated with syndromic neurodevelopmental disorders and reciprocal physiological conditions such as macro/microcephaly and high/low body mass index. To facilitate cellular and molecular investigations into these phenotypes, 65 clones of human induced pluripotent stem cells (hiPSCs) were generated from 13 individuals with 16p11.2 copy number variations (CNVs). To ensure these cell lines were suitable for downstream mechanistic investigations, a customizable bioinformatic strategy for the detection of random integration and expression of reprogramming vectors was developed and leveraged towards identifying a subset of 'footprint'-free hiPSC clones. Transcriptomic profiling of cortical neural progenitor cells derived from these hiPSCs identified alterations in gene expression patterns which precede morphological abnormalities reported at later neurodevelopmental stages. Interpreting clinical information-available with the cell lines by request from the Simons Foundation Autism Research Initiative-with this transcriptional data revealed disruptions in gene programs related to both nervous system function and cellular metabolism. As demonstrated by these analyses, this publicly available resource has the potential to serve as a powerful medium for probing the etiology of developmental disorders associated with 16p11.2 CNVs.

Dataset on the electrical energy consumption and its conservation in the cement manufacturing industry.

The cement industry consumes huge amount of electrical energy than the other sectors. The higher percentage of the energy cost was found in its total cost of production. The available resources and environmental constraints are becoming increasingly severe because of the continuous development in the economy of the country. Therefore, the energy-saving and the reduction in the emission of gases in the cement industries have become one of the choices for the process development. The concept of energy-saving determines the realization of the national goals of energy conservation. Taking the reference of one of the cement industry in India (Emami Cement Ltd, Baloda Bazaar, Chhattisgarh) as the main focus, this paper investigates on the energy-saving by implementing the variable speed drives (VSD) along with the cooling fan and motor across the system. This report also analyses the energy-saving potential of the cement manufacturing industry by assuming some different scenarios. The data analysis show that the electrical energy-saving potential of the cement industry is 53.5% with VSD and 51.89% with the use of light-emitting diode (LED) instead of using metal halide (MH) ultraviolet source. Thus, the improvement in energy efficiency can reduce the emission of the carbon dioxide from fuel, use of electrical energy and consequently it has the potential of reducing the cost of the cement production unit.

Role of environmental factors & oxidative stress with respect to in vitro fertilization outcome.

Background & objectives: Oxidative stress, lifestyle factors as also exposure to certain environmental factors are known to affect the fertility status in human beings. The aim of this study was to evaluate the role of OS and lifestyle and environmental factors affecting IVF outcome. Methods: A total of 253 couples were included, and biological samples such as blood, follicular fluid (FF), cumulus cells and semen were collected. Relevant biochemical parameters and metals namely lead (Pb), cadmium (Cd), copper (Cu) and zinc (Zn) were determined in the biological samples. ß-human chorionic gonadotropin levels ≥100 IU/l were considered to predict viable pregnancy on the 15th day of embryo transfer (ET). Results: The mean body mass index (BMI) was significantly lower in females with positive IVF outcome compared to those with negative outcome. Couples residing in the residential area showed more percentage of positive IVF outcomes as compared to couples residing in industrial/agricultural area. FF Zn level was significantly higher (P<0.001) among the females' participants who have undergone ET as compared to those who have not undergone ET. FF MDA and serum Cu levels were significantly higher (P<0.05) in the female participants with negative IVF outcome as compared to positive IVF outcome. Logistic regression revealed that maternal BMI (P=0.034) and FF MDA level (P=0.047) were significantly associated with the IVF outcome. Interpretation & conclusions: The success rate of IVF was about 31.8 per cent, and BMI was significantly lower in females with positive outcome. The higher levels of MDA in FF and SP might have a negative impact on IVF outcome, higher Zn level in SP, FF and serum might have a positive role in embryo transfer as well as IVF outcome. The role of stress management and nutrition supplementation during the IVF treatment may be explored.

Dynamical properties of EMIM-SCN confined in a SiO2 matrix by means of 1H NMR relaxometry.

1H nuclear magnetic resonance relaxometry is applied to investigate the translational and rotational dynamics of ionogels composed of an ionic liquid (IL): 1-ethyl-3-methyl-imidazolium-thiocyanate (EMIM-SCN) confined in a nanoporous SiO2 matrix. The relaxation studies were performed in the frequency range of 4 kHz-40 MHz and the temperature range of 223-248 K for different concentrations of the IL; the ratio (no. of moles of IL/no. of moles of SiO2) yields: 1/2, 3/5 and 7/10. A thorough analysis of this large set of experimental data was performed assuming the existence of two fractions of the liquid: a core fraction (near the pore center) and a surface fraction (near the confining walls). It was shown for all concentrations that the confinement does not significantly affect the translational motion near the pore center compared to the dynamics in bulk. The diffusion coefficients in the surface fraction are considerably smaller compared to the core fraction (from one to two orders of magnitude) and the difference becomes larger with increasing temperature. The diffusion coefficients become smaller for higher concentrations - this effect is not large, but visible. Very importantly, it was shown that, despite the interactions with the surface, the diffusion in the surface fraction remains of 3D character. As far as rotational dynamics in the surface fraction is concerned, it slows down compared to the bulk (and the core fraction), but this effect is of the order of factor 2-3.

A study of lip prints and its reliability as a forensic tool.

INTRODUCTION: Lip prints, like fingerprints, are unique to an individual and can be easily recorded. Therefore, we compared direct and indirect lip print patterns in males and females of different age groups, studied the inter- and intraobserver bias in recording the data, and observed any changes in the lip print patterns over a period of time, thereby, assessing the reliability of lip prints as a forensic tool. MATERIALS AND METHODS: Fifty females and 50 males in the age group of 15 to 35 years were selected for the study. Lips with any deformity or scars were not included. Lip prints were registered by direct and indirect methods and transferred to a preformed registration sheet. Direct method of lip print registration was repeated after a six-month interval. All the recorded data were analyzed statistically. RESULTS: The predominant patterns were vertical and branched. More females showed the branched pattern and males revealed an equal prevalence of vertical and reticular patterns. There was an interobserver agreement, which was 95%, and there was no change in the lip prints over time. Indirect registration of lip prints correlated with direct method prints. CONCLUSION: Lip prints can be used as a reliable forensic tool, considering the consistency of lip prints over time and the accurate correlation of indirect prints to direct prints.

Assessment of estrogenic potential of di-n-butyl phthalate and butyl benzyl phthalate in vivo.

Phthalate compounds are widely used industrial chemicals; when incorporated into polyvinyl chloride, they are not covalently bound and released into the surrounding media. Some of them have estrogenic potential in vitro but data on in vivo studies are scanty. For the 3-day uterotrophic assay, di-n-butyl phthalate (DBP;10 and 100 mg/kg), butyl benzyl phthalate (BBP; 20 and 200 mg/kg), and diethylstilbestrol (DES, 40 µg/kg, positive control) were administered orally to immature female rats for three consecutive days from postnatal day (PND) 21. For the 20-day pubertal onset assay, DBP (10 and 20 mg/kg), BBP (20 and 200 mg/kg), and DES (6 µg/kg) were administered orally from PND 21 daily for 20 days. In the uterotrophic assay, in groups treated with higher dose of DBP and BBP, the uterine wet weight significantly decreased in the higher dose, and there were minor variations in the ovary wet weight, while the wet weight of these organs increased significantly in DES-treated group. In the 20-day pubertal assay, the weight of uterus and ovary declined significantly and changes in vaginal weight were nonsignificant in DBP- and BBP-treated groups. However, in DES-treated group nonsignificant elevation in vagina weight was observed. All the DES-treated animals showed the vaginal opening (VO) on day 26.17 ± 0.16. However, VO was not observed in any of the animals in control, vehicle control, BBP-, and DBP-treated groups up to PND 42, except in one animal each in vehicle control and DBP (100 mg/kg)-treated groups. The data indicated that both DBP and BBP were unable to induce elevation in the uterine and ovarian weight. While DES treatment can accelerate the growth of uterus and ovary and alter the onset of puberty and estrous cyclicity in prepubertal rats. These suggest that these compounds may not have estrogenic potential in vivo.

Assessment of genetic damage among chewers of mixture containing mainly areca nut and tobacco.

UNLABELLED: Chewing mixture containing areca nut and tobacco is believed to be associated with oral cancer. Habit of chewing such mixture is prevalent among South Asian countries. This study aimed to evaluate the genotoxic effect of areca nut and tobacco on human lymphocytes. Peripheral blood from 107 subjects (nonchewers, 48; chewers, 59, including 20 subjects with oral submucous fibrosis [OSMF]) analyzed by cytokinesis-block micronucleus (CBMN) and alkaline comet assay. Nuclear anomalies, namely, binucleated cells with micronuclei (BN MN), total MN, nucleoplasmic bridge, and nuclear buds were higher in chewers whereas elevation in BN MN and total MN were significant among subjects with OSMF than nonchewers. DNA damage assessed by comet assay showed increased percentage of Tail DNA, Tail moment, and Olive tail moment among chewers as well as OSMF subjects. Significant positive correlation was observed between induction of CBMN and consumption of quids per day (r = .280, P = .033). RESULTS: suggested cytotoxic and genotoxic potential of mixture containing areca nut and tobacco.

Association between sperm quality, oxidative stress, and seminal antioxidant activity.

OBJECTIVES: To determine seminal antioxidant capacity, oxidative stress markers, and their association with semen quality as oxidative stress is considered to be a major etiological factor in male infertility. SUBJECTS AND METHODS: Semen samples were obtained from 138 men and categorized on the basis of sperm count, motility, and morphology. Seminal oxidative and antioxidant markers are as follows: lipid peroxidation (LPO), protein carbonyls (PC), superoxide dismutase (SOD), catalase (CAT), thiols, and ascorbic acid were determined. RESULTS: Sperm count significantly correlated positively with progressive sperm motility and normal morphology. Sperm count and normal morphology showed significant negative correlation with LPO and PC. Sperm count and progressive motility showed significant positive relationship with SOD. The SOD, CAT, and thiols positively whereas LPO and PC negatively associated with elevated sperm count. CONCLUSION: Insufficient antioxidant enzymes and increased oxidative stress may attribute to the risk of declining semen quality and hence protective role for antioxidant enzymes against the oxidative damage cannot be ruled out.

Toxicity assessment of dye containing industrial effluents by acute toxicity test using Daphnia magna.

Toxicity of dye containing effluent of tannery, textile, dyes and pulp-paper industries was evaluated in an acute toxicity test using Daphnia magna. The 48-hour EC(50) values were 4.33% and 19.5% for tannery effluents (Tn1 and Tn2). Textile effluents (Tx1-Tx7) had 48-hour EC(50) values; >100%, >100%, 62.9%, 63.0%, 40.3%, >100% and >100%, respectively. Dye industries (D1-D7) had 48-hour EC(50) values; 14.1%, 15.5%, 24.5%, 29.7%, 23.2%, >100% and >100%, respectively. Similarly pulp-paper effluents (P1-P5) showed acute toxicity as 100%, 77.87%, 46.44%, 69.55% and 82.84%, respectively. These results showed linear relationship with high degree of confidence (r(2) ≥ 0.84-0.99) between immobility and test concentrations. Toxicity classification criteria showed that out of five effluents from pulp-paper mill, four were minor acutely toxic having 48-hour EC(50) value in between >46%-100%. Out of seven textile effluents, four were not acutely toxic (48-hour EC(50) value >100%) and three were minor acutely toxic (48-hour EC( 50) value in the range of 40.3%-63.0%). Similarly, out of seven dye industrial effluents, two were not acutely toxic and five minor acutely toxic. One of the two tanneries was moderately acutely toxic and another one was minor acutely toxic. Classification based on toxic unit revealed that four out of five pulp-paper effluent, three out of seven textile effluents, five out of seven dye effluents and both the tannery effluents were toxic. Overall, 66.67% effluents were found toxic and 33.33% as non-toxic. In general, tannery and dyes effluents showed more toxicity than textile and paper mill effluents.