Now showing 1 - 10 of 1655
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    Simplified procedure for TEMPO-catalyzed oxidation: Selective oxidation of alcohols, α-hydroxy esters, and amides using TEMPO and calcium hypochlorite
    (01-12-2012)
    Reddy, Sabbasani Rajasekhara
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    Stella, Selvaraj
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    A wide range of primary and secondary multifunctional alcohols, α-hydroxyamides, and α-hydroxyesters were oxidized to their corresponding aldehydes, ketones, α-ketoamides, and α-ketoesters under mild reaction conditions using 2,2,6,6-tetramethylpiperidine-1-oxyl as a catalyst with calcium hypochlorite as an oxidant [TEMPO-Ca(OCl) 2]. This simplified method does not require any transition metals, acids, or bases and demonstrates controlled and selective oxidation of structurally diverse alcohols, affording moderate to excellent yields at room temperature. © 2012 Taylor & Francis Group, LLC.
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    Comparison of first trimester dating methods for gestational age estimation and their implication on preterm birth classification in a North Indian cohort
    (01-12-2021)
    Vijayram, Ramya
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    Damaraju, Nikhita
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    Xavier, Ashley
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    Desiraju, Bapu Koundinya
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    Thiruvengadam, Ramachandran
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    Misra, Sumit
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    Chopra, Shilpa
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    Khurana, Ashok
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    Wadhwa, Nitya
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    Bal, Vineeta
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    Bhatnagar, Shinjini
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    Das, Bhabatosh
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    Dash, Mahadev
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    Kshetrapal, Pallavi
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    Natchu, Uma Chandra Mouli
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    Rath, Satyajit
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    Sachdeva, Kanika
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    Sharma, Dharmendra
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    Singh, Amanpreet
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    Sopory, Shailaja
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    Maitra, Arindam
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    Majumder, Partha P.
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    Mukherjee, Souvik
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    Maiti, Tushar K.
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    Bahl, Monika
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    Bansal, Shubra
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    Mehta, Umesh
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    Sharma, Sunita
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    Sindhu, Brahmdeep
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    Arya, Sugandha
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    Bharti, Rekha
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    Chellani, Harish
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    Mittal, Pratima
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    Garg, Anju
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    Ramji, Siddharth
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    Tripathi, Reva
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    Goyal, Alpesh
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    Gupta, Yashdeep
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    Hari, Smriti
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    Tandon, Nikhil
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    Gupta, Rakesh
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    Salunke, Dinakar M.
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    Nair, G. Balakrish
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    Kang, Gagandeep
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    Background: Different formulae have been developed globally to estimate gestational age (GA) by ultrasonography in the first trimester of pregnancy. In this study, we develop an Indian population-specific dating formula and compare its performance with published formulae. Finally, we evaluate the implications of the choice of dating method on preterm birth (PTB) rate. This study’s data was from GARBH-Ini, an ongoing pregnancy cohort of North Indian women to study PTB. Methods: Comparisons between ultrasonography-Hadlock and last menstrual period (LMP) based dating methods were made by studying the distribution of their differences by Bland-Altman analysis. Using data-driven approaches, we removed data outliers more efficiently than by applying clinical parameters. We applied advanced machine learning algorithms to identify relevant features for GA estimation and developed an Indian population-specific formula (Garbhini-GA1) for the first trimester. PTB rates of Garbhini-GA1 and other formulae were compared by estimating sensitivity and accuracy. Results: Performance of Garbhini-GA1 formula, a non-linear function of crown-rump length (CRL), was equivalent to published formulae for estimation of first trimester GA (LoA, − 0.46,0.96 weeks). We found that CRL was the most crucial parameter in estimating GA and no other clinical or socioeconomic covariates contributed to GA estimation. The estimated PTB rate across all the formulae including LMP ranged 11.27–16.50% with Garbhini-GA1 estimating the least rate with highest sensitivity and accuracy. While the LMP-based method overestimated GA by 3 days compared to USG-Hadlock formula; at an individual level, these methods had less than 50% agreement in the classification of PTB. Conclusions: An accurate estimation of GA is crucial for the management of PTB. Garbhini-GA1, the first such formula developed in an Indian setting, estimates PTB rates with higher accuracy, especially when compared to commonly used Hadlock formula. Our results reinforce the need to develop population-specific gestational age formulae.
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    Analysis of kinetic data of pectinases with substrate inhibition
    Enzyme kinetics data play a vital role in the design of reactors and control of processes. In the present study, kinetic studies on pectinases were carried out. Partially purified polymethylgalacturonase (PMG) and polygalacturonase (PG) were the two pectinases studied. The plot of initial rate vs. initial substrate concentration did not follow the conventional Michaelis-Menten kinetics, but substrate inhibition was observed. For PMG, maximum rate was attained at an initial pectin concentration of 3 g/l, whereas maximum rate was attained when the initial substrate concentration of 2.5 g/l of polygalacturonic acid for PG I and PG II. The kinetic data were fitted to five different kinetic models to explain the substrate inhibition effect. Among the five models tested, the combined mechanism of protective diffusion limitation of both high and inhibitory substrate concentrations (semi-empirical model) explained the inhibition data with 96-99% confidence interval.
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    Chromogranin A: A novel susceptibility gene for essential hypertension
    (01-03-2010)
    Sahu, Bhavani S.
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    Sonawane, Parshuram J.
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    Chromogranin A (CHGA) is ubiquitously expressed in secretory cells of the endocrine, neuroendocrine, and neuronal tissues. Although this protein has long been known as a marker for neuroendocrine tumors, its role in cardiovascular disease states including essential hypertension (EH) has only recently been recognized. It acts as a prohormone giving rise to bioactive peptides such as vasostatin-I (human CHGA1-76) and catestatin (human CHGA352-372) that exhibit several cardiovascular regulatory functions. CHGA is over-expressed but catestatin is diminished in EH. Moreover, genetic variants in the promoter, catestatin, and 3'-untranslated regions of the human CHGA gene alter autonomic activity and blood pressure. Consistent with these findings, targeted ablation of this gene causes severe arterial hypertension and ventricular hypertrophy in mice. Transgenic expression of the human CHGA gene or exogenous administration of catestatin restores blood pressure in these mice. Thus, the accumulated evidence establishes CHGA as a novel susceptibility gene for EH.
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    Diminishing bioavailability and toxicity of P25 TiO2 NPs during continuous exposure to marine algae Chlorella sp.
    (01-10-2019)
    Thiagarajan, Vignesh
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    M., Pavani
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    S., Archanaa
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    R., Seenivasan
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    N., Chandrasekaran
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    Mukherjee, Amitava
    Titanium dioxide nanoparticles (TiO2 NPs) find applications in our day-to-day life because of unique physicochemical properties. Their release into the aquatic environment poses a possible risk to the organisms. However, the continuing exposure of NPs might reduce their bioavailability to marine organisms owing to aggregation and sedimentation in the aqueous systems thus significantly reducing their toxic impact. In this regard, the present study investigates the effect of continuous exposure of TiO2 NPs to marine microalgae Chlorella sp. under UV-A irradiation through “tanks in series” mode of experiments. In a three-cycle experiment, concentration of TiO2 NPs in the first cycle was fixed at 62.6 μM, and the interacted nanoparticles was subsequently exposed to fresh batches of algae in the next two cycles. After the interaction, the NPs underwent severe aggregation (mean hydrodynamic diameter 3000 ± 18.2 nm after cycle I) leading to gravitational settling in the medium and thus decreased bioavailability. The aggregation can be attributed to interactions between the particles themselves (homo-aggregation) further aggravated by the presence of the algal cells (hetero-aggregation). Cellular viability after cycle I was found to be only 24.2 ± 2.5%, and it was enhanced to 96.5 ± 2.8% after the cycle III in the course of continuous exposure. The results were validated with estimation of oxidative stress markers such as intracellular ROS (total ROS, superoxide and hydroxyl radicals) and LPO after each cycle of exposure. The continuing decrease in the EPS across the cycles further confirmed the diminishing toxicity of the NPs.
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    MicroRNA-106b-25 cluster targets β-TRCP2, increases the expression of Snail and enhances cell migration and invasion in H1299 (non small cell lung cancer) cells
    (17-05-2013)
    Savita, Udainiya
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    Lung cancer causes high mortality without a declining trend and non small cell lung cancer represents 85% of all pulmonary carcinomas. MicroRNAs (miRNAs) serve as fine regulators of proliferation, migration, invasion/metastasis and angiogenesis of normal and cancer cells. Using TargetScan6.2, we predicted that the ubiquitin ligase, β-TRCP2, could be a target for two of the constituent miRNAs of the miR-106b-25 cluster (miR-106b and miR-93). We generated a stable clone of miR-106b-25 cluster (CL) or the empty vector (EV) in H1299 (non small cell lung cancer) cells. The expression of β-TRCP2 mRNA was significantly lower in CL than that in EV cells. Transient expression of miR-93 but not antimiR-93 decreased the expression of β-TRCP2 mRNA in H1299 cells. β-TRCP2-3'UTR reporter assay revealed that its activity in CL cells was only 60% of that in EV cells. Snail protein expression was higher in CL than that in EV cells and H1299 cells exhibited an increase in the expression of Snail upon transient transfection with miR-93. miR-106b-25 cluster-induced migration of CL measured by scratch assay was more than that in EV cells and no significant difference in migration was observed between antimiR-93-transfected H1299 cells and the corresponding control-oligo-transfected cells. miR-106b-25 cluster-induced migration of CL cells was again confirmed in a Boyden chamber assay without the matrigel. CL cells were more invasive than EV cells when assessed using Boyden chambers with matrigel but there were no significant changes in the cell viabilities between EV and CL cells. Colony formation assay revealed that the CL cells formed more number of colonies than EV cells but they were smaller in size than those formed by EV cells. The supernatant from CL cells was more effective than that from EV cells in inducing tube formation in endothelial cells. Taken together, our data indicate that miR-106b-25 cluster may play an important role in the metastasis of human non-small cell lung cancer cells by directly suppressing the β-TRCP2 gene expression with a consequent increase in the expression of Snail. © 2013 Elsevier Inc.
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    Feeding enhances fibronectin adherence of quiescent lymphocytes through non-canonical insulin signalling
    (01-09-2023)
    Mallu, Abhiram Charan Tej
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    Sivagurunathan, Sivapriya
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    Paul, Debasish
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    Aggarwal, Hobby
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    Nathan, Abel Arul
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    Manikandan, Amrutha
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    Ravi, Mahalakshmi M.
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    Boppana, Ramanamurthy
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    Jagavelu, Kumaravelu
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    Santra, Manas Kumar
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    Nutritional availability during fasting and refeeding affects the temporal redistribution of lymphoid and myeloid immune cells among the circulating and tissue-resident pools. Conversely, nutritional imbalance and impaired glucose metabolism are associated with chronic inflammation, aberrant immunity and anomalous leukocyte trafficking. Despite being exposed to periodic alterations in blood insulin levels upon fasting and feeding, studies exploring the physiological effects of these hormonal changes on quiescent immune cell function and trafficking are scanty. Here, we report that oral glucose load in mice and healthy men enhances the adherence of circulating peripheral blood mononuclear cells (PBMCs) and lymphocytes to fibronectin. Adherence to fibronectin is also observed upon regular intake of breakfast following overnight fasting in healthy subjects. This glucose load-induced phenomenon is abrogated in streptozotocin-injected mice that lack insulin. Intra-vital microscopy in mice demonstrated that oral glucose feeding enhances the homing of PBMCs to injured blood vessels in vivo. Furthermore, employing flow cytometry, Western blotting and adhesion assays for PBMCs and Jurkat-T cells, we elucidate that insulin enhances fibronectin adherence of quiescent lymphocytes through non-canonical signalling involving insulin-like growth factor-1 receptor (IGF-1R) autophosphorylation, phospholipase C gamma-1 (PLCγ-1) Tyr783 phosphorylation and inside-out activation of β-integrins respectively. Our findings uncover the physiological relevance of post-prandial insulin spikes in regulating the adherence and trafficking of circulating quiescent T-cells through fibronectin–integrin interaction.
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    In silico evaluation of the impact of Omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT-qPCR assays for SARS-CoV-2 detection using whole genome sequencing
    (01-01-2023)
    Sharma, Divya
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    Notarte, Kin Israel
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    Fernandez, Rey Arturo
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    Lippi, Giuseppe
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    Henry, Brandon M.
    Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC) Omicron (B.1.1.529) has rapidly spread around the world, presenting a new threat to global public human health. Due to the large number of mutations accumulated by SARS-CoV-2 Omicron, concerns have emerged over potentially reduced diagnostic accuracy of reverse-transcription polymerase chain reaction (RT-qPCR), the gold standard diagnostic test for diagnosing coronavirus disease 2019 (COVID-19). Thus, we aimed to assess the impact of the currently endemic Omicron sublineages BA.4 and BA.5 on the integrity and sensitivity of RT-qPCR assays used for coronavirus disease 2019 (COVID-19) diagnosis via in silico analysis. We employed whole genome sequencing data and evaluated the potential for false negatives or test failure due to mismatches between primers/probes and the Omicron VoC viral genome. Methods: In silico sensitivity of 12 RT-qPCR tests (containing 30 primers and probe sets) developed for detection of SARS-CoV-2 reported by the World Health Organization (WHO) or available in the literature, was assessed for specifically detecting SARS-CoV-2 Omicron BA.4 and BA.5 sublineages, obtained after removing redundancy from publicly available genomes from National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Avian Influenza Data (GISAID) databases. Mismatches between amplicon regions of SARS-CoV-2 Omicron VoC and primers and probe sets were evaluated, and clustering analysis of corresponding amplicon sequences was carried out. Results: From the 1164 representative SARS-CoV-2 Omicron VoC BA.4 sublineage genomes analyzed, a substitution in the first five nucleotides (C to T) of the amplicon's 3′-end was observed in all samples resulting in 0% sensitivity for assays HKUnivRdRp/Hel (mismatch in reverse primer) and CoremCharite N (mismatch in both forward and reverse primers). Due to a mismatch in the forward primer's 5′-end (3-nucleotide substitution, GGG to AAC), the sensitivity of the ChinaCDC N assay was at 0.69%. The 10 nucleotide mismatches in the reverse primer resulted in 0.09% sensitivity for Omicron sublineage BA.4 for Thai N assay. Of the 1926 BA.5 sublineage genomes, HKUnivRdRp/Hel assay also had 0% sensitivity. A sensitivity of 3.06% was observed for the ChinaCDC N assay because of a mismatch in the forward primer's 5′-end (3-nucleotide substitution, GGG to AAC). Similarly, due to the 10 nucleotide mismatches in the reverse primer, the Thai N assay's sensitivity was low at 0.21% for sublineage BA.5. Further, eight assays for BA.4 sublineage retained high sensitivity (more than 97%) and 9 assays for BA.5 sublineage retained more than 99% sensitivity. Conclusion: We observed four assays (HKUnivRdRp/Hel, ChinaCDC N, Thai N, CoremCharite N) that could potentially result in false negative results for SARS-CoV-2 Omicron VoCs BA.4 and BA.5 sublineages. Interestingly, CoremCharite N had 0% sensitivity for Omicron Voc BA.4 but 99.53% sensitivity for BA.5. In addition, 66.67% of the assays for BA.4 sublineage and 75% of the assays for BA.5 sublineage retained high sensitivity. Further, amplicon clustering and additional substitution analysis along with sensitivity analysis could be used for the modification and development of RT-qPCR assays for detecting SARS-CoV-2 Omicron VoC sublineages.
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    A fourier transform infrared spectroscopy (FTIR) based assay for Candida parapsilosis ATCC 7330 mediated oxidation of aryl alcohols
    (19-06-2015)
    Sudhakara, Sneha
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    We present an FTIR based assay to monitor the whole cell mediated oxidation of aryl alcohols by measuring the characteristic IR absorption of the hydroxyl group [OH] of the substrate and the carbonyl group [CO] of the corresponding oxidized product. This method expedites the analysis of whole cell mediated catalysis which is usually done by GC and/or HPLC. The FTIR assay had linearity with R2≥0.980 and sensitivity up to 10μM. The accuracy and precision of FTIR assay was found ≥81% and ≥94%, respectively. This assay was validated by GC which exhibited ≥82% accuracy and ≥79% precision. The time of analysis taken by this assay was 2-3min per sample in comparison with 20-40min by GC.