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Evolutionary divergence of TLR9 through ancestral sequence reconstruction. Immunogenetics 2024; 76:203-211. [PMID: 38441635 DOI: 10.1007/s00251-024-01338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/24/2024] [Indexed: 05/12/2024]
Abstract
The transmembrane pattern recognition receptor, Toll-like receptor (TLR), are best known for their roles in innate immunity via recognition of pathogen and initiation of signaling response. Mammalian TLRs recognize molecular patterns associated with pathogens and initiate innate immune response. We have studied the evolutionary diversity of mammalian TLR genes for differences in immunological response. Reconstruction of ancestral sequences is a key aspect of the molecular evolution of TLR to track changes across the TLR genes. The comprehensive analysis of mammalian TLRs revealed a distinct pattern of evolution of TLR9. Various sequence-based features such as amino acid usage, hydrophobicity, GC content, and evolutionary constraints are found to influence the divergence of TLR9 from other TLRs. Ancestral sequence reconstruction analysis also revealed that the gradual evolution of TLR genes in several ancestral lineages leads to the distinct pattern of TLR9. It demonstrates evolutionary divergence with the progressive accumulation of mutations results in the distinct pattern of TLR9.
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Emerging resistome diversity in clinical Vibrio cholerae strains revealing their role as potential reservoirs of antimicrobial resistance. Mol Biol Rep 2024; 51:409. [PMID: 38461219 DOI: 10.1007/s11033-024-09313-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera. METHODS AND RESULTS Genotyping of representative strains, VC1 and VC2 was undertaken to characterize antimicrobial resistance genes (ARGs) against chloramphenicol, SXT, nalidixic acid and streptomycin against which they were found to be resistant by antibiogram analysis in our previous investigation. strAB, sxt, sul2, qace∆1-sul1 were detected by PCR. Genome annotation and identification of ARGs with WGS helped to detect the presence of almG, varG, strA (APH(3'')-Ib), strB (APH(6)-Id), sul2, catB9, floR, CRP, dfrA1 genes. Signatures of resistance determinants and protein domains involved in antimicrobial resistance, primarily, efflux of antibiotics were identified on the basis of 30-100% homology to reference proteins. These domains were predicted to be involved in other metabolic functions on the basis of 100% identity with 100% coverage with reference protein and nucleotide sequences and were predicted to be of a diverse taxonomic origin accentuating the influence of the microbiota on AMR acquisition. Sequence analysis of QRDR (quinolone resistance-determining region) revealed SNPs. Cytoscape v3.8.2 was employed to analyse protein-protein interaction of MDR proteins, MdtA and EmrD-2, with nodes of vital AMR pathways. Vital nodes involved in efflux of different classes of antibiotics were found to be absent in VC1 and VC2 justifying the sensitivity of these strains to most antibiotics. CONCLUSIONS The study helped to examine the resistome of VC isolated from recent outbreaks to understand the underlying reason of sensitivity to most antibiotics and also to characterize the ARGs in their genome. It revealed that VC is a reservoir of signatures of resistance determinants and serving as precursors for severe AMR crisis in cholera. This is the first study, to our knowledge, which has scrutinized and presented systematically, information on prospective domains which bear the potential of serving as AMR determinants in VC with the help of bioinformatic tools. This pioneering approach may help in the prediction of AMR landfalls and benefit epidemiological surveillance and early warning systems.
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Phylogeny and structural insights of lipase from Halopseudomonas maritima sp. nov., isolated from sea sand. Int Microbiol 2023; 26:1021-1031. [PMID: 37076723 DOI: 10.1007/s10123-023-00362-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
A Gram-negative, aerobic bacterial strain RR6T was isolated from the sea sand to produce lipase and proposed as a novel species of Halopseudomonas. The optimum growth occurred at 28-37 °C, and the pH was 6.0-8.0. The optimum growth occurred at 3.0 -6.5% (w/v) NaCl. The major cellular fatty acids were C10:0 3OH, C12:0, C16:1 ω7c/16:1 ω6c, 18:1 ω7c and/or 18:1 ω6c, and C16:0. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid, and unidentified lipids. The genome is 3.93 Mb, and the G + C content is 61.3%. The 16S rRNA gene sequences shared 99.73-99.87% sequence similarity with the closely related type strains of Halopseudomonas. The average nucleotide identity and average amino acid identity of strain RR6T with reference type strains were below 95-96%, and the corresponding in-silico DNA-DNA hybridization values were below 70%. Strain RR6T clustered with Halopseudomonas gallaeciensis V113T and Halopseudomonas pachastrellae CCUG 46540 T in the phylogenetic tree. Further, lipase produced by this bacterium belongs to α/β hydrolase lipase family and exhibits structural similarity to the lactonizing lipase. Based on the polyphasic analysis, the new isolates RR6T represent a novel species of Halopseudomonas for which Halopseudomonas maritima sp. nov. is proposed. The type strain is RR6T (= NBRC 115418 T = TBRC 15628 T).
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Emergence of Genomic Diversity in the Spike Protein of the "Omicron" Variant. Viruses 2023; 15:2132. [PMID: 37896909 PMCID: PMC10612054 DOI: 10.3390/v15102132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged "Omicron" variant has exhibited rapid transmission and divergence. The spike protein of SARS-CoV-2 has consistently been appearing as the mutational hotspot of all these VOCs. In order to determine a deeper understanding of the recently emerged and extremely divergent "Omicron", a study of amino acid usage patterns and their substitution patterns was performed and compared with those of the other four successful variants of concern ("Alpha", "Beta", "Gamma", and "Delta"). We observed that the amino acid usage of "Omicron" has a distinct pattern that distinguishes it from other VOCs and is significantly correlated with the increased hydrophobicity in spike proteins. We observed an increase in the non-synonymous substitution rate compared with the other four VOCs. Considering the phylogenetic relationship, we hypothesized about the functional interdependence between recombination and the mutation rate that might have resulted in a shift in the optimum of the mutation rate for the evolution of the "Omicron" variant. The results suggest that for improved disease prevention and control, more attention should be given to the significant genetic differentiation and diversity of newly emerging variants.
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Psychological Impacts of Retained Bullets From the Perspective of Survivors. Am Surg 2023; 89:3732-3738. [PMID: 37148273 PMCID: PMC10725717 DOI: 10.1177/00031348231171121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
INTRODUCTION Despite a high prevalence of retained bullet fragments (RBFs) after firearm related injury (FRI) there is limited data on the full spectrum of their consequences, particularly the psychological impacts on those injured. Further, the experiences of FRI survivors with RBFs are missing from existing literature. The objective of this study was to explore the psychological impacts of RBFs on individuals who have experienced recent FRI. METHODS Adult (18-65 years) survivors of FRI with radiographically confirmed RBFs were purposively selected from an urban Level 1 trauma center in Atlanta, Georgia, to participate in an in-depth interview. Interviews were conducted between March 2019 and February 2020. Thematic analysis was used to identify a range of psychological effects from RBFs. RESULTS Interviews from 24 FRI survivors were analyzed: the majority of participants were Black males (N = 22, 92%) with a mean age of 32 years whose FRI occurred ∼8.6 months prior to data collection. The psychological effects of RBFs were grouped into four categories: physical health (eg, pain, limited mobility), emotional well-being (eg, anger, fear), social isolation, and occupational welfare (eg, disability leading to inability to work). A range of coping mechanisms were also identified. CONCLUSION Survivors of FRI with RBFs experience a range of psychological impacts that are far-reaching and affect daily activities, mobility, pain and emotional wellbeing. Study results indicate a need for enhanced resources to support those with RBFs. Further, changes to clinical protocols are warranted on removal of RBFs and communication about the effects of leaving RBFs in situ.
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Laser-direct-drive fusion target design with a high-Z gradient-density pusher shell. Phys Rev E 2023; 108:035209. [PMID: 37849111 DOI: 10.1103/physreve.108.035209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023]
Abstract
Laser-direct-drive fusion target designs with solid deuterium-tritium (DT) fuel, a high-Z gradient-density pusher shell (GDPS), and a Au-coated foam layer have been investigated through both 1D and 2D radiation-hydrodynamic simulations. Compared with conventional low-Z ablators and DT-push-on-DT targets, these GDPS targets possess certain advantages of being instability-resistant implosions that can be high adiabat (α≥8) and low hot-spot and pusher-shell convergence (CR_{hs}≈22 and CR_{PS}≈17), and have a low implosion velocity (v_{imp}<3×10^{7}cm/s). Using symmetric drive with laser energies of 1.9 to 2.5MJ, 1D lilac simulations of these GDPS implosions can result in neutron yields corresponding to ≳50-MJ energy, even with reduced laser absorption due to the cross-beam energy transfer (CBET) effect. Two-dimensional draco simulations show that these GDPS targets can still ignite and deliver neutron yields from 4 to ∼10MJ even if CBET is present, while traditional DT-push-on-DT targets normally fail due to the CBET-induced reduction of ablation pressure. If CBET is mitigated, these GDPS targets are expected to produce neutron yields of >20MJ at a driven laser energy of ∼2MJ. The key factors behind the robust ignition and moderate energy gain of such GDPS implosions are as follows: (1) The high initial density of the high-Z pusher shell can be placed at a very high adiabat while the DT fuel is maintained at a relatively low-entropy state; therefore, such implosions can still provide enough compression ρR>1g/cm^{2} for sufficient confinement; (2) the high-Z layer significantly reduces heat-conduction loss from the hot spot since thermal conductivity scales as ∼1/Z; and (3) possible radiation trapping may offer an additional advantage for reducing energy loss from such high-Z targets.
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153P Molecular epidemiology of EGFR mutations in NSCLC: A single-center experience from India. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00407-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Sorption of long-lived 94Nb on magnetite: spectroscopic and electrochemical investigation of the associated mechanism. J Radioanal Nucl Chem 2023. [DOI: 10.1007/s10967-023-08867-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Development and evaluation of a simple PCR assay and nested PCR for rapid detection of clarithromycin-resistant Helicobacter pylori from culture and directly from the biopsy samples in India. Gut Pathog 2023; 15:7. [PMID: 36782212 PMCID: PMC9925366 DOI: 10.1186/s13099-023-00530-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Eradication of Helicobacter pylori provides the most effective treatment for gastroduodenal diseases caused by H. pylori infection. Clarithromycin, a member of the macrolide family, still remains the most important antibiotic used in H. pylori eradication treatment. But the increasing prevalence of clarithromycin resistant H. pylori strains due to point mutations in the V region of the 23S rRNA, poses a great threat in treating the ailing patients. So, we aimed for PCR-mediated rapid detection of the point mutation at 2143 position of 23S rRNA gene in H. pylori that is relevant to clarithromycin resistance from culture and simultaneously from biopsy specimens to avoid the empirical treatment. RESULTS Newly developed PCR assay using DNA of pure culture detected point mutation in 23S rRNA gene in 21 (8.04%) of 261 clinical strains tested. The agar dilution method showed that all these 21 strains were resistant to clarithromycin indicating the perfect match of the PCR based results. Additionally, the sequencing study also identified the A to G mutation at 2143 position in 23S rRNA gene of the resistant strains only. Consequently, the newly developed Nested-ASP-PCR dealing directly with 50 biopsy specimens demonstrated 100% sensitivity and specificity with the findings of agar dilution method taken as Gold standard. Bioinformatics based analysis such as accessibility analysis and dot plot clearly stated that the base pairing probability has increased due to mutation. Computational studies revealed that the point mutation confers more stability in secondary structure due to conversion of loop to stem. Furthermore, interaction studies showed binding affinity of the CLR to the mutant type is weaker than that to the wild type. CONCLUSION This assay outlines a rapid, sensitive and simple approach to identify point mutation that confers clarithromycin resistance as well as clarithromycin sensitive strains, providing rapid initiation of effective antibiotic treatment. Additionally, it is simple to adopt for hospital based diagnostic laboratories to evaluate the degree of regional clarithromycin resistance from biopsy specimens itself. Furthermore, in silico studies provide evidence or a signal that the prevalence of clarithromycin resistance may rise in the near future as a result of this point mutation.
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P19-15 Epigenetic alterations induced by occupational exposure to hexavalent chromium. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Empathy marketing during COVID-19 pandemic: decoding the impact and effectiveness on the brand image. CARDIOMETRY 2022. [DOI: 10.18137/cardiometry.2022.23.392398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
For brands, empathy can create a customer persona, which can help in effectively targeting their consumers. In terms of marketing, however, it means asking what customers truly value rather than what will sell. Moreover, by creating content that evokes empathy, consumers are more likely to take action – sharing, responding, and even prompting change within their communities. Nevertheless, why are brands suddenly realizing the power of empathy? This is because consumers today are not only interested in passively consuming content. Instead, they actively seek out content that prompts a change in themselves and the world around them. This need of the hour made the brand realize the power of effective communication and hence the rise of empathy as a useful marketing tool. The research used a qualitative approach to understand the effectiveness of Empathy marketing during the pandemic hit time. Focus Group Discussions were conducted to understand the importance and relevance of empathy-based communication. The findings established that this type of communication is useful and helps the consumer create a positive brand image and a recall, but this may not directly impact or lead to a purchase decision.
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Early atherosclerotic cardiovascular disease in high-risk women with polycystic ovary syndrome. Atherosclerosis 2022. [DOI: 10.1016/j.atherosclerosis.2022.06.1007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Natural selection shaped the evolution of amino acid usage in mammalian toll like receptor genes. Comput Biol Chem 2022; 97:107637. [DOI: 10.1016/j.compbiolchem.2022.107637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/09/2021] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
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Lung cancer: Premalignant biology and medical prevention. Semin Oncol 2022; 49:S0093-7754(22)00013-6. [PMID: 35305831 DOI: 10.1053/j.seminoncol.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/08/2022] [Indexed: 11/11/2022]
Abstract
Lung cancer (both adenocarcinoma and squamous cell) progress through a series of pre-malignant histologic changes before the development of invasive disease. Each of these carcinogenic cascades is defined by genetic and epigenetic alterations in pulmonary epithelial cells. Additionally, alterations in the immune response, progenitor cell function, mutational burden, and microenvironmental mediated survival of mutated clones contribute to the risk of pre-malignant lesions progressing to cancer. Medical preventions studies have been completed and current and future trials are informed by the improved understanding of pre-malignancy. This will lead to precision chemoprevention trials based on lesional biology and histologic characteristics.
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Association of adult attachment with delays in accessing specialist care in women with ovarian cancer. J Psychosoc Oncol 2022; 40:491-505. [PMID: 35112658 DOI: 10.1080/07347332.2022.2025510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Advanced stage at diagnosis and delayed presentation are common in ovarian cancer (OC). The objective of the current study was to explore the association of adult attachment pattern with delays in accessing specialist oncology care in patients with OC. METHODS A cross-sectional structured interview study of patients with OC presenting to an Indian cancer center was undertaken. Consenting patients completed Experiences of Close Relationships-Relationship Style questionnaire (ECR-RS) and Medical Outcome Survey-Social Support Survey (MOS-SSS). Multivariate linear regression with "time to presentation to cancer specialist" as the dependent variable was undertaken. RESULTS In all, 132 of 155 (85%) patients with OC who were invited were interviewed. An increased ECR-RS attachment anxiety score (P = .01) and being part of a multigenerational extended household (P = .04) were both independently associated with delay in presentation to a cancer specialist. There was no association between delay in presentation and social support. CONCLUSIONS Among patients with OC, adult attachment may contribute to delays in presentation. It may be important for the cancer symptom awareness efforts in primary care to include educating physicians on recognizing and interacting with patients with insecure attachment styles. The association of delays in presentation for women with OC living in multigenerational extended households needs more indepth exploration. Supplemental data for this article is available online at https://doi.org/10.1080/07347332.2022.2025510 .
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Utilization of thermal neutron induced in-situ chain reactions and the (n,p) reaction with fast neutrons for compositional characterization of lithium titanate. Anal Chim Acta 2022; 1191:339295. [PMID: 35033239 DOI: 10.1016/j.aca.2021.339295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/11/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
A methodology has been developed for the complete compositional characterization of lithium titanate (LTO) using neutron activation, which is quite challenging and no literature report is available so far. The concept of thermal neutron induced in-situ chain reactions 6Li(n,α)3H and 16O(3H,n)18F has been used for the determination of Li and O through the measurement of 18F activity. The method is capable of analyzing Li and O in percentage level as reported in the present analysis of two types of lithium titanate samples. Spectroscopic interference of the elements which can directly or indirectly affect the outcome, were evaluated meticulously. Determination of Ti was carried out using fast neutron activation through the product isotopes like 47Sc, 48Sc, generated via (n,p) nuclear reactions. Fast neutron activation methodology seems to be advantageous for Ti determination over thermal neutron activation, as it offers self validation through different isotopes and multiple gamma lines.
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Journeys: understanding access, affordability and disruptions to cancer care in India. Ecancermedicalscience 2022; 16:1342. [PMID: 35242223 PMCID: PMC8831108 DOI: 10.3332/ecancer.2022.1342] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background Much of the global cancer burden is in low- and middle-income countries (LMICs). Along with the high incidence of cancer, most LMICs have unevenly distributed health care resources. This study is a qualitative exploration of the journey of patients accessing cancer care in India and their caregivers. Methods The study followed a cross-sectional qualitative design. Participants were recruited by stratified purposive sampling, and all common cancers in India as reported by the GLOBOCAN database were included in the study. Consenting patients and their caregivers were interviewed using in-depth interview techniques. The data was analysed using principles of qualitative content analysis. Results Cancer patients (n = 100) and their caregivers (n = 48) were interviewed for the study. The six themes that emerged were related to a) the journey of patients to access care, b) the psychological journey of patients, c) stigma of cancer patients, d) decision-making and adherence to treatment, e) economic costs of cancer care and its impact and f) modifiers to accessing cancer care. Conclusions Planning and policymaking in the future of cancer care delivery need to consider the views expressed by the cancer patients and their caregivers as regards to access, adherence and disruptions to cancer care in India. Future policies will hopefully address some of the difficulties faced by patients.
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'Wine Glass' sign following COVID-19 vaccination in a previously healthy adult. Neurologia 2022; 37:820-823. [PMID: 36468431 PMCID: PMC9609644 DOI: 10.1016/j.nrleng.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/22/2022] [Indexed: 11/07/2022] Open
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Underlying selection for the diversity of spike protein sequences of SARS-CoV-2. IUBMB Life 2021; 74:213-220. [PMID: 34780121 PMCID: PMC8652778 DOI: 10.1002/iub.2577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023]
Abstract
The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present article, we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.
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Interplay of Val66Met and BDNF methylation: effect on reward learning and cognitive performance in major depression. Clin Epigenetics 2021; 13:149. [PMID: 34325733 PMCID: PMC8323304 DOI: 10.1186/s13148-021-01136-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/16/2021] [Indexed: 12/02/2022] Open
Abstract
Background There is a growing interest in the role of brain-derived neurotrophic factor (BDNF) in major depressive disorder (MDD). BDNF potentially exhibits opposite effects in the pathways linked to anhedonia and reward learning on the one hand and cognitive performance, on the other hand. However, the epigenetic mechanisms behind this remain unknown. In the present study, we aimed to investigate the interplay of DNA methylation of different BDNF exons and the common Val66Met polymorphism on anhedonia, reward learning and cognitive performance in MDD. Methods We recruited 80 depressed patients and 58 age- and gender-matched healthy controls. Participants underwent clinical assessment including neuropsychological testing and a probabilistic reward task to assess reward learning. Val66Met polymorphism and DNA methylation of BDNF promoters I, IV and exon IX were assessed from whole blood derived DNA, using pyrosequencing. Results BDNF promoter I methylation was lower in MDD patients (p = 0.042) and was negatively associated with self-reported anhedonia. In depressed patients, both Val66Met polymorphism and DNA methylation of promoter I were significantly associated with reward bias (p < 0.050 and p = 0.040, respectively), without an interaction effect. On the other hand, methylation of exon IX had a negative impact on executive functioning (p = 0.002) and mediated the effect of Val66Met on this outcome in patients with MDD. Conclusions Our results provide the first evidence of Val66Met susceptibility to differential epigenetic regulation of BDNF exons in reward learning and executive functioning in MDD, which needs to be further explored. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01136-z.
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EFFICACY AND SAFETY OF TISAGENLECLEUCEL (TISA‐CEL) IN ADULT PATIENTS (PTS) WITH RELAPSED/REFRACTORY FOLLICULAR LYMPHOMA (R/R FL): PRIMARY ANALYSIS OF THE PHASE 2 ELARA TRIAL. Hematol Oncol 2021. [DOI: 10.1002/hon.85_2879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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PATIENT‐REPORTED QUALITY OF LIFE (QOL) FOLLOWING TISAGENLECLEUCEL (TISA‐CEL) INFUSION IN ADULT PATIENTS (PTS) WITH RELAPSED/REFRACTORY FOLLICULAR LYMPHOMA (R/R FL). Hematol Oncol 2021. [DOI: 10.1002/hon.178_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Liquid Biopsy using “Cell – Free DNA” as Predictive Marker of Response after Radiotherapy in Solid Tumors. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Utilization of unsaponifiable matter from rice bran oil fatty acid distillate for preparing an antioxidant-rich oleogel and evaluation of its properties. GRASAS Y ACEITES 2020. [DOI: 10.3989/gya.0938182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rice bran oil fatty acid distillate (RBOFAD) is an important by-product obtained from the physical refining process. This fatty acid distillate contains high a amount of Unsaponifiable Matter (γ-oryzanol 3.27 gm/100gm UM; total tocopherol 10.93 mg/100 g UM; total phytosterol 21.81 g/100g UM; squalene 1.15 g/100 g UM and total fatty alcohol 73.34 g/100 g UM) and free fatty acids. Antioxidant-rich Oleogels were obtained from rice bran wax (RBW), rice bran oil fatty acid distillate (RBOFAD) and refined rice bran oil. The main objective of this study was to utilize the antioxidant-rich unsaponifiable matter of RBOFAD (UMRBOFAD) as an organogelator along with rice bran wax, which also acts as a good organogelator. Antioxidant-rich oleogel was prepared using UMRBFAD, ethylcellulose (EC) and RBW at 2%, 2%, 3% on weight basis, respectively, in refined rice bran oil and this antioxidant-rich oleogel was compared with rice bran oil oleogel using RBW at 7% on weight basis of rice bran oil. These oleogels were evaluated using a combination of techniques such as differential scanning calorimetry (DSC), polarized light microscopy (PLM), Viscosity, synchrotron radiation X-ray diffraction (SR-XRD) and FTIR Spectroscopy. The differential scanning calorimetry (DSC) measured the thermal properties of rice bran oil oleogel and high antioxidant-rich oleogel. Polarized light microscopy images revealed needle-like crystals for RBW. SR-XRD measurements were used for clarification of the crystal structures of the building blocks of these oleogels. The antioxidant activities of oleogels were evaluated involving DPPH and ABTS assays.
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Inherited and acquired thrombophilia as a modifier of clinical course of chronic immune thrombocytopenia. JOURNAL OF APPLIED HEMATOLOGY 2020. [DOI: 10.4103/joah.joah_75_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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A simple fermentative process for ensuring safety and nutrition of legume and legume wheat based sourdoughs. QUALITY ASSURANCE AND SAFETY OF CROPS & FOODS 2019. [DOI: 10.3920/qas2018.1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
Bluetongue (BT) is an economically important, infectious and non-contagious disease of ruminant animals. BT disease is caused by bluetongue virus (BTV) of the genus Orbivirus (the family Reoviridae). BTV is transmitted by certain species of biting midges of the genus Culicoides. Although originally BT was restricted to African continent, now it is present in all the continents except Antarctica. Conventional BT vaccines such as live attenuated and inactivated vaccines showed different degree of success in BT control. However, conventional vaccines have certain disadvantages of reversion to virulent strain and frequent booster dose requirement. Several BT outbreaks in India and the rest of the world open a new insight for development of better vaccines. The development in molecular biology techniques allowed the development and validation of several modern vaccines such as subunit vaccine, recombinant vector vaccine, disabled infections single cycle (DISC) vaccine, differentiating infected from vaccinated animals (DIVA) approach etc. Most of these vaccines are considered as safer, having better protective immune response and provided cross-protective immunization against more than one serotype. Keywords: bluetongue virus; live vaccine; inactivated vaccine; DISC; recombinant vaccine.
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ELARA: A PHASE 2 TRIAL INVESTIGATING THE EFFICACY AND SAFETY OF TISAGENLECLEUCEL IN ADULT PATIENTS WITH REFRACTORY/RELAPSED FOLLICULAR LYMPHOMA. Hematol Oncol 2019. [DOI: 10.1002/hon.6_2632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Effect of metformin and flutamide on insulin, lipogenic and androgen-estrogen signaling, and cardiometabolic risk in a PCOS-prone metabolic syndrome rodent model. Am J Physiol Endocrinol Metab 2019; 316:E16-E33. [PMID: 30153063 PMCID: PMC6417686 DOI: 10.1152/ajpendo.00018.2018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023]
Abstract
Polycystic ovary syndrome (PCOS) is highly associated with cardiometabolic risk and the metabolic syndrome (MetS), predisposing women to increased risk of developing type 2 diabetes and cardiovascular disease. Metformin is commonly used to treat insulin resistance-glucose intolerance, and flutamide, an androgen receptor (AR) antagonist, is used to target hyperandrogenemia and dyslipidemia. Currently, the physiological mechanism of action of these treatments on androgen, lipidogenic, and insulin signaling pathways remains unclear in PCOS. The aim of this study was to investigate the effects and mechanisms of action of metformin and flutamide on plasma lipid-apolipoprotein (Apo)B-lipoprotein and insulin-glucose metabolism, and endocrine-reproductive indices in a PCOS-prone MetS rodent model. PCOS-prone rodents were treated with metformin (300 mg/kg body wt), flutamide (30 mg/kg body wt), or metformin + flutamide combination treatment for 6 wk. Metformin was shown to improve fasting insulin and HOMA-IR, whereas flutamide and combination treatment were shown to reduce plasma triglycerides, ApoB48, and ApoB100, and this was associated with decreased intestinal secretion of ApoB48/triglyceride. Flutamide and metformin were shown to reduce plasma androgen indices and to improve ovarian primary and preovulatory follicle frequency. Metformin treatment increased hepatic estrogen receptor (ER)α, and metformin-flutamide decreased intestinal AR and increased ERα mRNA expression. Metformin-flutamide treatment upregulated hepatic and intestinal insulin signaling, including insulin receptor, MAPK1, and AKT2. In conclusion, cardiometabolic risk factors, in particular ApoB-hypertriglyceridemia, are independently modulated via the AR, and understanding the contribution of AR and insulin-signaling pathways further may facilitate the development of targeted interventions in high-risk women with PCOS and MetS.
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Hierarchical Bayes versus empirical Bayes density predictors under general divergence loss. Biometrika 2018. [DOI: 10.1093/biomet/asy073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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P3.03-25 Squamous Cell Carcinoma-Associated Bronchial Dysplasias Demonstrate Altered T-helper Lymphocyte Differentiation. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Single-walled and multi-walled carbon nanotubes induce epigenetic alterations in association with the nuclear deposition in 16 HBE cells. Toxicol Lett 2018. [DOI: 10.1016/j.toxlet.2018.06.918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Fresh vs. frozen donor oocytes (DO) - looking at the big picture, is one superior? Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Isolation of the unsaponifiable matter (squalene, phytosterols, tocopherols, γ-oryzanol and fatty alcohols) from a fatty acid distillate of rice bran oil. GRASAS Y ACEITES 2018. [DOI: 10.3989/gya.1112172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rice bran oil is characterized by its unique composition of unsaponifiable matter such as oryzanol, squalene, sterols, tocopherols and fatty alcohols. Rice bran oil fatty acid distillate (RBOFAD) is an important by-product of physical refining plants. In the present study, an appropriate fractionation methodology is proposed for isolating the unsaponifiable matter into two fractions, squalene, phytosterols and fatty alcohols as fraction 1; tocopherols and γ- oryzanol as fraction 2. The two fractions together constitute the total unsaponifiable matter in the RBOFAD. The individual unsaponifiable matter components (γ-oryzanol 1.78g/100g, squalene 209.63 mg/100g, tocopherol 2.45mg/100g, total phytosterols 3.79g/100g and fatty alcohols 94.23g/100g) were isolated from RBOFAD by combining a chemical esterification process and liquid-liquid extraction process with 95% ethanol which extracted tocopherol, γ-oryzanol, sterols, squalene, FFA, monoglycerides; later with hexane extraction of the alkaline phase to remove squalene, sterols and fatty alcohols. The alkaline salts of tocopherols and γ-oryzanol are decomposed by the acidification and extraction of the unsaponifiable matter with n-hexane.
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Survival and prognostic factors for glioblastoma multiforme: Retrospective single-institutional study. Indian J Cancer 2018; 54:362-367. [PMID: 29199724 DOI: 10.4103/ijc.ijc_157_17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor in adults. The standard management has been maximum surgical resection followed by adjuvant radiotherapy with concurrent chemotherapy followed by adjuvant chemotherapy. Although the survival rate of patients with GBM has improved with recent advancements in treatment, the prognosis remains generally poor. The median survival rates are in the range of 9-12 months and 2-year survival rates are in the range of 8%-12%. MATERIALS AND METHODS A single-institution retrospective review of 61 patients of GBM from 2012 to 2014. Data regarding patient factors, disease factors, and treatment factors were collected and survival has been calculated. RESULTS A total of 61 patients with GBM were analyzed. GBM is commonly seen in sixth decade of life. Male to female ratio is 2.6:1. The right side of the brain is commonly involved with right frontal lobe being the most common site. The median follow-up was 4.6 months. The median survival of our patients was 8 months. The 1-year and 2-year survival rates were 20% and 3.27%, respectively. CONCLUSIONS The overall survival and prognosis in patients with GBM remains poor despite of constant research and studies. Concurrent chemoradiotherapy followed by adjuvant chemotherapy with temozolomide should be used after maximal resection to improve the survival.
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915 Maternal occupation is associated with maternal global dna (hydroxy) methylation in the second trimester of pregnancy. Epidemiology 2018. [DOI: 10.1136/oemed-2018-icohabstracts.384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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P3.03-026 Cell-CT® Differential Detection of Dysplastic Bronchial Epithelial Cells from Patient Explants. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Organic-Inorganic Composite Films Based on Gd 3Ga 3Al 2O 12:Ce Scintillator Nanoparticles for X-ray Imaging Applications. ACS APPLIED MATERIALS & INTERFACES 2017; 9:37310-37320. [PMID: 28990750 DOI: 10.1021/acsami.7b11289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Organic-inorganic nanocomposite self-standing films of Gd3Ga3Al2O12 (GGAG) uniformly dispersed in poly(methyl methacrylate) (PMMA) and polystyrene polymer are prepared for radiography application. GGAG:Ce nanoscintillator has been chosen because of its high light output and fast decay time. The nanopowder of GGAG is synthesized by coprecipitation method and dispersed in the polymer matrix by a simple blending technique. The nanocomposite films of thickness in the range of 150-450 μm with a very high inorganic content is achieved by this technique. These films are characterized by their uniformity, optical absorption, photoluminescence, and radioluminescence. These films are further tested for their application in radiography by recording X-ray images using a commercially available charge-coupled device camera. A resolution of 10 lp/mm is obtained using GGAG:PMMA composite film with 50% loading, confirming their application in imaging devices.
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Rapid quantification of cholesterol in dairy powders using Fourier transform near infrared spectroscopy and chemometrics. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Most nutritional studies on the development of children focus on mother-infant interactions. Maternal nutrition is critically involved in the growth and development of the fetus, but what about the father? The aim is to investigate the effects of paternal methyl-group donor intake (methionine, folate, betaine, choline) on paternal and offspring global DNA (hydroxy)methylation, offspring IGF2 DMR DNA methylation, and birth weight. Questionnaires, 7-day estimated dietary records, whole blood samples, and anthropometric measurements from 74 fathers were obtained. A total of 51 cord blood samples were collected and birth weight was obtained. DNA methylation status was measured using liquid chromatography-tandem mass spectrometry (global DNA (hydroxy)methylation) and pyrosequencing (IGF2 DMR methylation). Paternal betaine intake was positively associated with paternal global DNA hydroxymethylation (0.028% per 100 mg betaine increase, 95% CI: 0.003, 0.053, P=0.03) and cord blood global DNA methylation (0.679% per 100 mg betaine increase, 95% CI: 0.057, 1.302, P=0.03). Paternal methionine intake was positively associated with CpG1 (0.336% per 100 mg methionine increase, 95% CI: 0.103, 0.569, P=0.006), and mean CpG (0.201% per 100 mg methionine increase, 95% CI: 0.001, 0.402, P=0.049) methylation of the IGF2 DMR in cord blood. Further, a negative association between birth weight/birth weight-for-gestational age z-score and paternal betaine/methionine intake was found. In addition, a positive association between choline and birth weight/birth weight-for-gestational age z-score was also observed. Our data indicate a potential impact of paternal methyl-group donor intake on paternal global DNA hydroxymethylation, offspring global and IGF2 DMR DNA methylation, and prenatal growth.
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Polymorphism in 5′ untranslated region of heat-shock protein 70 gene as marker of post-partum anoestrus in Murrah buffaloes. Reprod Domest Anim 2017; 52:505-512. [DOI: 10.1111/rda.12941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/10/2017] [Indexed: 12/25/2022]
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High-Performance Liquid Chromatography Determination of Praziquantel in Rat Plasma; Application to Pharmacokinetic Studies. Indian J Pharm Sci 2017. [DOI: 10.4172/pharmaceutical-sciences.1000304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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DNA methylation alterations by carbon nanotubes. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.07.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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In vitro demonstration of potential virulence determinants among clinical isolates of various Candida species and its clinical implication in a Teaching Hospital in Eastern India. Indian J Med Microbiol 2016; 34:406-7. [PMID: 27514982 DOI: 10.4103/0255-0857.188385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Congenital macrothrombocytopenia is a heterogeneous disorder in India. Haemophilia 2016; 22:570-82. [DOI: 10.1111/hae.12917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2016] [Indexed: 11/27/2022]
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Determination of Deltamethrin in Mice Plasma and Immune Organs by Simple Reversed-Phase HPLC. ACTA CHROMATOGR 2016; 28:193-206. [DOI: 10.1556/1326.2016.28.2.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
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Lower respiratory tract infection in two tertiary hospitals of Kolkata and carbapenem resistance. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract P6-07-01: Multigene profiling to identify clinically relevant actionable mutations in breast cancer: An Indian study. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-07-01] [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
Background: Numerous chemotherapeutic agents are available against breast cancer (BC), but a vast majority of patients diagnosed with this disease still develop treatment resistance and eventually succumb to disease. It remains an unmet need to identify specific molecular defects against which targeted therapy are available for improving clinical outcomes in BC. Our study aims to identify frequent hotspot mutations in BCs and determine their clinical impact.
Methods: 200 women with BC(early diagnosed and/or metastatic) aged 26-75 yrs (median age 50.5yrs) diagnosed at HCG from April 2013-15 were consented to be profiled by targeted deep sequencing for hotspot mutations in 48 cancer-related genes using Illumina's TSCAP panel and MiSeq technology in an IRB-approved prospective study in a CLIA compliant laboratory. All the cases had pathology review for stage, histological type, hormonal status and Ki67. The average coverage across 220 hot spots was greater than 1000X. Data was processed using Strand Avadis NGS™. Mutations identified in the tumor were assessed for 'actionability' i.e. response to therapy and impact on prognosis. Results: Somatic variants were detected in 75% of cases with direct impact on therapy or prognosis. Genetic aberrations were identified in PI3K/AKT/ mTOR signalling pathway in substantial fraction (27%) of breast cancer cases, out of which 17% had PIK3CA activating mutations,13 and 5 cases had PTEN and AKT deletions or truncating mutations respectively. Aberration in this pathway was more prevalent in HR+ve (53%) and HER2-ve including TNBC (61%) than in HR+/HER2+ve tumors (10.6%) of IDC histology. However, no correlation was found with stage and Ki67 index of the tumor. Notably 80% of BC cases presented with liver metastasis at the time of diagnosis were detected with PIK3CA mutation indicating its role as a surrogate marker of organ specific metastasis. PIK3CA was found to be co mutated with p53 in 16 cases (9%) of which 4 cases showed npCR post NACT. Also disruptive and non-disruptive mutations in TP53 alone were found in 25% of BC, varying widely among different histologies. A follow up of few cases showed shorter PFS and poor outcome in resected BC treated with NACT indicating its robust prognostic value in NACT setting. Furthermore, two patients were detected with cKIT mutations indicating sensitivity to imatinib and therefore enrolled on a clinical trial. The other variants were found in RB1(n=8),Her2 (n=2),FGFR amplification(n=1), KRAS(n=2),NRAS(n=3)CDH1(n=1),FBXW7(n=2) and EGFR(n=1).All these variants detected indicated resistance to conventional therapy and suggested sensitivity to available targeted therapy, either approved or in clinical trials. The response and outcome are being monitored in about 20 (10%) patients who have been enrolled in clinical trials and receiving mutation specific targeted therapy. Conclusions: This study confirms the utility of multigene profiling in early diagnosed and advanced BC patients, to stratify them on their molecular profile who could potentially benefit from targeted therapy. Prospective studies and randomized clinical trials are ongoing to confirm the independent prognostic and therapeutic value of the mutations in a larger cohort of Indian population.
Citation Format: Ghosh M, Sheela ML, Choudhury S, Bahadur U, Patil S, Satheesh CT, Murugan K, Nayak R, Sridhar PS, Rao N, Mahesh B, Shashidhara HP, Krishnamoorthy N, Gupta V, Sankaran S, Subramanian K, Ajaikumar BS. Multigene profiling to identify clinically relevant actionable mutations in breast cancer: An Indian study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-01.
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Abstract P6-06-06: Comprehensive analysis of BRCA (BRCAm) and other germline mutations (GRm) with a clinicopathological association in breast cancer: An Indian study. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-06-06] [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
Background: BRCAm and other GRm testing using next generation sequencing (NGS) in early diagnosed and/or metastatic breast cancer (BC) helps in the identification of both unambiguously defined deleterious mutations and sequence variants of unknown clinical significance (VUS). The early detection of these mutations in the proband and the family members help in risk stratification and instituting effective monitoring, surveillance and disease management strategies.
Methods: Out of total 200 patients diagnosed with BC (April 2013-15) 77 unrelated individuals were consented to be profiled by NGS on MiSeq platform using TruSight Cancer panel (consisting of 94 genes including 13 genes highly associated with risk of inherited breast and/or ovarian cancer) in an IRB-approved prospective study in a CLIA compliant laboratory. Paired end sequencing was done with an average coverage of > 450X. Data was processed using STRAND software and interpreted using "Strand Omics" platform. The paired tumor samples were analysed for pathological stage, histological type and hormonal status.
Results: GRm were detected in 61 cases (79%). Among all mutations detected, BRCA1/2 were found in 51% (31% in BRCA1, 20% in BRCA2) of cases. BRCA1 was found to be co-mutated with BRCA2 in 2 cases. Out of 37 deleterious mutations in BRCA1/2 genes only 10 were reported to be pathogenic (6 in BRCA1 and 4 in BRCA2) and rest were VUS. Mutation frequencies were higher among high grade IDC with HER2-ve tumors including TNBC (53%, p<0.05) with an early onset of the disease. TNBC with BRCAm were found to have no/incomplete pCR on conventional TAC regimen , subsequently started with platinum therapy and the outcome being monitored. Interestingly, 4 BRCA1 mutations including 3 non-sense and 1 frameshift mutation were found in two unrelated individuals suggesting them to be founder mutations in Indian population. The other GRm frequency (alone/ co-mutated with BRCA) was also found to be significantly high (49%) and include BRIP1, CHEK2, ERCC2, CDH1, SDHB, APC, MSH6, TP53, PALB2 and RAD51C. Stratification based on age of diagnosis(dx) showed a detection rate significantly higher in the age group of 25-50 yrs (74%) as compared to the 50-75 yrs (26%). Also a strong association of GRm status with the family history(Hx) of BC in 1st or 2nd degree relatives was indicated.
Table 1: Correlation of GRm with Dx and HxGenen%Age at dx(yrs)Family Hx (Yes=Y, No=N,Unknown=UK)BRCA1193125-50 (n=23) 50-75(n=8)Y(n=13) N(n=3) UK(n=3)BRCA2122025-50(n=21) 50-75(n=9)Y(n=8) N(n=2) UK(n=2)PALB211.7>50YCHEK258.825-50 (n=4) 50-75(n=1)YATM610.525-50 (n=4) 50-75(n=2)Y(n=5) N(n=1)RAD5111.7<50Y
Conclusions: Our study in a small cohort clearly highlighted the significance of germline testing and classifying the variant in larger cohort of BC patients with a strong family Hx of cancer particularly in BRCA1/2 positive families , and in women <50yrs for early detection and risk assessment. The study also indicates BRCAm to be an important contributor to the etiology of high grade HER2-/ TNBC in Indian patients. Expanded testing of this subtype is warranted to impact management of the disease with PARP inhibitors and/or platinum therapy.
Citation Format: Ghosh M, ML S, Upasana M, Chodhury S, Mannan AU, Southekal S, Manjima C, Patil S, Murugan K, Mahesh B, Nayak R, Sridhar PSS, Rao N, Krishnamoorthy N, Gupta V, Satheesh CT, Subramanian K, Ajaikumar BS. Comprehensive analysis of BRCA (BRCAm) and other germline mutations (GRm) with a clinicopathological association in breast cancer: An Indian study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-06-06.
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