Pulmonary Spindle Cell Carcinoma: As Rare as a Hen's Teeth.

This case is about a 70-year-old man who presented with symptoms and laboratory reports that indicated differentials toward an infectious disease (pneumonia and tuberculosis). A lung mass was found in his chest X-ray and in the computerized tomography (CT) scan of his thorax. A biopsy was taken from the lung mass, and histopathological examination and immunohistochemical staining of the biopsy were done. The results revealed the presence of spindle cell carcinoma (SpCC) with vimentin and cytokeratin positivity. Spindle cell lung cancer is a rare type of non-small cell lung carcinoma, for which all available research indicates a poor prognosis. Due to the rarity of diagnosis, there is a dearth of information about the epidemiology and overall survival of affected patients.

The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection.

SARS-CoV-2 infection-induced aggravation of host innate immune response not only causes tissue damage and multiorgan failure in COVID-19 patients but also induces host genome damage and activates DNA damage response pathways. To test whether the compromised DNA repair capacity of individuals modulates the severity of COVID-19 infection, we analyze DNA repair gene expression in publicly available patient datasets and observe a lower level of the DNA glycosylase NEIL2 in the lungs of severely infected COVID-19 patients. This observation of lower NEIL2 levels is further validated in infected patients, hamsters and ACE2 receptor-expressing human A549 (A549-ACE2) cells. Furthermore, delivery of recombinant NEIL2 in A549-ACE2 cells shows decreased expression of proinflammatory genes and viral E-gene, as well as lowers the yield of viral progeny compared to mock-treated cells. Mechanistically, NEIL2 cooperatively binds to the 5'-UTR of SARS-CoV-2 genomic RNA to block viral protein synthesis. Collectively, these data strongly suggest that the maintenance of basal NEIL2 levels is critical for the protective response of hosts to viral infection and disease.

A Rare Case of Primary Adenocarcinoma of the Gallbladder With Lymphoid Stroma.

Adenocarcinoma of the gallbladder is the most common gallbladder carcinoma. But lymphoid stroma in gallbladder carcinoma is one of the rarest presentations. A unique case of gallbladder adenocarcinoma with lymphoid stroma in a 47-year-old female is presented in this report. The surgically resected gallbladder demonstrated invasive adenocarcinoma with lymphoid stroma, though it was radiologically diagnosed as xanthogranulomatous cholecystitis. Adenocarcinoma was immunohistochemically positive for pancytokeratin (AE1/AE3), cytokeratin 7 (CK7), cytokeratin 20 (CK20), and carcinoembryonic antigen (CEA). Lymphoid stroma was positive for CD45, where B-cell zones were CD20 and CD79a positive, and T-cell zones were CD3 positive, with a larger T-cell subset being positive for CD4 than CD8. This is the fourth reported case of gallbladder adenocarcinoma with lymphoid stroma, which needs to be studied for pathogenesis, prognosis, and future therapy, if any.

Synchronous Adenocarcinoma Stomach With Marginal Zone Lymphoma: A Sporadic Occurrence and Review of Literature.

Synchronous adenocarcinoma of the stomach with lymphoma is extremely rare. We report a case of a 65-year-old male patient with synchronous adenocarcinoma of the stomach with nodal marginal zone lymphoma. Initial endoscopic biopsy suggested invasive moderately differentiated adenocarcinoma and a locoregional disease, per contrast-enhanced computed tomography (CECT) scans. The patient was started on neo-adjuvant chemotherapy with the 5FU, leucovorin, oxaliplatin, docetaxel (FLOT) regime and, after response evaluation, underwent radical gastrectomy. Histopathology and immunohistochemistry suggested synchronous adenocarcinoma of the stomach with marginal zone lymphoma in perigastric lymph nodes. This case is probably the first such synchronous malignancy case reported from India. The prognosis of multiple primary malignancies is usually poor because no standard guidelines are available regarding optimum treatment and sequencing of available treatment modalities. The frequency of synchronous primary cancers has been increasing in recent years, probably due to better diagnostic modalities, and second primary in patients with cancer should be considered as one of the differential diagnoses.

A Case Report of Rare and Lethal Methicillin-Resistant Staphylococcus aureus (MRSA) Peritonitis in Infancy.

Peritoneal inflammation without a discernible intraperitoneal source is referred to as primary peritonitis. Only 2% of pediatric acute abdominal crises are diagnosed preoperatively. Association with other infections is uncommon and is often limited to hepatic and urinary pathogens. Here, we describe a case of primary peritonitis in a one-month-old child who had laparotomy and appendicectomy as per the recommended treatment plan. There were no accompanying hepatic and urinary diseases. In this instance, methicillin-resistant Staphylococcus aureus (MRSA) was the responsible bacteria. The use of linezolid, as per the culture sensitivity report of intraperitoneal pus, ensured a smooth recovery in this case.

SHAPE to Probe RNA Structure and RNA-Protein Interactions In Vitro.

Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) is used to distinguish between the levels of flexibility of nucleotides regulated by base pairing or protein binding. In this method, a reagent reacts with the 2' hydroxyl group to form an adduct, which is then detected by reverse transcription reaction. The number of RNA molecules with an adduct at a specific nucleotide position indicates the SHAPE reactivity of that nucleotide. Here, we describe the method for probing the structure of an RNA in a protein-free or a protein-bound state by in vitro SHAPE.

Chemical Probing of RNA Structure In Vivo Using SHAPE-MaP and DMS-MaP.

The functional roles of RNAs are often regulated by their structure. Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) and dimethyl sulfate (DMS) base reactivity can be employed to investigate the flexibility of nucleotides and correlate it to the constraints imparted by base-pairing and/or protein-binding. In vivo, a multitude of proteins could bind an RNA molecule, regulating its structure and function. Hence, to obtain a more comprehensive view of the RNA structure-function relationship in vivo, it may be required to characterize both the RNA structure and the RNA-protein interaction network. In this chapter, we describe methods for characterizing the in vivo nucleotide flexibility of RNA in cells by SHAPE-MaP (SHAPE by Mutational Profiling) and DMS-MaP. In another chapter, we will discuss the characterization of RNA-protein interaction network by RNP-MaP.

Analysis of RNA-Protein Interaction Networks Using RNP-MaP.

RNA-protein interactions regulate a myriad of biological functions through formation of ribonucleoprotein complexes. These complexes may consist of one or more RNA-protein interaction network(s) providing additional layers of regulatory potential to the RNA. Moreover, since the protein-binding also regulates local and global structure of the RNA by structurally remodeling the latter, it is important to correlate RNA nucleotide flexibility with the site of protein-binding. We have discussed methods for chemical probing of structure of the RNA in the protein-free and protein-bound states in the preceding chapters. In this chapter, we describe a ribonucleoprotein mutational profiling (RNP-MaP) method for probing RNA-protein interaction networks.

Clinical outcomes of bronchiectasis in India: data from the EMBARC/Respiratory Research Network of India registry.

BACKGROUND: Identifying risk factors for poor outcomes can help with risk stratification and targeting of treatment. Risk factors for mortality and exacerbations have been identified in bronchiectasis but have been almost exclusively studied in European and North American populations. This study investigated the risk factors for poor outcome in a large population of bronchiectasis patients enrolled in India. METHODS: The European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) and Respiratory Research Network of India (EMBARC-India) registry is a prospective observational study of adults with computed tomography-confirmed bronchiectasis enrolled at 31 sites across India. Baseline characteristics of patients were used to investigate associations with key clinical outcomes: mortality, severe exacerbations requiring hospital admission, overall exacerbation frequency and decline in forced expiratory volume in 1 s. RESULTS: 1018 patients with at least 12-month follow-up data were enrolled in the follow-up study. Frequent exacerbations (≥3 per year) at baseline were associated with an increased risk of mortality (hazard ratio (HR) 3.23, 95% CI 1.39-7.50), severe exacerbations (HR 2.71, 95% CI 1.92-3.83), future exacerbations (incidence rate ratio (IRR) 3.08, 95% CI 2.36-4.01) and lung function decline. Coexisting COPD, dyspnoea and current cigarette smoking were similarly associated with a worse outcome across all end-points studied. Additional predictors of mortality and severe exacerbations were increasing age and cardiovascular comorbidity. Infection with Gram-negative pathogens (predominantly Klebsiella pneumoniae) was independently associated with increased mortality (HR 3.13, 95% CI 1.62-6.06), while Pseudomonas aeruginosa infection was associated with severe exacerbations (HR 1.41, 95% CI 1.01-1.97) and overall exacerbation rate (IRR 1.47, 95% CI 1.13-1.91). CONCLUSIONS: This study identifies risk factors for morbidity and mortality among bronchiectasis patients in India. Identification of these risk factors may support treatment approaches optimised to an Asian setting.

Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly.

We recently reported that serine-arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. Excess U1 snRNP selectively displaces some of the SR protein molecules from the pre-mRNA generating the substrate for splice signal-specific, sequential recognition by U1 snRNP, U2AF65 and U2AF35. Our work thus identifies a novel function of U1 snRNP in mammalian splicing substrate definition, explains the need for excess U1 snRNP compared to other U snRNPs in vivo, demonstrates how excess SR proteins could inhibit splicing, and provides a conceptual basis to examine if this mechanism of splicing substrate definition is employed by other splicing regulatory proteins.

Utility of tru-cut biopsy in diagnosis of palpable pediatric soft tissue neoplasms.

Context: Soft tissue neoplasms are infrequent in children with sarcomas accounting for approximately 7% of all pediatric malignancies. Morphologic diagnosis is challenging due to overlapping features. Subtyping and categorization of these lesions are difficult on fine-needle aspiration cytology (FNAC) alone owing to tumor heterogeneity and limited material in some cases. Tru-cut biopsies obtain adequate tumor tissue for ancillary studies besides conventional histology. Aim: The study aims to explore the role of tru-cut biopsy to arrive at a definitive diagnosis. The study also highlights the correlation between FNAC and histopathology on tru-cut biopsy besides explaining the significance of a panel of immunohistochemistry (IHC) markers for histological categorization and subtyping. Materials and Methods: A total of 61 children from infancy to 18 years were included in the study. Closed biopsy procedures like FNAC and tru-cut biopsy were performed, and the tru-cut biopsy specimen was subjected to a panel of immunohistochemical markers. Results: Fisher's exact test for sensitivity and specificity towards detection of malignancy was 83% and 86%, respectively for FNAC. For tru-cut biopsy, sensitivity was 94% and specificity was 91%. The two-sided P value (<0.0001) was extremely significant. Cohen's Kappa coefficient value for tru-cut biopsy was 0.772 suggesting a substantial strength of agreement. Tru-cut with IHC had a Kappa value of 0.866 suggesting greater agreement with histopathology. Conclusion: Tru-cut biopsy is a simple, safe, and reliable adjunct to the FNAC. Instead, immunohistochemistry enhances the diagnostic accuracy.

Immune Response to COVID-19 in India through Vaccination and Natural Infection.

In India, COVID-19 (Corona Virus Disease-2019) continues to this day, although with subdued intensity, following two major waves of viral infection. Despite ongoing vaccination drives to curb the spread of COVID-19, the relative potential of the administered vaccines to render immune protection to the general population and their advantage over natural infection remain undocumented. In this study, we examined the humoral and cell-mediated immune responses induced by the two vaccines Covishield and Covaxin, in individuals living in and around Kolkata, India. We also compared the immune responses induced separately by vaccination and natural infection. Our results indicate that although Covishield generates a better humoral immune response toward SARS-CoV-2, both vaccines are almost equivalent in terms of cell-mediated immune response to the virus. Both Covishield and Covaxin, however, are more effective toward the wild-type virus than the Delta variant. Additionally, the overall immune response resulting from natural infection in and around Kolkata is not only similar to that generated by vaccination but the cell-mediated immune response to SARS-CoV-2 also lasts for at least ten months in some individuals after the viral infection.

Paraganglioma of Urinary Bladder: An Uncommon Entity in Uropathology.

Paraganglioma of the urinary bladder is a rare neoplasm. It may be functional, secreting catecholamines, or nonfunctional. Clinically and histopathologically, it has the potential to be misdiagnosed as a more common urothelial carcinoma, especially in nonfunctional cases. A high index of suspicion on the part of pathologist can help in identification of characteristic histopathologic feature which coupled with immunohistochemistry can help in establishing the correct diagnosis. We present a case of paraganglioma in a 78-year-old male patient presenting with haematuria. Clinical provisional diagnosis rendered based on cystoscopic findings and radiology was urothelial carcinoma; however, was confirmed to be a case of paraganglioma of bladder on histopathological and immunohistochemical evaluation. A long follow-up is warranted. Herein, we also briefly review the relevant literature.

Diagnostic Yield of Closed Pleural Biopsy in Undiagnosed Exudative Pleural Effusions.

Introduction: In our practice, etiological diagnosis of pleural effusion is sometimes difficult despite cytological, biochemical and microbiological tests. The aim of the present study was to make an etiological diagnosis by means of closed pleural biopsy in undiagnosed pleural effusions. Methods:The study group consisted of patients with exudative pleural effusion where etiology was not determined by means of conventional cytological, biochemical and microbiological investigations. Pleural tissue was obtained by Abrams pleural biopsy needle. Pleural biopsy was subjected to histopathology, Ziehl-Neelsen (Z-N) staining and mycobacterial culture. Results:Four hundred fifty eight patients with pleural effusion were screened over three years and 82 of them were found to have undiagnosed exudative effusion after investigations, as mentioned in the Method section. The age of the 82 subjects [56 (68.29%) men and 26 (31.71%) women] ranged from 15 to 65 years (mean 32.6). Histopathology showed epitheloid granuloma with caseation necrosis in 50 (60.9%) patients and non-specific chronic inflammation in 14 (17.1%) subjects. Ziehl-Neelsen stain was positive for acid fast bacilli (AFB) in 10 (12.2%) patients and culture of pleural tissue showed the presence of Mycobacterium tuberculosis in 18 (21.9%) patients. Conclusion:In the era of thoracoscopy, percutaneous closed needle pleural biopsy still holds a significant role in cases of undiagnosed exudative pleural effusions where thoracoscopy is not available, being also a cost effective approach for developing countries. It can achieve specific diagnosis among 86.6% of cases with undiagnosed exudative pleural effusions.

High-Resolution Ultrasound Study of Morphological Changes of the Pylorus in the Postoperative Cases of Infantile Hypertrophic Pyloric Stenosis.

AIMS: The aim of this study was to find & compare the pyloric Canal Length (CL), Pyloric muscle thickness (MT) by using the High Resolution Ultrasonography (HRUS) in Preoperative & postoperative period (after Ramstedt Pyloromyotomy) for Infantile Hypertrophic Pyloric Stenosis (IHPS). METHODS: From January 2018 to June 2019, we have performed HRUS for 40 patients of clinically diagnosed cases of IHPS. & Ultrasonography machine: Phillips HD 7 machine & Alpinion E-CUBE with 3-12MHz linear probe, 3.5-5 MHz curvilinear probe and 5-7.5 MHz sector probe were used. The sonographic criteria for positive IHPS are Pyloric muscle thickness (MT) > 3 mm, pyloric Canal length (CL) >14 mm. Postoperative MT & CL at 2 month, 4 month & 6 month were determined and results were analysed with the preoperative pyloric parameters. Statistical analysis used: Mean and standard deviation of values were obtained by using Microsoft excel and statistical significance was analysed by regression study of grouped variables showing p - value by Microsoft excel. RESULTS: Pyloric parameters (MT & CL ) gradually attain normal values over months and 80 % of patients showed resolution of pyloric MT & CL values by 6 months. MT assessment shows statistical significance at six months scan ( p- value <0.05). CONCLUSIONS: Serial postoperative HRUS in IHPS cases show gradual ( mostly by 6 months) resolution of pyloric parameters ( MT & CL ) to normal. MT appears to be a consistent parameter for serial assessment.

Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code.

The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of 3D structural scaffold of AdML-a model pre-mRNA substrate-guiding early spliceosomal components to the splice signal sequences. We find that mutations in the non-cognate splice signal sequences impede recruitment of early spliceosomal components due to disruption of the global structure of the pre-mRNA. We further find that the pre-mRNA segments potentially interacting with the early spliceosomal component U1 snRNP are distributed across the intron, that there is a spatial proximity of 5' and 3' splice sites within the pre-mRNA scaffold, and that an interplay exists between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components can recognize a 3D structural scaffold beyond the short splice signal sequences, and that in our model pre-mRNA, this scaffold is formed across the intron involving the major splice signals. This provides a conceptual basis to analyze the contribution of recognizable 3D structural scaffolds to the splicing code across the mammalian transcriptome.

Invasive Mucormycosis - An Enigma.

Mucormycosis is an emerging infection in the present post-COVID-19 era, associated with high morbidity and mortality. We are reporting an interesting case of invasive rhino-orbital-cerebral mucormycosis in a 65-year-old female who presented with left nasal and orbital swelling after COVID-19 infection associated with uncontrolled diabetes mellitus. Histopathological and microbiology examination favored mucormycosis. Finally, endoscopic debridement of the lesion was done with left orbital exenteration. The patient at present is clinically stable. As these cases have been seen in many suspected and confirmed COVID-19 cases, early diagnosis and treatment will salvage the patient.

Pancreatico Duodenal Trauma in Children: Two-Year Experience at a Regional Referral Center and Tertiary Care Teaching Hospital.

BACKGROUND: Pancreatico-Duodenal injuries, though rare, pose a mighty challenge to the surgeon in both diagnosis and treatment. More so in children, where the patho-physiologic threshold is low. Added to this is the absence of any strong guidelines to guide and ensure standardised care in these children for best outcome. MATERIALS AND METHODS: The trauma patients' records in the emergency department, operation theatre, inpatient departmrnt, outpatient department (OPD) for the period of December 2016 to December 2018 in the institution were retrospectively reviewed, to find out the cases of pancreaticoduodenal trauma proven radiologically, biochemically and/or on laparotomy. Those cases then studied with respect to diagnosis, treatment and short term outcome. RESULTS: Of the 256 cases of abdominal trauma, suspected pancreatico duodenal (PD) trauma were in nine but on laparotomy actually eight of them had PD trauma. All were blunt abdominal traumas sustained in road traffic accidents. Of these one was combined pancreatico duodenal while three were pure pancreatic and four were pure duodenal. One had associated superior mesenteric vein trauma. All were managed operatively. There were no mortality, one fourth had major complications. Mean hospital stay was 22.25 days. Follow up period varied from six to 32 months. CONCLUSION: Though PD traumas are rare but are potentially very morbid and may prove fatal. Proactive individualized management, multidisciplinary approach and good perioperative support can yield good results.