Analysis of SARS-CoV-2 genome evolutionary patterns.

The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.

A rare case of peritoneal metastases from oropharyngeal squamous cell carcinoma in a young male after completion of chemoradiotherapy.

ABSTRACT: Distant metastases are frequent in head and neck squamous cell carcinomas (HNSCC), but they are limited to some organs like lungs, bone, mediastinum, liver and brain. Peritoneal metastases (PMs) from HNSCC are extremely rare. A 28-year-old chronic smoker and alcoholic was diagnosed with squamous cell carcinoma of oropharynx. Patient was admitted and was given six cycles of concurrent chemo and radiotherapy (CCRT) and was discharged. Two months later, he presented with abdominal pain and lump. Contrast-enhanced CT revealed ascites, peritoneal implants and subcutaneous deposit which were proved to be metastases by histopathology. The present case is the seventh reported case of PM from HNSCC. • Patients of HNSCC shall be screened for distant metastases. • Differential diagnosis of HNSCC needs consideration when encountered with peritoneal metastases. • Research is required to understand the basis of PM in HNSCC while on CCRT to suggest management modifications.

Changes in the Status of Spastic Diplegic Children in Terms of Gross Motor Function Classification System and Functional Mobility Scale Following Surgical Intervention: A Single Centre Experience.

Introduction Most centers in low- to mid-income countries (LMICs) lack facilities for a comprehensive instrumented gait analysis (IGA) which is often considered the preferred method for assessment of the functional results of surgery in children with spastic diplegia. We aimed to study if there were any changes in the Gross Motor Function Classification System (GMFCS) levels and Functional Mobility Scale (FMS) scores after surgery and whether they can be used as an indirect indicator of change in the functional status of a child. Methods This prospective study was conducted at the Pediatric Orthopedic unit of a teaching hospital on spastic diplegic children requiring surgical intervention. GMFCS levels and FMS scores were recorded before the surgery and at each follow-up visit, with the latest record being two years post-surgery. The change in the scores was indicated as an improvement, deterioration, or no change from the baseline and compared to the score of the preceding visit. In addition, it was examined whether the age at surgery had any effect on the temporal change in the scores. Results A total of 25 children were included for analysis after excluding those who failed to fulfill the predefined inclusion and exclusion criteria. Both the GMFCS levels and FMS scores improved from the third month to one-year post-surgery, after which a few patients had a worsening of their scores at the two years follow-up visit. The age at which surgery was performed had no significant effect on the pattern of change in the scores. Most children sought consultations with the physical therapy department only when they visited the surgical team for follow-up. Conclusion This study shows that surgical interventions do improve the functional outcomes in children with spastic CP when assessed using FMS scores while maintaining an undeteriorated GMFCS level in most children. While a peak improvement can be expected one year after surgery in most patients, possible of worsening from baseline scores do exist, and the parents must be informed of the same. Any decision for surgery must involve the parents, and the usefulness of postoperative physical therapy must be impressed upon them before the surgery and during each follow-up visit too.

Knowledge of handling medical emergencies among general dental practitioners pan India: a cross-sectional survery.

BACKGROUND: Medical emergency situations in dental clinics have been contemplated to be an issue in most of the countries by reason of dentist's lack of knowledge and preparedness to attend emergency situations in dental offices. The aim of this paper is to observe the knowledge, attitude, and perceived confidence of the general dental practitioners regarding emergency medical care and its practical application. Questionnaire on knowledge assessment was circulated among 500 dentists using printed questionnaire formats and various social media platforms. The questionnaire included details on treating hypertensive patients, cardiopulmonary resuscitation training, accessibility of medical emergency equipments in the dental clinics, prevalence of medical emergency cases in the dental office and the self-assessed competence to handle medical emergency situations in the dental clinics. Data was surveyed and scrutinized using the Statistical Package for Social Sciences (SPSS), version 17 (SPSS Inc., Chicago IL). Descriptive statistics was tabulated and Chi square tests was applied. FINDINGS: 500 general dental practitioners pan India were involved in the study (294 were females and 207 were males). They were grouped into different age groups (20-30 yrs, 30-40 yrs, 40-50 yrs, 50 and above) and experience (0-5 yrs, 5-10 yrs and more than 10 years). 279 participants did not attend any medical emergency training whereas, 222 participants from all groups attended training program. It was observed that with increased experience in the field, the knowledge, awareness and confidence to treat medical emergency situation in the dental clinics was better. Dentists should update themselves from time-to-time with the latest technologies in the field and need to attend training programs to handle any medical emergency situations in the dental offices. Medical emergencies in a dental clinic can be encountered at any point of time and the clinician should have apt knowledge in handling such situations. Majority of the dentists feel subdued in managing medical situations in dental offices. Training and workshops for handling medical situations in the dental offices should be mandated at the undergraduate and postgraduate levels. This will help the dentist to shape one's confidence in managing such situations without apprehension. Availability of proper infrastructure and equipments is recommended in every dental clinics so as to ease the handling of the situation. CONCLUSION: This paper enlightens the need of basic life support training on regular basis among the dentists to improve the competence among them and to improve the confidence in handling such situations.

Challenges and Opportunities of Metal Chelation Therapy in Trace Metals Overload-Induced Alzheimer's Disease.

Essential trace metals like zinc (Zn), iron (Fe), and copper (Cu) play an important physiological role in the metabolomics and healthy functioning of body organs, including the brain. However, abnormal accumulation of trace metals in the brain and dyshomeostasis in the different regions of the brain have emerged as contributing factors in neuronal degeneration, Aß aggregation, and Tau formation. The link between these essential trace metal ions and the risk of AD has been widely studied, although the conclusions have been ambiguous. Despite the absence of evidence for any clinical benefit, therapeutic chelation is still hypothesized to be a therapeutic option for AD. Furthermore, the parameters like bioavailability, ability to cross the BBB, and chelation specificity must be taken into consideration while selecting a suitable chelation therapy. The data in this review summarizes that the primary intervention in AD is brain metal homeostasis along with brain metal scavenging. This review evaluates the impact of different trace metals (Cu, Zn, Fe) on normal brain functioning and their association with neurodegeneration in AD. Also, it investigates the therapeutic potential of metal chelators in the management of AD. An extensive literature search was carried out on the "Web of Science, PubMed, Science Direct, and Google Scholar" to investigate the effect of trace elements in neurological impairment and the role of metal chelators in AD. In addition, the current review highlights the advantages and limitations of chelation therapies and the difficulties involved in developing selective metal chelation therapy in AD patients.

COVID Associated Invasive Aspergillosis.

To study the possible association between invasive fungal sinusitis (aspergillosis) and coronavirus disease. An observational study was conducted at a tertiary care centre over 6 months, involving all patients with aspergillosis of the paranasal sinuses suffering from or having a history of COVID-19 infection. 92 patients presented with aspergillosis, all had an association with COVID-19 disease. Maxillary sinus (100%) was the most common sinus affected. Intraorbital extension was seen in 34 cases, while intracranial extension was seen in 5 cases. Diabetes mellitus was present in 75 of 92 cases. All had a history of steroid use during their coronavirus treatment. New manifestations of COVID-19 are appearing over time. The association between coronavirus and aspergillosis of the paranasal sinuses must be given serious consideration. Uncontrolled diabetes and overzealous use of steroids are two main factors aggravating the illness, and both of these must be properly checked.

Fibronectin containing alternatively spliced extra domain A interacts at the central and c-terminal domain of Toll-like receptor-4.

Extra domain A of cellular fibronectin (FN-EDA) is known to cause insulin resistance, atherosclerosis, tissue fibrosis, ischemic stroke and exaggerated myocardial reperfusion injury through Toll-like receptor 4 (TLR4). However, the FN-EDA-TLR4 interacting site is not well established. Therefore, in-silico approaches have been used to study FN-EDA and TLR4 interactions at the interface. In the present study, molecular docking studies of FN-EDA with TLR4-myeloid differentiation factor 2 (MD2) heterodimer have been performed to unravel the FN-EDA-TLR4 interacting sequence. Furthermore, the modulatory role of FN-EDA adjacent domains FNIII(11) and FNIII(12) on its interaction with TLR4-MD2 was investigated. The results show that FN-EDA interacting sequence "SPEDGIRELF" selectively interacts with TLR4 directly near its central and C-terminal domain region. The regulatory domains, FN type III 11 facilitate and 12 impede the FN-EDA-TLR4 interaction. Furthermore, the molecular dynamic simulation studies confirmed that FN-EDA forms a stable complex with TLR4-MD2 heterodimer. In conclusion, FN-EDA interacts and forms a stable complex through its "SPEDGIRELF" sequence at the central and C-terminal domain region of TLR4. The revelation of FN-EDA and TLR4 interacting sites may help design novel therapeutics for drug discovery research.

Baicalein: promising therapeutic applications with special reference to published patents.

Baicalein is a medicinally important flavonoid present in Scutellaria baicalensis, which has numerous biological benefits like anti-oxidant, anti-inflammatory, antihepatotoxicity, anticancer properties, etc. Recent studies have revealed that baicalein is an efficient antihepatoma agent and has the strongest antiproliferative effect toward cancerous bladder cell lines, and suppression of cell cycle progression in prostate cancer cells. This natural substance has a high commercial value because it strengthens the heart and cerebral vessels and protects the nervous system and also reduces diabetes and diabetic complications. In addition, baicalein is known to decrease inflammatory markers such as IL-1ß, IL-6 and TNF-α. In this review, we have attempted to compile the list of recent therapeutic patents of baicalein used for treating different disorders.

Cochlear Implantation in Goldenhar Syndrome.

Goldenhar syndrome is a rare genetic condition characterized by hemifacial microsomia, mandibular hypoplasia, auricular malformations, and epibulbar dermoids. The syndrome has both sporadic and familial occurrence. Incidence of congenital hearing loss in these patients is 1:1000 in children with a male to female ratio of 3:2. In our case study we report a case of Goldenhar Syndrome who underwent cochlear implantation. The patient had right side microtia, right hemifacial microsomia and right side torticollis, pterygium in her right eye, right hypoplastic thumb and unilateral right side kidney. Radiologically, there was narrow duplicated internal auditory canal on right side with absent right cochlear nerve with normal anatomy on left side and the left side showed malformed facial nerve at tympani segment and second genu. Therefore, the patient was planned for left side cochlear implantation. Intraoperatively, there were malformed ossicles with anomalous facial nerve covering whole of oval window and partially the round window. Thus, a separate cochleostomy was done. Impedance was < 5 Hertz in all electrodes and electrically evoked action potential (ECAP) thresholds were obtained on all electrodes.

Assessment of Accuracy of Fine Needle Aspiration Cytology and Ultrasonography in Relation to Histopathology in Cases of Solitary Thyroid Nodule.

The thyroid gland is an endocrine gland situated in the lower part of front and the sides of the neck. Thyroid nodules are very common with estimated prevalence that ranges from 4% by palpation to 67% by Ultrasonography. The main purpose of our study was to detect cases of thyroid carcinoma preoperatively in patients with solitary thyroid nodules and subsequently advise surgery in these selected patients only, without missing any malignancy. The goal of the investigating modalities used was that they should detect maximum (ideally all) cases of carcinoma and minimize the number of patients who might end up with unnecessary surgery. The present study was to be undertaken for assessment of accuracy of FNAC & USG in relation to Histopathology in cases of solitary thyroid nodule (accuracy in terms of sensitivity, specificity, positive predictive value, negative predictive value). In our series of total 102 pateints, 90 patients were females (88.2%) and 12 cases were males (11.8%). The overall incidence of malignancy in solitary thyroid nodules is 15.68%. In our series the sensitivity and specificity of Fine needle aspiration cytology and Ultrasonography was 81.25% & 98.84% and 75% and 77.91% respectively. The closest method to ideal was fine needle aspiration cytology. However, a combination of techniques, rather than a single technique, give optimum results & avoid unnecessary surgery in a greater number of patients without missing any malignancy.

Diagnostic Efficacy of Thyrotropin to Thyroglobulin Ratio in Correlation with Histopathology of Euthyroid Patient Having Solitary Thyroid Nodule.

In patients with solitary thyroid nodules, the first course of action is to determine whether the nodule is benign or malignant. Many investigations are used to differentiate between benign and malignant nodules so as to avoid surgery in those who don't need it. Among these, FNAC and USG are commonly used in association with clinical features but there are drawbacks of each technique. The present study was undertaken to assess the diagnostic effectivity of thyrotropin (also known as TSH) to thyroglobulin ratio in correlation with histopathology in euthyroid patients having solitary thyroid nodule. This is a prospective study carried out on 48 euthyroid cases of solitary thyroid nodule. All patients subjected to FNAC, USG, thyrotropin and thyroglobulin assay. Then, they underwent surgery and histopathological examination (HPE) of the specimens done. Finally, the histopathology reports were correlated with the thyrotropin to thyroglobulin ratio in order to evaluate their sensitivity and specificity by statistical methods. The sensitivity and specificity of thyrotropin to thyroglobulin ratio was 100% and 100% respectively. All malignant lesions according to thyrotropin to thyroglobulin ratio were confirmed by histopathology indicating its excellence. Therefore, TSH to thyroglobulin ratio helps in planning the correct management and avoids second surgery. It was found that serum TSH:Tg is a safe, reliable and effective diagnostic modality with a high sensitivity and specificity and is the single best investigation for preoperative evaluation of solitary thyroid nodule to differentiate between benign and malignant nodules.

Molecular Mechanisms of Oncogenesis through the Lens of Nucleosomes and Histones.

At the cellular level, cancer is the disease of both the genome and the epigenome, and the interplay between genetic mutations and epigenetic states may occur at the level of elementary chromatin units, the nucleosomes. They are formed by a segment of DNA wrapped around an octamer of histone proteins. In this review, we survey various mechanisms of cancer etiology and progression mediated by histones and nucleosomes. In particular, we discuss the effects of mutations in histones, changes in their expression and slicing on epigenetic dysregulation and carcinogenesis. The links between cancer phenotypes and differential expression of histone variants and isoforms are summarized. Finally, we discourse the geometric and steric effects of DNA compaction in nucleosomes on DNA mutation rate, interactions with transcription factors, including pioneer transcription factors, and prospects of cancer cells' genome and epigenome editing.

Cochlear Implantation in Pierre Robin Syndrome.

Hereditary hearing loss accounts for nearly 60% of deafness in developed countries and about 30% of them are syndromic. Pierre Robin Syndrome is one such condition. The patient with this syndrome usually presnts with triad of micrognathia, glossoptosis and cleft palate. Hearing loss is mostly conductive but there can be sensorineural hearing loss also. Here we present a case of Pierre Robin Syndrome who presented with congenital hearing loss. He also had bilateral serous otitis media. He underwent cochlear implant surgery and was prescribed antihistaminics and steroid spray for middle ear effusion. Therefore, proper clinical evaluation is required.

Conformational dynamics of Ribonuclease Sa and its S48P mutant: Implications for the stability of the mutant protein.

The optimization of ß-turns has been used as a strategy to increase protein thermal stability. One example is the S48P mutation in Ribonuclease Sa, introduced to optimize a ß-turn, which increases the stability of the protein as determined experimentally. Here, we have studied 48SYGY51 ß-turn and its S48P mutant from RNase Sa, as a peptide and as part of the protein, using molecular dynamics simulations. The turn propensity of the region 48SYGY51 shows an increase in both the peptide and protein models on S48P mutation. The mutant protein shows an overall decrease in conformational dynamics and a decrease in conformational heterogeneity as compared to the wildtype protein. A comparatively restricted sampling of the φ-ψ region of GLN47, a pre PRO48 residue, in the mutant protein and some local changes in hydrogen bonding patterns involving residues 20-24 might be contributing to the mutant protein stability. In addition, some long-range hydrogen bonding interactions involving the 60s loop and the salt-bridge interaction involving ASP17-ARG63 could also be contributing to the increase in rigidity and stability of the mutant protein.

To Study the Association of the Size and Site of Tympanic Membrane Perforation with the Degree of Hearing Loss.

Chronic suppurative otitis media is a serious health problem worldwide. It has been a general view that the hearing loss increases with the size of the perforation, more so if it is in the postero- inferior quadrant. The present study is an effort to test the validity of above concepts. With Institutional ethical committee clearance, an observational study was carried at SMS medical college, Jaipur. A total of 90 cases were studied. All cases between the age group 15-50 years with dry tympanic membrane perforations were divided into 3 groups Group I (0-9 mm²), Group II (9-30 mm²), Group III (>30 mm²) with 30 in each group based on size of perforation. Hearing loss was calculated as average of hearing loss at 500, 1000, 2000 Hz. Similarly the site of perforation was grouped as perforation involving anterior quadrant, posterior quadrant and multiple quadrant as Group A, Group B, Group C respectively. At the end of study, data was compiled systematically and analyzed using Post Hoc test. The age group ranges between 15 and 50 years with mean age of 25.6 years. Hearing loss was found to be directly proportional to the size of perforation in our study. (p = 0.000, highly significant). We also observed that hearing loss was more in posterior and multiple perforations than in anterior perforations. (p = 0.000, highly significant). Overall this study has shown significant correlation between the size and the site of the perforation to the degree of hearing loss.

Hematopathological alterations of major tumor suppressor cascade, vital cell cycle inhibitors and hematopoietic niche components in experimental myelodysplasia.

Myelodysplastic syndrome (MDS) is a poorly understood dreadful hematopoietic disorder that involves maturational defect and abnormalities in blood cell production leading to dysplastic changes and peripheral blood pancytopenia. The present work aims in establishing the mechanistic relationship of the expressional alterations of major tumor suppressor cascade, vital cell cycle inhibitors and hematopoietic microenvironmental components with the disease pathophysiologies. The study involves the development of N-N' Ethylnitrosourea (ENU) induced mouse model of MDS, characterization of the disease with blood film and bone marrow smear studies, scanning electron microscopic observation, mitochondrial membrane potential determination, flowcytometric analysis of osteoblastic and vascular niche components along with the expressional study of cleaved caspase-3, PCNA, Chk-2, p53, Ndn, Gfi-1, Tie-2, Sdf-1, Gsk-3ß, p18 and Myt-1 in the bone marrow compartment. Dysplastic features were found in peripheral blood of MDS mice which seemed to be the consequence of three marrow pathophysiological conditions viz; aberrant rise of cellular proliferation, increased apoptosis and crowding of abnormal blast population. Expressional decline of the p53 cascade involving Chk-2, p53, Ndn, Gfi-1 along with the downregulation of major cell cycle inhibitors seemed to be associated with the hyper-proliferative nature of bone marrow cells during MDS. Moreover the disruption of osteoblastic niche components added to the decreased hematopoietic quiescency. Increased marrow vascular niche components signified the pre-malignant state of MDS. Elevated cellular apoptosis and rise in the blast burden were also found to be associated with the p53 expression dependent collapsing of mitochondrial membrane potential and upregulation of Tie-2 respectively. The study established the mechanistic correlation between the alterations of the mentioned signaling components and hematopoietic anomalies during MDS which may be beneficial for the development of therapeutic strategies for the disease.

Impact of Turn Propensity on the Folding Rates of Z34C Protein: Implications for the Folding of Helix-Turn-Helix Motif.

The rate-limiting step for the folding of the helix-turn-helix (HTH) protein, Z34C, involves ß-turn region 20DPNL23. This reverse turn has been observed to be part of the transition state in the folding process for Z34C, influencing its folding rates. Molecular dynamics simulations were performed on this turn peptide and its two mutants, D20A and P21A, to study turn formation using GROMOS54A7 force field. We find that this region has a turn propensity of its own, and the highest turn propensity is observed for the wild-type, which correlates well with available experimental results. We also find that a slight unfavorable change in ΔG turn folding causes a drastic change in the folding rates of HTH motif and a mechanistic interpretation is given. Implications of these observations for the folding of the HTH protein Z34C are discussed.