Evolution and Phylodynamics of the Hemagglutinin Protein of Influenza A/(H1N1)pdm09 Virus Isolates from India from 2009 to 2020.

Influenza A/(H1N1)pdm09 virus evolves through continuous antigenic variation in both surface antigens, such as hemagglutinin (HA) and neuraminidase (NA) proteins, which affect its pathogenicity, the effectiveness of the host immune response, and drug resistance. This study reports the evolution and dynamics of 527 HA protein sequences of influenza A/(H1N1)pdm09 Indian isolates submitted from 2009 to 2020. These isolates were aligned with a reference sequence and 22 sequences representing different clades using MEGA X, and subjected to phylogenetic analysis. The strains were predominantly grouped in clades 6B.1 and 6B.2. Prediction of glycosylation sites using the BioEdit and NetNglyc servers showed 12 glycosylation sites distributed in both the stem and globular head regions of HA. Functional evaluation showed that there were 22 deleterious mutations that could affect the function of HA. In addition, 403 unique mutations were distributed across various isolates, indicating the dynamics of antigenic variation in Indian isolates. These results provide an understanding of the frequency, phylodynamics, and impact of mutations in Indian isolates of influenza A/(H1N1)pdm09 relative to global isolates. Monitoring the genomic evolution of the virus will support studies on strain selection for vaccine development and devising control and prevention measures to manage this respiratory infection.

Industrial functional safety assessment for WSN using QoS metrics.

Wireless Sensor Networks are increasingly getting deployed for the safety use cases in industrial applications. While several research papers discuss about the Quality & Reliability improvement techniques in WSN systems to achieve minimal delay, higher node life, optimal routing etc., very limited work is witnessed on assessment of safety integrity levels of WSN systems. In this paper we tried to bridge this gap by bringing out a QoS metric-based safety integrity assessment for the end-to-end industrial Wireless Sensor Network (WSN) system. To identify relevant QoS metrics for monitoring the safety integrity levels, we also bring out a 4-step mapping methodology to link the QoS metrics and communication defenses/safety mechanisms. This mapping approach is expected to serve the network safety design engineers. Finally, a simulation case example is discussed to illustrate safety integrity assessment and we conclude by bringing out future research opportunities to improve safety integrity levels of industrial WSN systems.

Body composition reference values in Singaporean adults using dual-energy X-ray absorptiometry-The Yishun study.

OBJECTIVES: This study establishes age- and sex-specific reference values for fat mass index (FMI), lean mass index (LMI), appendicular LMI (aLMI), and body fat distribution indices including Android/Gynoid % fat ratio and Trunk/Limb % fat ratio in multi-ethnic Singaporean adults. METHODS: A population-based cross-sectional study using dual-energy X-ray absorptiometry (Hologic Discovery Wi) was carried out to measure whole body and regional fat and lean mass in community-dwelling adults. A total of 537 adults (57.5% women), aged from 21 to 90 years, were recruited from the large north-eastern residential town of Yishun. Age- and sex-specific percentile reference values were generated for FMI, LMI, aLMI, Android/Gynoid % fat ratio and Trunk/Limb % fat ratio using the Lambda-Mu-Sigma method. The relationship between the parameters and age were assessed through the Pearson's correlation coefficient. RESULTS: All parameters demonstrated significant correlation with age (p < 0.05) for both men and women, except for LMI in women, with the strength of r ranging from 0.12 (weak correlation) to 0.54 (strong correlation). LMI (r = -0.45) and appendicular LMI (r = -0.54) were negatively associated with age in men while none (r = -0.06) to weak correlation (r = -0.14) were shown in women for the same parameters respectively. The Android/Gynoid % fat ratio and Trunk/Limb % fat ratio were positively related to age for both men (r = 0.37 & 0.43, p < 0.001) and women (r = 0.52 & 0.48, p < 0.001). CONCLUSION: We have established DXA-based body composition reference data for the Singapore adult population. These reference data will be particularly useful in geriatric, obesity and oncology clinics, enabling the prescription of appropriate therapy to individuals at risk of morbidity from unfavorable body composition phenotypes. It also adds on to the limited reference database on Southeast Asian body composition.

Epitope Identification and Designing a Potent Multi-epitope Vaccine Construct against SARS-CoV-2 Including the Emerging Variants.

Introduction: The emergence of a novel coronavirus in China has turned into a SARS-CoV-2 pandemic with high fatality. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering immune responses against the virus. Methods: In this study, we adopted an immunoinformatics-aided approach for developing a new multi-epitope vaccine construct (MEVC). In silico approach was taken for the identification of B-cell and T-cell epitopes in the Spike protein, for MEVC various cytotoxic T-lymphocyte, helper T-lymphocyte, and B-cell epitopes with the highest affinity for the respective HLA alleles were assembled and joined by linkers. Results: The computational data suggest that the MEVC is nontoxic, nonallergenic and thermostable and elicit both humoral and cell-mediated immune responses. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the emerging variants having multiple unique mutations in S protein. Conclusions: Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

Immunoinformatic Approach for the identification of T Cell and B Cell Epitopes in the Surface Glycoprotein and Designing a Potent Multiepitope Vaccine Construct Against SARS-CoV-2 including the new UK variant

The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates.

BACKGROUND: From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe. METHODS: We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India. RESULTS: We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade. CONCLUSIONS: The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10-3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.

Hemosuccus pancreatitis due to a ruptured splenic artery pseudoaneurysm - diagnosis and endovascular management.

Hemosuccus pancreatitis is a rare and potentially fatal cause of upper gastrointestinal bleeding characterized by hemorrhage from the ampulla of Vater via the pancreatic duct. In this case, a patient with chronic pancreatitis on a background of chronic alcoholism is found to have a splenic artery pseudoaneurysm that was bleeding into the pancreatic duct. This was identified on contrast-enhanced computed tomography imaging and successfully managed via microcoil embolization.

Bone mineral density reference values in Singaporean adults and comparisons for osteoporosis establishment - The Yishun Study.

BACKGROUND: While there have been studies in Singapore on the prevalence and economic burden of osteoporotic hip fracture, there is a severe lack of reference data on bone mineral density and prevalence of osteoporosis. The purpose of this study is to establish the reference values for BMD and compare prevalence of osteoporotic conditions using other available reference values so as to better understand the status of bone health in Singaporean adults. METHODS: We carried out a population-based cross-sectional study using dual-energy x-ray absorptiometry (Hologic Discovery Wi) to measure the bone mineral density of Singaporean adults aged ≥21 years. A total of 542 participants were recruited from the large north-eastern residential town of Yishun. We computed T- scores (denoted by TSG) for each individual in the study. Similar diagnoses were also done based on T-scores provided by the densitometer (TDXA), NHANES database (TNHANES), and China (TCHN), and the differences in prevalence compared. We then compared the concordance between TSG and TDXA in the classification of osteoporosis. Osteoporosis was defined according to criteria by the World Health Organization (WHO). RESULTS: Peak lumbar spine BMD was 1.093 ± 0.168 g/cm2 in women, and 1.041 ± 0.098 g/cm2 for men. Peak whole-body BMD was 1.193 ± 0.93 g/cm2 in women at, and 1.224 ± 0.112 g/cm2 for men. Prevalence of osteoporosis based on lumbar spine was 9.3% in postmenopausal women, and 0.7% in men after 50 years of age. The percentage difference in prevalence range from 60.5-163.6%, when using reference values from TDXA, TNHANES, and TCHN. Comparing diagnosis using TDXA and TSG cut-off values, 28 versus 15 women were diagnosed as osteoporotic respectively.  The kappa statistics was 0.81 for women and 0.85 for men. CONCLUSION: Our study shows that T-scores provided by DXA manufacturer over-diagnosed osteoporosis in Singaporeans, and the prevalence of osteoporotic conditions is not accurately represented. This over-diagnosis may result in unnecessary treatment in some individuals.

Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories.

Background & objectives: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. Methods: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. Results: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. Interpretation & conclusions: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.

Interventional radiology and COVID-19: evidence-based measures to limit transmission.

As we face an explosion of COVID-19 cases and deal with an unprecedented set of circumstances all over the world, healthcare personnel are at the forefront, dealing with this emerging scenario. Certain subspecialties like interventional radiology entails a greater risk of acquiring and transmitting infection due to the close patient contact and invasive patient care the service provides. This makes it imperative to develop and set guidelines in place to limit transmission and utilize resources in an optimal fashion. A multi-tiered approach needs to be devised and monitored at the administrative level, taking into account the various staff and patient contact points. Based on these factors, work site and health force rearrangements need to be in place while enforcing segregation and disinfection parameters. We are putting forth an all-encompassing review of infection control measures that cover the dynamics of patient care and staff protocols that such a situation demands of an interventional department.

Balloon-occluded retrograde transvenous obliteration of colonic varices: a case report.

BACKGROUND: Ectopic varices are uncommon and typically due to underlying liver cirrhosis. They can be located in the duodenum, small intestines, colon or rectum, and may result in massive haemorrhage. While established guidelines exist for the management of oesophageal and gastric variceal bleeding, this is currently lacking for colonic varices. Beta-blockers, transjugular intrahepatic portosystemic shunt insertion and subtotal colectomy have been reported as management methods. However, there are only two other cases that have reported successfully treating colonic varices using balloon-occluded retrograde transvenous obliteration (BRTO), an endovascular procedure typically performed for gastric varices. CASE PRESENTATION: A 55-year-old man with background of alcoholic liver cirrhosis presented with per-rectal bleeding due to caecal varices. Grade 2-3 oesophageal varices were identified on oesophago-gastro-duodenoscopy, and computed tomography showed multiple right para-colic portosystemic collaterals around the hepatic flexure and ascending colon. Colonoscopy confirmed fresh blood in the colon up to the caecum, with a submucosal varix deemed the most likely source of haemorrhage. As transjugular intrahepatic portosystemic shunt insertion was potentially technically difficult, due to left portal vein thrombosis and a small right portal venous system, he underwent BRTO, which successfully embolised and thrombosed the colonic varices without complications. CONCLUSIONS: Whilst further studies are required to conclude its effectiveness and efficacy, BRTO may be considered a viable solution in managing ectopic, colonic, variceal haemorrhage especially when traditional techniques are unsuccessful or contraindicated.

Tract sealing with normal saline after percutaneous transthoracic lung biopsies.

INTRODUCTION: In the present study, we aimed to assess whether normal saline injection for sealing the biopsy track is useful in reducing the incidence of pneumothorax after computed tomography (CT)-guided percutaneous transthoracic lung biopsy (PTLB). METHODS: We retrospectively compared the incidence of pneumothorax in 100 consecutive biopsies (n = 100, group A) that had injection of saline along the track, with historical cohort of same number of consecutive patients who underwent PTLB without injection of saline along the needle track (n = 100, group B). CT-guided biopsies were performed by coaxial technique and 1-3 ml of saline was injected along the tract. Patient chjmirocteristics, lesion size, location and other baseline pjmirometers were compared. Incidence of pneumothorax and number of patients who underwent catheter drainage of pneumothorax was compared in both groups. RESULTS: Baseline chjmirocteristics were compjmiroble in both groups. Track sealing with saline was successful in all patients. Pneumothorax rate was 46% for patients in group B and 32% in group A (P < 0.05). Seven patients (7%) had insertion of chest drain for pneumothorax in the group B and only 1% in the group A (P < 0.05). No mortality was observed in both groups. No complications were observed in any of the patients due to saline injection. CONCLUSION: Track sealing with saline is a simple and safe technique which significantly reduces the incidence of pneumothorax and chest tube insertion after PTLB.

Synergetic effects of thymoquinone-loaded porous PVPylated Fe3O4 nanostructures for efficient pH-dependent drug release and anticancer potential against triple-negative cancer cells.

Porous iron oxide nanostructures have attracted increasing attention due to their potential biomedical applications as nanocarriers for cancer and many other therapies as well as minimal toxicity. Herbal anti-cancer agent thymoquinone loaded on Fe3O4 nanoparticles is envisaged to offer solution towards cancer treatment. The purpose of the present study was to investigate the efficacy of thymoquinone-loaded PVPylated Fe3O4 magnetic nanoparticles (TQ-PVP-Fe3O4 NPs) against triple-negative breast cancer (TNBC) cells. The porous PVPylated Fe3O4 NPs were prepared by a simple solvothermal process, whereas the thymoquinone drug was loaded via the nanoprecipitation method. Fourier transform infrared (FTIR) spectroscopic analysis confirmed the molecular drug loading, and surface morphological observation further confirmed this. The quantity of thymoquinone adsorbed onto the porous PVPylated Fe3O4 NPs was studied by thermogravimetric analysis (TGA). The positive surface charge of TQ-PVP-Fe3O4 NPs facilitates the interaction of the NPs with cancer (MDA-MB-231) cells to enhance the biological functions. In addition, the anticancer potential of NPs involving cytotoxicity, apoptosis induction, reactive oxygen species (ROS) generation, and changes in the mitochondrial membrane potential (ΔΨ m) of TNBC cells was evaluated. TQ-PVP-Fe3O4 NP-treated cells effectively increased the ROS levels leading to cellular apoptosis. The study shows that the synthesized TQ-PVP-Fe3O4 NPs display pH-dependent drug release in the cellular environment to induce apoptosis-related cell death in TNBC cells. Hence, the prepared TQ-PVP-Fe3O4 NPs may be a suitable drug formulation for anticancer therapy.

Usefulness of ultrasonography in diagnosis, percutaneous management and follow up of post-traumatic scalp pseudoaneurysms.

Pseudoaneurysms of the scalp are rare. Most common etiology is trauma. The patients usually present clinically with persistent painful swelling in the scalp few days after the trauma. The lesion may or may not be pulsatile clinically. Ultrasonography (US) is the best modality to assess these pseudoaneurysms. It not only helps in the diagnosis, but also to trace the offending arterial branch and helps in treatment. We present two cases of post-traumatic scalp pseudoaneurysms which were diagnosed with US and were managed by US-guided thrombin injection. Follow up US showed complete resolution. We highlight the importance of US scan in diagnosis, management, and follow up of scalp pseudoaneurysms.