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.

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.

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.

Role of Doppler Ultrasound in Diagnosis of Hepatocellular Carcinoma with Histopathological Correlation

Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world and the leading cause (possibly third) of cancer mortality. In a present scenario, HCC displays a challenging clinical problem worldwide. Good-quality ultra sound with careful evaluation of the hepatobiliary system can be a screening examination for HCC in patients at risk. The aim of the study was to determine the diagnostic accuracy of the Doppler sonography for differentiation of hepatocellular carcinoma (HCC) from other focal liver lesions. It was a cross-sectional survey, conducted in the Department of Radiology& Imaging, Mymensingh Medical College, Mymensingh, Bangladesh from January 2017 to December 2018. A total of 70 patients with space occupying lesions on ultrasound were included in this study while pregnant women were excluded. All patients were examined by gray scale ultrasonography, color Doppler and FNAC. To visualize the blood flow, standard color Doppler sonography was used for each lesion. Within the lesions, pulsed Doppler samples were assessed whenever possible on the basis of pulsatile flow & finally resistive index (RI) of intra-tumoral and peritumoral arterial flow was studied. After evaluating by Doppler sonography (CDFI and Spectral analysis), FNAC was done and the specimen was sent to the Department of Pathology for Cytopathological examination. Cytopathology were assessed for confirmation of positive and negative cases of HCC. The detection rate of arterial flow in malignant tumors was 85.1% and in benign lesions were 30.4%. Doppler spectrum analysis showed that the resistive index in primary malignant tumors were 0.76±0.12 and in metastatic tumors were 0.80±0.12 and below 0.6 in benign lesions. The difference was significant (p<0.001). This difference was related with its Cytopathological report. The arterial flow identified by CDFI within the liver lesion with RI >0.6 can be regarded as a criterion of malignant tumors and RI<0.6 can be regarded as benign lesions. This study concluded that the combination of color Doppler flow imaging and RI are more useful in differential diagnosis of liver neoplasms.

Assessment of the Relationship between Non-motor features and Severity of Parkinson's Disease Patients in Bangladesh

Parkinson's disease (PD) is second most common neurodegenerative disorder after Alzheimer's disease that may present with both motor and non-motor symptoms (NMSs). Many of the ignored NMSs may potentiate further deterioration of the patient's quality of life (QoL). But there is scarcity of data regarding NMSs of PD patients and their relationship with the disease severity in Bangladesh. This study was aimed to investigate the frequency of NMSs and assess their debatable impact on the severity of PD patients in Bangladesh. This cross-sectional type of observational study was conducted in neurology department of Dhaka Medical College Hospital, Bangladesh from January 2012 to June 2013 which recruited 60 eligible PD patients. The PD patients and disease severity was demonstrated by UK Parkinson's Disease Society Brain Bank criteria for idiopathic PD and the Hoehn and Yahr scale respectively. Whereas, NMSs were demonstrated by the self-structured questionnaire which had encountered 30 common symptoms of PD. The mean age of our study cohort was found 57.88±10.56 years with male female ration 2:1. According to the Hoehn and Yahr (H & Y) severity scale 38.3%, 38.3%, 20.1% and 3.3% patients had been suffering from stage ?, stage II, stage III and stage ?V Parkinson's disease respectively. Irrespective of the severity of the PD the frequency of NMSs was nocturia (66.7%), sadness or blues (65.0%), memory disturbance (61.7%), anxiety (58.3%), insomnia (56.7%), orthostatic hypotension (55.0%), erectile dysfunction (50.0%), urinary urgency (46.7%), anhedonia (45.0%), olfactory disturbance (38.3%), constipation (38.3%), hyper or hypo sexuality (31.7%) and restless leg syndrome (31.7%). However, after head-to-head NMSs analysis, daytime dribbling of saliva (p=0.024), urinary urgency (p=0.036), nocturia (p=0.001), weight loss (p=0.001), anhedonia (p=0.027), excessive daytime sleepiness (p=0.024), insomnia (p=0.007), vivid dream (p=0.024), REM behavior disorder (p=0.010), restless leg syndrome/ periodic leg movements (p=0.043) had significantly been reported higher among the stage II PD patients than that of stage I patients. Whereas fall (p=0.001), dysphagia or choking (p=0.002), constipation (p=0.003), fecal incontinence (p=0.033), excessive daytime sleepiness (p=0.033), anxiety (p=0.036) and anhedonia (p=0.044) were significantly more prevalent among the advanced stage (III) than stage (II) PD patients. Mean total NMS increased significantly with PD severity based on H and Y staging with a mean NMSQ-T (Non-Motor Symptoms Questionnaire Test) of 5.43 in stage 1, 9.22 in stage 2, 13.75 in stage 3 and 17.0 in stage 4 (p=0.0001). This study revealed that there was high frequency of NMSs among the PD patients and most common symptoms were nocturia, sadness, memory impairment, anxiety, insomnia, orthostatic hypotension, erectile dysfunction, anhedonia, urinary urgency and constipation. Finally, the more advanced disease as indicated by a higher H&Y stage was associated with significantly higher number of reported NMSs.

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.

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.

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.

Role of Transabdominal Ultrasonogram for Evaluation of Placental Maturity in Relation with Fetal Gestational Age

In this study our main goal is to evaluate the role of ultrasonography (USG) for determination of placental maturity and fetal gestational age. This cross-sectional study was done at the Department of Radiology and Imaging (USG section) Mymensingh Medical College and Hospital, Mymensingh from July 2008 to June 2010, where 60 patients included in this study, who was attending in the department of Radiology & Imaging for transabdominal ultrasonography with early and late pregnancy related complaints. In this study among the 60 patients, the youngest one was eighteen years and oldest one was thirty-nine years old age. Thirty five percent (35.0%) patients were from 26-30 years age group. About 33 patients out of 60(55.0%) were house wives. Most of the patients were presented with amenorrhea (65.0%) 39 out of 60. Among 60 patients, 20 patients (33.3%) were in gestational age within 12-28 weeks, 20 patients (33.3%) were in gestational age within 29-36 weeks and 20 patients (33.3%) were within >36 weeks gestational age. Among them, 20 patients (33.3%) had grade III placenta, 20 patients (33.3%) had grade II placenta, 12 patients (20%) had grade I placenta and 08 patients (13.3%) had grade 0 placenta. Out of 60 patients, 18 patients (30.0%) were in high risk group and 70.0% were normal. Six (6) patients (10.0%) suffered from HTN, 3 patients had RH negative (5.0%) blood group, 3(5.0%) patients suffered from APH, 3 patients suffer from DM and 3 from IUGR. In this study showed hypertension and IUGR had strong correlation with accelerated placental maturation. Maternal DM and Rh sensitization were associated with delayed maturation of the placenta. This study concludes that, USG appears to be the best imaging modality for the evaluation of placenta and its grading. USG is relatively less expensive and it is good considering the diagnostic accuracy in pregnancy profile. It is noninvasive procedure without any radiation hazards and better visualization of the lesion in different section, but this study is not a complete reflection of overall incidence and statistics regarding the ailment in our country. For this a more extensive study over a longer period covering different section of society is very much needed for better outcome.

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.

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.

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. 

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.

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.

A Rare Case of Polyorchidism: Sonographic and MR Evaluation of Four Testes

Polyorchidism is a rare congenital anomaly reported about 200 cases in the world text. A number of theories have been planned concerning the making of polyorchidism, but the real explanation is still not acknowledged. Here we are going to present a case study of polyorchidism. A 70 years old gentleman complained with left supernumerary testes in the left hemiscrotum. His left hemiscrotum was painless with mass. Polyorchidism without malignancy or any other concomitant features were revealed by both ultrasound and MRI examinations. In most cases the ultrasonograph alone is diagnostic. In complicated cases of polyorchidism MRI may provide additional information.

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.

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.

Metal contaminations in sediment and associated ecological risk assessment of river Mahanadi, India

Mahanadi is one of the major rivers of peninsular India. Like other Indian rivers, it is contaminated with sewages, industrial discharges, and agricultural runoff. Thus, necessity was felt to monitor its pollution status. Present work was part of that program and aimed to assess the sediment contamination due to the trace metals Cd, Cr, Cu, Mn, Pb, and Zn during 2012-2015. Sediment pollution status and ecological risks were evaluated calculating contamination factor (CF), geo-accumulation (I_geo), pollution load index (PLI), potential ecological risk (EⁱR), etc. The recorded metal concentrations were Cd BDL of flame mode of AAS; Cr BDL - 73.9; Cu BDL - 44.4; Mn 37.2 - 1887.0; Pb BDL - 29.5; and Zn BDL - 92.5 mg kg^-1. As per US EPA guidelines, Cr concentrations at many locations were in the moderately polluted range. I_geo, CF, mC_d, PLI, and EⁱR indicated low pollution levels and low ecological risks due to the trace metals assessed. The sediment quality guidelines (SQGs) indicated that Cr and Cu concentrations exceeded (16% sample) the threshold effect concentrations and may occasionally exhibit adverse biological effects. The association of sediment organic matter, conductivity and content of Cu, and their grouping in component 1 of PCA revealed that the anthropogenic input was dominant and so also the component 2 where Cr exhibited moderately good correlation with organic matter. Cluster analysis of the sampling sites based on pollution status yielded 3 groups: relatively uncontaminated (S3, S4), low to moderately contaminated (S2), and moderately contaminated (S1, S5, S6) stretches.

Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing

Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem-loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.

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.

Borderline serous ovarian neoplasm: case report of a diagnostic challenge in intraoperative frozen sections

Surface epithelial tumors of the ovary account for 25% of all ovarian neoplasms. When composed predominantly of fibrous stroma, with glands and cysts forming a minor component, their appearance on imaging is often complex; cystic- to solid-appearing masses often raise suspicion of a malignant tumor. An accurate frozen histopathological diagnosis of a benign cystadenofibroma of this tumor can facilitate appropriate surgical management. However, it is equally important to diagnose areas of borderline changes/malignancy arising in these tumors, particularly when large or complex surface and inner papillary areas with multilayering or stratification are seen microscopically. We present here a case of bilateral complex ovarian mass in a 68-year-old woman, which was equivocal for malignancy on radiology, per operative gross examination as well as on frozen section evaluation. It was finally diagnosed as a borderline serous tumor (BOT) in a cystadenofibroma on histopathological examination.

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Borderline tumors among surface epithelial tumors with a prominent stromal component are uncommon.

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Adhesions & bilaterality with a prominent stromal component result in radiological interpretation of a complex ovarian mass.

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The Risk of Malignancy Index is usually <200 if the CA125 is low.

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Intraoperative surgical decisions are based on frozen section examination which are challenging.

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A benign tumor diagnosis may results in inadequate surgery, additional interventions later and possible tumor spread.

Status of pesticide residues in water, sediment, and fishes of Chilika Lake, India

Chilika Lake is the largest coastal lagoon in Asia and the second largest in the world covering an area of 1100 km² and spread over three districts of Odisha state of India. It is the first Indian wetland designated as a wetland of international importance under the Ramsar Convention in 1981. The lake ecosystem sustains large and diversified resources of plants and animals including fisheries. Pollution of the ecosystem caused by residues of pesticides originating from different sources was assessed through multiple sampling from 2012 to 2016 from three potential sites of contamination, viz., Palur Bridge, Daya River Estuary, and Makara River. Incidence of organochlorinated (OC) pesticide residues was noticed in about 25% water samples. HCH (α, γ&δ), DDD (op^|), DDE (op^|&pp.^|) and heptachlor were the OCs detected in concentration varying from 0.025 to 23.4 μg/l. None of the eight targeted synthetic pyrethroid (SP) pesticides was found in water, but among the organophosphates (OP), chlorpyrifos (0.019-2.73 μg/l), and dichlorvos (0.647 μg/l) were recorded. In sediment samples, residues of OC or OP pesticides were not present, but one SP pesticide was recorded. Fish samples were contaminated to the extent of 55%, mostly with residues of OCs and OPs and less with SPs. However, their concentrations were below the permissible limit, so there was no direct threat of health hazards to humans.

Synchronous Bilateral Wilms Tumor: Five-Year Single-Center Experience with Assessment of Quality of Life

Context:

Synchronous Bilateral Wilms tumor (sBWT).

Aims:

This study aimed to assess the outcome of patients with sBWT treated on SIOP protocol.

Settings and Design:

Retrospective and prospective randomized study.

Subjects and Methods:

SIOP 93-01 protocol was used to study nine patients of sBWT in a single center and followed up over a period from 2 to 5 years.

Statistical Analysis Used:

Unpaired t-test and Mann–Whitney U-test were used for analysis.

Results:

Of nine patients, six were included in the study as three patients lost to follow-up. Among the six patients, there were four girls and two boys with a median age of 2 years. Mean regression in the size of tumor was 87% in four out of six patients. Tumor with unfavorable histology showed 32% response (ratio of favorable: unfavorable histology 2:1). Event-free survival rate was 81.3% and overall survival was 90% over 2–5 years. Recurrence was seen in two patients of whom one had Denys–Drash syndrome. Mean DTPA glomerular filtration rate was 91.4/ml/min/1.73 m² preoperatively and that of 3 months after completion of treatment was 84/ml/min/1.73 m². Health-related quality of life (HRQOL) using Pediatric Quality of Life Inventory and Lansky Play Performance Scale revealed significant improvement results of all functioning domains such as physical, social, emotional, and school subscales with P < 0.05 and performance scale (P < 0.04).

Conclusions:

We suggest SIOP protocol for sBWT and bilateral nephron-sparing surgery in two stages. However, long-term follow-up is required to assess the ultimate renal function outcome. HRQOL is an essential guide in improving the conditions of pediatric cancer survivors.

Spontaneous Asymptomatic Migration of Ventriculoperitoneal Shunt into Thoracic Cavity: A Case Report with Review of Literature

Intrathoracic migration of ventriculoperitoneal shunt is a rare complication and usually complicated with pneumonia or cerebrospinal fluid hydrothorax, which leads to diagnosis and early interventions. Very rarely patient remains asymptomatic. Here is a case report of a 6-year-old boy with a rare asymptomatic intrathoracic migration of ventriculoperitoneal shunt.

Ultraslow isomerization in photoexcited gas-phase carbon cluster [Formula: see text]

Isomerization and carbon chemistry in the gas phase are key processes in many scientific studies. Here we report on the isomerization process from linear [Formula: see text] to its monocyclic isomer. [Formula: see text] ions were trapped in an electrostatic ion beam trap and then excited with a laser pulse of precise energy. The neutral products formed upon photoexcitation were measured as a function of time after the laser pulse. It was found using a statistical model that, although the system is excited above its isomerization barrier energy, the actual isomerization from linear to monocyclic conformation takes place on a very long time scale of up to hundreds of microseconds. This finding may indicate a general phenomenon that can affect the interstellar medium chemistry of large molecule formation as well as other gas phase processes.

Bright nanowire single photon source based on SiV centers in diamond

The practical implementation of many quantum technologies relies on the development of robust and bright single photon sources that operate at room temperature. The negatively charged silicon-vacancy (SiV^-) color center in diamond is a possible candidate for such a single photon source. However, due to the high refraction index mismatch to air, color centers in diamond typically exhibit low photon out-coupling. An additional shortcoming is due to the random localization of native defects in the diamond sample. Here we demonstrate deterministic implantation of Si ions with high conversion efficiency to single SiV^- centers, targeted to fabricated nanowires. The co-localization of single SiV^- centers with the nanostructures yields a ten times higher light coupling efficiency than for single SiV^- centers in bulk diamond. This enhanced photon out-coupling, together with the intrinsic scalability of the SiV^- creation method, enables a new class of devices for integrated photonics and quantum science.

Demographic Study and Management of Colonic Atresia: Single-Center Experience with Review of Literature

Context and Aim

The aim of this study is to highlight the rarity of this disorder and its associated anomalies and our objective was to review our experience in the management of colonic atresia (CA) with respect to staged surgery versus one-step procedure for a better outcome of the disease.

Settings and Design

A randomized, controlled, single-center study conducted over a period of 4 years from October 2013 to 2017.

Subjects and Methods

Nine cases were operated for CA of which three underwent primary anastomosis and six underwent initial colostomy followed by definitive surgery. Age, sex, body weight, clinical presentation, type of atresia, site, time interval of operation, associated anomalies, initial procedure, postoperative complications, final procedure, biopsy, hospital stay, and outcome were noted.

Statistical Analysis Used

Microsoft Excel was used for statistical analysis.

Results

Out of 9 patients, 6 were males and 3 were females, 7 patients survived and 2 patients died (mortality 22.2%), of which one patient with primary anastomosis had leak and sepsis and one patient with primary anastomosis had associated Hirschsprung's disease (HD). Mean time gap for operation was 12.8 h and mean hospital stay was 3.5 days for initial colostomy and 21 days for primary anastomosis. Wound dehiscence occurred in 4 patients. Malrotation was found in 3 patients, HD in 2 patients, cardiac anomaly in 2, Meckel's diverticulum in 1, and cleft lip in 1 patient. Type IIIa atresia was found in in 6 patients, Type I in 2, and Type II in 1 patient. The most common site was transverse colon (n = 5).

Conclusion

Diagnosis and management of CA is a challenge. Early presentation and diagnosis should be prompt. Staged procedure with initial colostomy followed by definitive procedure is the preferred choice. Associated anomaly HD must be ruled out.

Demographic, clinical, biochemical, radiological and etiological characteristics of malignant pleural effusions from Eastern India

CONTEXT

There are very limited data regarding clinical, radiological and etiological aspects of malignant pleural effusion (MPE) from Eastern India.

AIMS

To review natural history, clinical features, radiological features and etiology of MPEs.

SETTING AND DESIGN

Hospital based cross-sectional descriptive study.

MATERIALS AND METHODS

We had reviewed166 diagnosed cases of MPEsregarding demography; clinical, radiological and biochemical characteristics, diagnostic modalities and etiologies.

RESULTS

Out of 166 patients, 72.89% were males and 27.11% were females. Mean age of presentation among males was 64.3 ± 12.7 and among females was 52.5 ± 14.8. Most common presenting symptom was dry cough (87.9%) and most common presenting sign was clubbing (54.5%). Massive effusion was found in 45.78% of cases. Pleural fluid macroscopic appearance was haemorrhagic in 54.82% of cases. Mean adenosine deaminase activity in MPE was 24.05 U/L. Mean pleural fluid/serum protein ratio was 0.65, mean pleural fluid/serum lactate dehydrogenase ratio was 1.01. Most of the cases (84.94%) were diagnosed by pleural fluid cytology for malignant cells. Primary cancer was diagnosed in 136 (81.93%) cases; among which 121 (88.97%) cases were lung cancers, among which adenocarcinoma (52.89%) was the most common histology.

CONCLUSIONS

Pleural fluid cytologies for malignant cells are usually sufficient to diagnose MPE in nearly 85% of cases and in remaining cases if thoracoscopyis not available, blind pleural biopsy can be helpful. The most common primary in cases of MPE is lung cancer with adenocarcinoma being the commonest culprit.

Autoresonance Cooling of Ions in an Electrostatic Ion Beam Trap

Autoresonance (AR) cooling of a bunch of ions oscillating inside an electrostatic ion beam trap is demonstrated for the first time. The relatively wide initial longitudinal velocity distribution is reduced by at least an order of magnitude using AR acceleration and ramping forces. The hot ions escaping the bunch are not lost from the system but continue to oscillate in the trap outside of the bunch and may be further cooled by successive AR processes. Ion-ion collisions inside the bunch close to the turning points in the trap's mirrors contribute to the thermalization of the ions. This cooling method can be applied to any mass and any charge.

An experimental setup to study delayed electron emission upon photoexcitation of trapped polyatomic anions

A Velocity Map Imaging (VMI) spectrometer has been designed and integrated with an electrostatic ion beam trap to study delayed electron emission from trapped polyatomic anions upon photodetachment. The VMI spectrometer is small in size and can record a wide range of photoelectron energies, with variable magnification. Delayed electron emission can be recorded in our experimental setup for any time duration after the photoexcitation of the polyatomic anions. Experiments were carried out with trapped O^- and C₅^- ions to demonstrate the capability of the spectrometer. Delayed electron emissions from C₅^- as well as prompt photoelectrons from O^- were detected by the VMI spectrometer upon photoexcitation. The design and performance of the spectrometer are presented in detail.

The Fourier decomposition method for nonlinear and non-stationary time series analysis

for many decades, there has been a general perception in the literature that Fourier methods are not suitable for the analysis of nonlinear and non-stationary data. In this paper, we propose a novel and adaptive Fourier decomposition method (FDM), based on the Fourier theory, and demonstrate its efficacy for the analysis of nonlinear and non-stationary time series. The proposed FDM decomposes any data into a small number of 'Fourier intrinsic band functions' (FIBFs). The FDM presents a generalized Fourier expansion with variable amplitudes and variable frequencies of a time series by the Fourier method itself. We propose an idea of zero-phase filter bank-based multivariate FDM (MFDM), for the analysis of multivariate nonlinear and non-stationary time series, using the FDM. We also present an algorithm to obtain cut-off frequencies for MFDM. The proposed MFDM generates a finite number of band-limited multivariate FIBFs (MFIBFs). The MFDM preserves some intrinsic physical properties of the multivariate data, such as scale alignment, trend and instantaneous frequency. The proposed methods provide a time-frequency-energy (TFE) distribution that reveals the intrinsic structure of a data. Numerical computations and simulations have been carried out and comparison is made with the empirical mode decomposition algorithms.

Observation of longitudinal quadrupole ion bunch oscillations in an electrostatic ion beam trap

Ions in an ion bunch trapped inside an Electrostatic Ion Beam Trap (EIBT) exhibit collective oscillations within the bunch under the influence of an external driving force. These internal oscillations have been measured explicitly using a new method with a particle detector outside the EIBT. In this approach, the evolving ion bunch is monitored along the entire trap length, in contrast to the localized single point measurements that are often carried out in other techniques. In the present study, quadrupole oscillations have been measured for the first time in an EIBT along with the dipole oscillations that were measured previously. The frequency of the quadrupole oscillation is found to be about twice the dipole oscillation frequency. This is in agreement with the prediction of a theoretical model.