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Talukdar J, Karmakar A, Dhar R, Kumar A, Karmakar S. Non Government Organizations (NGO)-The gap fillers during COVID-19 lockdown in Assam, India. ASIAN JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.3126/ajms.v12i6.36488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
COVID-19 pandemic caused due to SARS-CoV2 has disrupted the spectrum of health care. The wide arrays of supportive and palliative care needed for patients with ailments were grossly neglected, due to the diversion of resources and healthcare professionals in COVID management. This deficiency was further exaggerated by extended lockdown and closure of outdoor patient care services resulting in unprecedented crisis in disease management. Further, COVID-19 has been associated with increased risk of morbidity and mortality arising from associated risk factors in geriatric subjects and those with other high risk co-morbidities like hypertension, COPD, diabetes and cancer. North East Indian states and the adjoining regions seem to have suffered substantially during the COVID-19 crisis due to their pre-existing vulnerabilities and under developed health care infrastructure and logistics. This deficiency, however, seems to have been fulfilled substantially by the participation of NGO (Non-Government Organizations) and other volunteer services who has actively participated to provide basic healthcare and other life support to cancer patients in this crisis.
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Jee B, Dhar R, Singh S, Karmakar S. Heat Shock Proteins and Their Role in Pregnancy: Redefining the Function of "Old Rum in a New Bottle". Front Cell Dev Biol 2021; 9:648463. [PMID: 33996811 PMCID: PMC8116900 DOI: 10.3389/fcell.2021.648463] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Pregnancy in humans is a multi-step complex physiological process comprising three discrete events, decidualization, implantation and placentation. Its overall success depends on the incremental advantage that each of the preceding stages passes on to the next. The success of these synchronized sequels of events is an outcome of timely coordination between them. The pregnancy events are coordinated and governed primarily by the ovarian steroid hormones, estrogen and progesterone, which are essentially ligand-activated transcription factors. It's well known that intercellular signaling of steroid hormones engages a plethora of adapter proteins that participate in executing the biological functions. This involves binding of the hormone receptor complex to the DNA response elements in a sequence specific manner. Working with Drosophila melanogaster, the heat shock proteins (HSPs) were originally described by Ferruccio Ritossa back in the early 1960s. Over the years, there has been considerable advancement of our understanding of these conserved families of proteins, particularly in pregnancy. Accumulating evidence suggests that endometrial and uterine cells have an abundance of HSP27, HSP60, HSP70 and HSP90, implying their possible involvement during the pregnancy process. HSPs have been found to be associated with decidualization, implantation and placentation, with their dysregulation associated with implantation failure, pregnancy loss and other feto-maternal complications. Furthermore, HSP is also associated with stress response, specifically in modulating the ER stress, a critical determinant for reproductive success. Recent advances suggest a therapeutic role of HSPs proteins in improving the pregnancy outcome. In this review, we summarized our latest understanding of the role of different members of the HSP families during pregnancy and associated complications based on experimental and clinical evidences, thereby redefining and exploring their novel function with new perspective, beyond their prototype role as molecular chaperones.
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Jindal SK, Aggarwal AN, Jindal A, Talwar D, Dhar R, Singh N, Singh V, Krishnaswamy UM, Chetambath R, Nath A, Bhattacharya P, Chaudhary D, Gupta PR, Gupta ML, Koul P, Swarankar R, Kant S, Ghoshal A. COPD exacerbation rates are higher in non-smoker patients in India. Int J Tuberc Lung Dis 2021; 24:1272-1278. [PMID: 33317671 DOI: 10.5588/ijtld.20.0253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is common among non-smokers exposed to solid fuel combustion at home. Different clinical characteristics in these patients may have significant therapeutic and prognostic implications.METHODS: We used medical record review and a questionnaire among COPD patients at 15 centres across India to capture data on demographic details, different types of exposures and clinical characteristics. Chest radiography and pulmonary function testing were performed in all 1984 cases; C-reactive protein and exhaled breath nitric oxide were measured wherever available.RESULTS: There were 1388 current or ex-smokers and 596 (30.0%) non-smokers who included 259 (43.5%) male and 337 (56.5%) female patients. Sputum production was significantly more common in smokers with COPD (P < 0.05). The frequency of acute symptomatic worsening, emergency visits and hospitalisation were significantly higher (P < 0.05) in non-smokers with COPD; however, intensive care unit admissions were similar in the two groups. There was no significant difference with respect to the use of bronchodilators, inhalational steroids or home nebulisation among smoker and non-smoker patients. The mean predicted forced expiratory volume in 1 sec in smokers (43.1%) was significantly lower than in non-smokers (46.5%).CONCLUSION: Non-smoker COPD, more commonly observed in women exposed to biomass fuels, was characterised by higher rate of exacerbations and higher healthcare resource utilisation.
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Dhar R, Jee B, Karmakar S. Balancing Healthcare and Economy Amidst the COVID-19 Pandemic: An Indian Experience. Risk Manag Healthc Policy 2021; 14:827-833. [PMID: 33664604 PMCID: PMC7924119 DOI: 10.2147/rmhp.s291084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/27/2021] [Indexed: 11/23/2022] Open
Abstract
With its 1.3 billion population and faced with the COVID-19 pandemic, India is at the junction of two crucial decisions, balancing healthcare and the economy. To prevent the community spread of the virus, the Indian Government imposed a nationwide lockdown. Though initially successful to some extent in containing the disease spread, the extended lockdown eventually leads to a spiraling out effect resulting in the slowdown of the economy, which, in turn, lead to widespread consequences affecting the lives of millions of people, mostly those at the base of the social pyramid. We investigated the implications of few government policies taken during this pandemic and their impact on society, thereby suggesting short-term crisis management with long-term solutions. Here, we present a comprehensive account of Indian policy in dealing with the COVID-19 crisis, balancing both economic and public health. We also explored a future contingency plan for risk mitigation along with few recommendations. This viewpoint will be useful for effective healthcare management and the economy in Asia's populous nation in the COVID-19 and prepare for a future crisis of this nature.
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Chattopadhyay I, Dhar R, Pethusamy K, Seethy A, Srivastava T, Sah R, Sharma J, Karmakar S. Exploring the Role of Gut Microbiome in Colon Cancer. Appl Biochem Biotechnol 2021; 193:1780-1799. [PMID: 33492552 DOI: 10.1007/s12010-021-03498-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Dysbiosis of the gut microbiome has been associated with the development of colorectal cancer (CRC). Gut microbiota is involved in the metabolic transformations of dietary components into oncometabolites and tumor-suppressive metabolites that in turn affect CRC development. In a healthy colon, the major of microbial metabolism is saccharolytic fermentation pathways. The alpha-bug hypothesis suggested that oncogenic bacteria such as enterotoxigenic Bacteroides fragilis (ETBF) induce the development of CRC through direct interactions with colonic epithelial cells and alterations of microbiota composition at the colorectal site. Escherichia coli, E. faecalis, F. nucleatum, and Streptococcus gallolyticus showed higher abundance whereas Bifidobacterium, Clostridium, Faecalibacterium, and Roseburia showed reduced abundance in CRC patients. The alterations of gut microbiota may be used as potential therapeutic approaches to prevent or treat CRC. Probiotics such as Lactobacillus and Bifidobacterium inhibit the growth of CRC through inhibiting inflammation and angiogenesis and enhancing the function of the intestinal barrier through the secretion of short-chain fatty acids (SCFAs). Crosstalk between lifestyle, host genetics, and gut microbiota is well documented in the prevention and treatment of CRC. Future studies are required to understand the interaction between gut microbiota and host to the influence and prevention of CRC. However, a better understanding of bacterial dysbiosis in the heterogeneity of CRC tumors should also be considered. Metatranscriptomic and metaproteomic studies are considered a powerful omic tool to understand the anti-cancer properties of certain bacterial strains. The clinical benefits of probiotics in the CRC context remain to be determined. Metagenomic approaches along with metabolomics and immunology will open a new avenue for the treatment of CRC shortly. Dietary interventions may be suitable to modulate the growth of beneficial microbiota in the gut.
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Pethusamy K, Seethy AA, Kulandhasamy M, Garg P, Chowdhury D, Agarwal S, Kumar A, Dhar R, Karmakar S. Effects of 469 E/K polymorphism of ICAM1 gene in ischemic stroke and its association with stroke severity and outcome. ASIAN JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.3126/ajms.v12i1.30985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: Stroke is the second leading cause of death globally and it is a major cause of long-term, physical, psychological, and social disability among the elderly. Increasing evidence shows that ischemic injury and inflammation account for its pathogenic progression. So, we studied the association of Intercellular Adhesion Molecule 1 (ICAM1) polymorphism with ischemic stroke, stroke severity, and outcome.
Aims and Objectives: To compare ICAM1 469 E/K polymorphism in ischemic stroke patients with healthy controls, and to study its association with stroke severity and outcome.
Materials and Methods: Fifty patients of ischemic stroke and hundred healthy individuals were included. The stroke severity was assessed clinically and radiologically. Outcome was measured at three and six months of stroke onset. Genomic DNA was used for Allele-Specific PCR to detect ICAM1 469 E/K polymorphism. The subjects were categorized into EE, EK, and KK genotypes.
Results: The odds of EK genotype to develop stroke was 0.41 (95 % CI; 0.17 - 0.92) (p = 0.07) and of KK genotype was 0.41 (95 % CI; 0.11 - 0.87) (p = 0.04) compared to EE genotype. Subjects with ICAM1K allele had significantly reduced risk of stroke compared with those with E allele. (RR: 0.55; 95% CI: 0.35-0.87) (p=0.03).
Conclusion: Subjects with ICAM1K allele had significantly reduced the risk of developing stroke. 469 E/K polymorphism of the ICAM1 gene does not significantly affect stroke severity, mortality, and outcome.
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Dhar R, Singh S, Mukherjee I, Pethusamy K, Purkayastha K, Das P, Sharma JB, Shyam Sharma R, Karmakar S. EMTiness in pseudo-malignant behavior of trophoblasts during embryo implantation. Front Biosci (Landmark Ed) 2021; 26:717-743. [PMID: 33049691 DOI: 10.2741/4915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Implantation in humans is a multistep process that involves apposition, adhesion, and invasion of the developing blastocyst into the receptive maternal endometrium. Though significant volume of research in this direction has identified important players orchestrating this delicate process, there are still gaps in our understanding of all the sequence of events during embryo implantation. Also, the early pregnancy-related complications that lead to fetal loss and miscarriage often occur in this critical window of implantation, which is primarily defined as the time when the maternal endometrium is supposed to be most receptive to the free blastocyst that emerges out from the zona pellucida. Studies in humans and rodents have identified several mediators like folliculin, LIF, IL11Ra, splicing factor SC35, etc. to be essential for early implantation. Trophoblasts, that form the outer epithelial layer of the blastocyst, participate in the formation of the placenta. During placentation, invasive extravillous trophoblasts (EVTs), migrate into the endometrium, and a transient epithelial to mesenchymal transition (EMT) and remodel the uterine arteries for blood and nutrient exchange.
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Dhar R, Jee B, Pethusamy K, Seethy A, Kumar A, Karmakar S. The scars of COVID19: Preparing for the collateral damages. ASIAN JOURNAL OF MEDICAL SCIENCES 2020. [DOI: 10.3126/ajms.v11i6.30660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
COVID-19 is a pandemic of disproportionate magnitude. Its devastating effect seems to have a more significant impact on the emerging economies like India and the rest of SE Asia, which also has regions harbouring some of the world's highest population density living under poor socio-economic condition. What seems to have originated from one just one province in China, rapidly speard like wildfire across international territories, affecting millions and crippling the health care system. After about eight months into COVID-19, we realized that the fallout is not only humongous but also stretched across multiple avenues of the society and different aspects of our life. The scars of COVID-19 are much more than the virus itself. With a global shutdown in business and financial institutions, the economy is in free fall. Markets plummeted, stocks crashed and unemployment numbers skyrocketed. Apart from the economy, COVID-19 related shutdown has a tremendous impact on the healthcare system for those with preventable ailments, which were either compromised or delayed affecting millions who need hospitalization for non-COVID causes. COVID crisis also seems responsible for the emergence of a new culture system and mindset that was unprecedented before. With schools and other academic institutions closed, online teaching through electronic media and work from home became the new normal. In this editorial, we summarized the collateral damage on society, economy, and human health in the COVID crisis and few suggestions to chalk out a new plan and strategy to address the challenges for a future episode of similar nature. Though we could still remain vulnerable against similar contagious agents, an advanced planning strategy and preparedness will surely help us better in effective damage control and risk mitigation, not only to reduce mortality, but also from economic downfall.
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Seethy AA, Singh S, Mukherjee I, Pethusamy K, Purkayastha K, Sharma JB, Sharma RS, Dhar R, Karmakar S. Potential SARS-CoV-2 interactions with proteins involved in trophoblast functions - An in-silico study. Placenta 2020; 103:141-151. [PMID: 33126048 PMCID: PMC7581362 DOI: 10.1016/j.placenta.2020.10.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/29/2020] [Accepted: 10/22/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Though a large number of pregnant females have been affected by COVID-19, there is a dearth of information on the effects of SARS-CoV-2 infection on trophoblast function. We explored in silico, the potential interactions between SARS-CoV-2 proteins and proteins involved in the key functions of placenta. METHODS Human proteins interacting with SARS-CoV-2 proteins were identified by Gordon et al. (2020). Genes that are upregulated in trophoblast sub-types and stages were obtained by gene-expression data from NCBI-GEO and by text-mining. Genes altered in pathological states like pre-eclampsia and gestational diabetes mellitus were also identified. Genes crucial in placental functions thus identified were compared to the SARS-CoV-2 interactome for overlaps. Proteins recurring across multiple study scenarios were analyzed using text mining and network analysis for their biological functions. RESULTS The entry receptors for SARS-CoV-2 - ACE2 and TMPRSS2 are expressed in placenta. Other proteins that interact with SARS-CoV-2 like LOX, Fibulins-2 and 5, NUP98, GDF15, RBX1, CUL3, HMOX1, PLAT, MFGE8, and MRPs are vital in placental functions like trophoblast invasion and migration, syncytium formation, differentiation, and implantation. TLE3, expressed across first trimester placental tissues and cell lines, is involved in formation of placental vasculature, and is important in SARS-CoV (2003) budding and exit from the cells by COPI vesicles. CONCLUSION SARS-CoV-2 can potentially interact with proteins having crucial roles in the placental function. Whether these potential interactions identified in silico have effects on trophoblast functions in biological settings needs to be addressed by further in vitro and clinical studies.
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Karmakar S, Dhar R, Purkayastha K, Seth R, Karmakar S. Abstract 3127: To investigate the role of BRAF V600E co-occurring mutations in Langerhans cell histiocytosis (LCH). Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
a. Introduction :
Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia caused by alterations of several genes in the MAPKinase pathway. The cell of origin is a white blood cell known as a dendritic cell priviously called as histiocyte characterized by a unique cytoplasmic organelle, the Birbeck granule, and the expression of CD1a and class II major histocompatibility complex molecules . The mutations cause these dendritic cells to attract other white blood cells and cause a “lesion” in any organ of the body. LCH has multi-orgnan involvement affecting skin bones, lymph nodes, brain etc. Systemic symptoms may include fever, bone pain, weight loss, jaundice, diabetes insipidus.
b. Description:
LCH is a rare sporadic, non-hereditary and non-malignant disease with unknown etiology characterized with a clonal proliferation of pathologic cells.Recent discovery of recurrent somatic mutations, BRAFV600E in MAPK pathway genes at critical stages of myeloid hematopoietic differentiation in LCH patients supports redefinition of the disease as a myeloproliferative disorder and provides opportunities to develop novel approaches to diagnosis and therapy. In the present proposal, we intend to analyze the BRAFV600E status along with other co-occurring mutations in a cohort of pediatric LCH patients by DNA sequencing in bone marrow samples or Peripheral Blood. Additionally we approach the above unanswered questions by applying an improved machine learning approach for classification and defining an algorithm for disease into different clusters for immediate clinical implication and to address its clinical heterogeneity.
c. Results :
We screened about 5 LCH patients and performed tageted exome seq to asertain the mutational profile of these patients. Sequencing detected BRAF V600E mutation in 3 of 5 samples for a mutation frequency of 60%. IHC based immunofloroscence shows that the intensity of phospho-MEK and phospho-ERK staining shows no significant alterations samples with mutation in BRAF. We are currently investigating mutations in other members of MAK pathways
d. Conclusion :
BRAF-V600E mutations were detected in few of our LCH patients. Neverless seeing the disease heterogeneity, we expect additionall mutations. More studies are needed to investigate mutations in the MAPK pathways that could efffect the course of disease management.We further plan to integrate the clinical and genomic findings to design a predictive model for the disease outcome.
Citation Format: Subhradip Karmakar, R Dhar, K Purkayastha, R Seth, S Karmakar. To investigate the role of BRAF V600E co-occurring mutations in Langerhans cell histiocytosis (LCH) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3127.
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Jindal SK, Aggarwal AN, Christopher DJ, Dhar R, Jindal A. Face masks - a sustainable measure to mitigate COVID-19. Int J Tuberc Lung Dis 2020; 24:645-647. [PMID: 32552995 DOI: 10.5588/ijtld.20.0220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Marklin G, O'Sullivan C, Dhar R. Prone Ventilation in Brain-Dead Organ Donors Acutely Increases Oxygenation and Results in More Lungs Transplanted. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Musbahi A, Abdulhannan P, Bhatti J, Dhar R, Rao M, Gopinath B. Outcomes and risk factors of cholecystectomy in high risk patients: A case series. Ann Med Surg (Lond) 2020; 50:35-40. [PMID: 31956409 PMCID: PMC6956681 DOI: 10.1016/j.amsu.2019.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 01/11/2023] Open
Abstract
Introduction Many studies looked at outcomes and risk factors in laparoscopic cholecystectomies in general, including a few studies on risk factors and scoring systems in predicting conversion to open surgery. Little data has been produced on high-risk patients undergoing cholecystectomy. Identifying risk factors in this group could help stratify decision making regarding best management strategies. The aim of this study was to investigate outcomes of laparoscopic cholecystectomies in patients with ASA 3 and 4. Methods Data was collected and collated from a prospectively maintained database of all laparoscopic cholecystectomies performed by 13 general surgeons in a single unit. Case notes were reviewed for all patients with ASA 3 and 4 between 2013 and 2017. Data analysis was performed using R studio v 3.4. Results 244 cases were reviewed. Common bile duct was dilated in 52 cases (21.31%). Gall bladder wall was thick in 102 (41.8%) of the patients. Surgery was elective in 203 (83.2%) of the patients. ERCP was performed in 41 (16.9%) of the patients prior to surgery. 150 patients (62.2%) stayed for 1 day while 36 (14.9%) stayed for 2 days and the remaining 55 (22.9%) stayed for 3 days or more. Complications occurred in 37 (15.16%) of the patients while 23 (9.43%) of the patients were readmitted. 7 patients (2.87%) returned to theatre and 8 (3.28%) stayed in ITU post-op. Two patients died (0.82%). Conclusion Laparoscopic cholecystectomies in higher risk populations are safe. Alternative methods such as cholecystostomy and ERCP may be of benefit in these patients. Gallstone disease represents a significant volume of elective and emergency work in the United Kingdom. The primary aim of the study was to explore the factors that lead to complications in high risk patients (ASA 3-4). Histological gallbladder thickness and emergency surgery were the factors most strongly associated with negative outcomes. Age greater than 65 as an independent variable does not lead to an increase in negative outcomes. Cholecystectomy is a relatively safe procedure in what is typically considered higher risk patients.
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Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, Srivastava T, Sarkar S, Mandal V, Karmakar M, Gupta S, Ghosh A, Karmakar S. Draft genome of Ompok bimaculatus (Pabda fish). BMC Res Notes 2019; 12:825. [PMID: 31878964 PMCID: PMC6933649 DOI: 10.1186/s13104-019-4867-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/19/2019] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Pabda (Ompok bimaculatus) is a freshwater catfish, largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. This fish is highly valued for its fabulous taste and high nutritional value and is very popular as a rich source of proteins, omega-3 and omega-6 fatty acids, vitamins and mineral for growing children, pregnant females and elders. We performed de-novo sequencing of Ompok bimaculatus using a hybrid approach and present here a draft assembly for this species for the first time. DATA DESCRIPTION The genome of Ompok bimaculatus (Fig. 1: Table 1, Data file 3) from Ganges river, has been sequenced by hybrid approach using Illumina short reads and PacBio long reads followed by structural annotations. The draft genome assembly was found to be 718 Mb with N50 size of 81 kb. MAKER gene annotation tool predicted 21,371 genes.
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Yadav N, Swaminathan V, Panov VP, Dhar R, Vij JK. Elucidation of the de Vries behavior in terms of the orientational order parameter, apparent tilt angle, and field-induced tilt angle for smectic liquid crystals by polarized infrared spectroscopy. Phys Rev E 2019; 100:052704. [PMID: 31870006 DOI: 10.1103/physreve.100.052704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Indexed: 11/07/2022]
Abstract
We report experimental results of the orientational order parameter, the apparent tilt angle, and the field-induced tilt angle for three chiral smectic liquid crystalline materials investigated using infrared (IR) polarized spectroscopy. The common feature in these materials is use of the core 5-methyl-2- pyrimidine benzoate as the central part of the mesogen. This core is terminated by siloxane or carbosilane chains on one of the ends and by the chiral alkoxy chains on the opposite. These compounds exhibit low concomitant layer shrinkage at the smectic A^{*} (SmA^{*}) to smectic C^{*} (SmC^{*}) transition temperature and within the SmC^{*} phase itself. The maximum layer shrinkage in SmC^{*} is observed as ∼1.5%. We calculate the apparent orientational order parameter, S_{app} in the laboratory reference frame from the observed IR absorbance for homeotropic aligned samples, and the true order parameter, S, is calculated using the measured tilt angle and is also interpolated from Iso-SmA^{*} transition temperature closer to SmC^{*} phase. The apparent tilt angle in the SmA^{*} phase calculated from a comparison of order parameters S and S_{app} is found to be significantly large. A low magnitude of S_{app} found for homeotropic aligned samples in the SmA^{*} phase indicates that the order parameter plays a vital role in determining the de Vries characteristics, especially of exhibiting larger apparent tilt angles. Furthermore there is a significant increase in the true order parameter at temperatures close to SmA^{*} to SmC^{*} transition temperature in all three compounds. The planar-aligned samples are used to study the dependence of induced tilt angle on the applied electric field. The generalized Langevin-Debye model given by Shen et al. reasonably fits the experimental data on the field-induced tilt angle. The results show that the dipole moment of the tilt correlated domain in SmA^{*} diverges as temperature is lowered to the SmA^{*}-SmC^{*} transition temperature. The generalized Langevin-Debye model is also found to be extremely effective in confirming some of the conclusions of the de Vries behavior.
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Dhar R, Seethy A, Pethusamy K, Singh S, Rohil V, Purkayastha K, Mukherjee I, Goswami S, Singh R, Raj A, Srivastava T, Acharya S, Rajashekhar B, Karmakar S. De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. Gigascience 2019; 8:5488106. [PMID: 31077316 PMCID: PMC6511069 DOI: 10.1093/gigascience/giz038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/30/2018] [Accepted: 03/18/2019] [Indexed: 01/23/2023] Open
Abstract
Background The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford Nanopore technology (ONT). Results ONT sequencing gave ∼2.3-fold sequencing coverage, whereas Illumina generated 150–base pair paired-end sequence data at 284.6-fold coverage from 5 libraries. Subsequently, we generated a 0.915-gigabase pair de novo assembly of the peacock genome with a scaffold N50 of 0.23 megabase pairs (Mb). We predict that the peacock genome contains 23,153 protein-coding genes and 75.3 Mb (7.33%) of repetitive sequences. Conclusions We report a high-quality assembly of the peacock genome using a hybrid approach of sequences generated by both Illumina and ONT. The long-read chemistry generated by ONT was useful for addressing challenges related to de novo assembly, particularly at regions containing repetitive sequences spanning longer than the read length, and which could not be resolved with only short-read–based assembly. Contig assembly of Illumina short reads gave an N50 of 1,639 bases, whereas with ONT, the N50 increased by >9-fold to 14,749 bases. The initial contig assembly based on Illumina sequencing reads alone gave 685,241 contigs. Further scaffolding on assembled contigs using both Illumina and ONT sequencing reads resulted in a final assembly of 15,025 super-scaffolds, with an N50 of ∼0.23 Mb. Ninety-five percent of proteins predicted by homology matched with those in a public repository, verifying the completeness of our assembly. Like other phylogenetic studies of avian conserved genes, we found P. cristatus to be most closely related to Gallus gallus, followed by Meleagris gallopavo and Anas platyrhynchos. Compared with the recently published peacock genome assembly, the current, superior, hybrid assembly has greater sequencing depth, fewer non-ATGC sequences, and fewer scaffolds.
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Dhar R, Rath GK, Karmakar S. FBXO4 as a novel ubiquitin ligase that targets Cyclin D in the pathogenesis of breast cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14722 Background: Members of ubiquitin ligase family are reported to be associated with cancer. Genome wide RNAi screen using Dharmacon on target Plus RNAi library identified FBXO4 as one of the potential hit . We therefore aimed to study its detailed role on proliferation of MCF7 breast cancer cells with special focus on cell cycle genes. We want to expand it further and study its involvement in context to E2 signaling in breast cancer. We hypothesized that increase in CCND1 expression, could mimic some of the E2 transcriptional regulation and that CCND1 overexpression could lead to E2 independent ER alpha binding to estrogen response element (ERE). Methods: Cell lines: MCF7 grown in MEM alpha supplemented with 10% FBS . For stimulation studies, cells were maintained in phenol free MEM alpha supplemented with 10% FBS and 10 nM estradiol. RNAi knockdown studies: On-target plus siRNA were used to knockdown FBXO4 in MCF7 cells. Western Blot: Western Blot was performed following standard protocols. IHC/Tissue Array: Paraffin embedded malignant breast cancer (ER/PR/EGFR +ve) tissue samples that are scored by pathologist were used for the study. Gene Expression Studies: Microarray and NGS based approach. Results: FBXO4 has been identified as a potential hit in our RNAi screen showing a hyper-proliferative phenotype in MCF7 cellsupon its knockdown. Western blot and ubiquitination assay identified cyclin D (CCND1) as a dedicated FBXO4 target as revealed by confocal microscopy where FBXO4 knockdown showed an enrichment of CCND1 in cytoplasm. Ingenuity pathway analysis and ChIP assay revealed an exploitation of E2 signaling and enhanced recruitment of ER alpha to estrogen response element (ERE) in FBXO4 depleted cells. CCND1 further seems to co-occupy ESR binding motifs thereby representing ER functions. These effects were observed even in absence of any E2 stimulation. Further we observed a significant overlap of differentially expressed genes in E2 stimulated and FBXO4 knockdown cells that were nullified by CCND1 siRNA. Conclusions: Our study elucidated that CCND1 is spared from degradation following loss of FBXO4 which in turn leads to a hyper-proliferative state. Our findings co-related with TCGA and METABRIC databases indicating a poor patient survival and relapse in FBXO4 low and CCND1 high cohorts of ER +ve breast cancer thereby implying a diagnostic value. Along with traditional hormonal therapy, an effective targeted therapy in breast cancer should be aimed to restore FBXO4 levels.
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Koul P, Chaudhari S, Chokhani R, Christopher D, Dhar R, Doshi K, Ghoshal A, Luhadiya SK, Mahashur A, Mehta R, Nene A, Rahman M, Swarnakar R. Pneumococcal disease burden from an Indian perspective : Need for its prevention in pulmonology practice. Lung India 2019. [DOI: 10.4103/0970-2113.257714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Alfouzan W, Dhar R, Nicolau D. In vitro activity of newer and conventional antimicrobial agents, including fosfomycin and colistin, against selected gram-negative bacilli in Kuwait. J Infect Public Health 2019. [DOI: 10.1016/j.jiph.2018.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Dhar R, AlFouzan W, Sheikh S, Recalde G. Candida growth in urine cultures: contemporary analysis of species and current trends in antifungal susceptibility in a general hospital in Kuwait. J Infect Public Health 2019. [DOI: 10.1016/j.jiph.2018.10.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Dhar R, Paramesh A, Marklin G. A Randomized Controlled Trial of Naloxone for Optimization of Hypoxemia in Lung Donors. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Singh U, Singh D, Kumar S, Dhar R, Pandey M. The optical properties of quantum dots in anisotropic media. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yadav N, Panov VP, Swaminathan V, Sreenilayam SP, Vij JK, Perova TS, Dhar R, Panov A, Rodriguez-Lojo D, Stevenson PJ. Chiral smectic-A and smectic-C phases with de Vries characteristics. Phys Rev E 2017; 95:062704. [PMID: 28709233 DOI: 10.1103/physreve.95.062704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 11/07/2022]
Abstract
Infrared and dielectric spectroscopic techniques are used to investigate the characteristics of two chiral smectics, namely, 1,1,3,3,5,5,5-heptamethyltrisiloxane 1-[4^{'}-(undecyl-1-oxy)-4-biphenyl(S,S)-2-chloro-3-methylpentanoate] (MSi_{3}MR_{11}) and tricarbosilane-hexyloxy-benzoic acid (S)-4'-(1-methyl-hexyloxy)-3'-nitro-biphenyl-4-yl ester (W599). The orientational features and the field dependencies of the apparent tilt angle and the dichroic ratio for homogeneous planar-aligned samples were calculated from the absorbance profiles obtained at different temperatures especially in the smectic-A* phase of these liquid crystals. The dichroic ratios of the C-C phenyl ring stretching vibrations were considered for the determination of the tilt angle at different temperatures and different voltages. The low values of the order parameter obtained with and without an electric field applied across the cell in the Sm-A^{*} phase for both smectics are consistent with the de Vries concept. The generalized Langevin-Debye model introduced in the literature for explaining the electro-optical response has been applied to the results from infrared spectroscopy. The results show that the dipole moment of the tilt-correlated domain diverges as the transition temperature from Sm-A^{*} to Sm-C^{*} is approached. The Debye-Langevin model is found to be extremely effective in confirming some of the conclusions of the de Vries chiral smectics and gives additional results on the order parameter and the dichroic ratio as a function of the field across the cell. Dielectric spectroscopy finds large dipolar fluctuations in the Sm-A^{*} phase for both compounds and again these confirm their de Vries behavior.
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Abstract
Major neurologic morbidity, such as seizures and encephalopathy, complicates 20-30% of organ and stem cell transplantation procedures. The majority of these disorders occur in the early posttransplant period, but recipients remain at risk for opportunistic infections and other nervous system disorders for many years. These long-term risks may be increasing as acute survival increases, and a greater number of "sicker" patients are exposed to long-term immunosuppression. Drug neurotoxicity accounts for a significant proportion of complications, with posterior reversible leukoencephalopathy syndrome, primarily associated with calcineurin inhibitors (i.e., cyclosporine and tacrolimus), being prominent as a cause of seizures and neurologic deficits. A thorough evaluation of any patient who develops neurologic symptoms after transplantation is mandatory, since reversible and treatable conditions could be found, and important prognostic information can be obtained.
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