International Journal of Environmental Research, 2014
The extent of groundwater arsenic (As) contamination and associated health-risks were studiedin t... more The extent of groundwater arsenic (As) contamination and associated health-risks were studiedin the four villages: Chaukia and Terahrasiya (Vaishali); Mamalkha and Masharu (Bhagalpur) in Bihar, India.Groundwater samples were tested using the standard Silverdiethyledithiocarbamate method at 520nm byThermo UV-1 spectrophotometer. The As levels in both the districts exceeded the WHO standard of 10μg/Lfor drinking water with a maximum value of 20μg/L in Vaishali and 143μg/L in Bhagalpur. However, the FAOstandard of 100μg/L of As for irrigation water was only exceeded in Bhagalpur. The calculated range of thehazard index (HI) for Vaishali was 0.9 to 10, and for Bhagalpur was 10.40 to 40.47. Both ranges exceed theaccepted normal toxic HI of 1.00. The cancer risk was derived as 1-5/1000 people to 5-16/10,000 people inVaishali, and 7-21/1000 and 5-16/1000 people in Bhagalpur. Prevalence of skin pigmentation was double inVaishali in comparison to Bhagalpur. The analysis of principal componen...
Eighty patients with primary carcinoma of the gallbladder were studied by ultrasonography. Two br... more Eighty patients with primary carcinoma of the gallbladder were studied by ultrasonography. Two broad groups were defined. In group I (72.5%), the gallbladder lumen was identified along with a mass lesion, and in group II (27.5%), a large mass totally replacing the gallbladder was seen. Group I was further categorized into three subtypes according to the morphology of the lesion: type 1—a mass almost filling the lumen; type 2—a polypoidal mass projecting into the lumen; and type 3—an infiltrating mass. Associated findings of infiltration of the liver, presence of calculi, biliary tree obstruction, liver metastasis, and lymphadenopathy further supported the diagnosis.Ultrasonography was found to be highly reliable in the diagnosis of carcinoma of the gallbladder. In addition, it provided guidance for biopsy/aspiration of nonpalpable tumors. Its shortcomings appear to be its inability to assess peritoneal and bowel involvement, as well as that of the omentum and posterior rectus sheath.
Weldment characteristics like bead width, bead height, penetration and weldment cross-sectional a... more Weldment characteristics like bead width, bead height, penetration and weldment cross-sectional areas are the factors that contribute the weld quality. Submerged arc welding (SAW) is mostly used to join the heavy structures around the world because of its high deposition rate and good weld quality. The present investigation deals with single pass double side full penetration SAW butt joints with process parameters for minimizing the welding distortions. The plates were without having any edge preparation and welded from both the sides using full factorial design of experiments with process parameters such that full penetration was achieved. The shrinkage forces from both the sides of the joints acted in opposite direction to minimize distortions. The process was modelled using adaptive neuro – fuzzy inference system (ANFIS) technique to predict the effects of process parameters on weldment characteristics and angular distortion of SAW butt joint. The ANFIS model has been developed o...
Two hundred and three multi-transfused children with thalassemia attending the Thalassemia Clinic... more Two hundred and three multi-transfused children with thalassemia attending the Thalassemia Clinic of the Charak Palika Hospital, New Delhi were screened for human immunodeficiency virus (HIV) antibodies by ELISA and all positive cases were confirmed by Western Blot. Of the 203 children screened, 18 (8.9%) were HIV positive, and in these children a detailed immunological work up was done and compared to 18 age-matched HIV negative thalassemics as controls. The tests included absolute lymphocyte counts (ALC), absolute and percentages of CD4+ and CD8+ cells and their ratios (CD4/CD8), immunoglobulin levels (IgG, IgM and IgA) and delayed cutaneous hypersensitivity (DCH) test by Multitest CMI in all the cases and the controls. Of the 18 HIV positive children, 6 were diagnosed to have clinical AIDS as per the WHO criteria. After immunological testing, the children were further classified according to the CDC criteria. By these criteria, 11 children were classified as P1 A (asymptomatic in...
Even in cases where there is no obvious family history of disease, genome sequencing may contribu... more Even in cases where there is no obvious family history of disease, genome sequencing may contribute to clinical diagnosis and management. Clinical application of the genome has not yet become routine, however, in part because physicians are still learning how best to utilize such information. As an educational research exercise performed in conjunction with our medical school human anatomy course, we explored the potential utility of determining the whole genome sequence of a patient who had died following a clinical diagnosis of idiopathic pulmonary fibrosis (IPF). Medical students performed dissection and whole genome sequencing of the cadaver. Gross and microscopic findings were more consistent with the fibrosing variant of nonspecific interstitial pneumonia (NSIP), as opposed to IPF per se. Variants in genes causing Mendelian disorders predisposing to IPF were not detected. However, whole genome sequencing identified several common variants associated with IPF, including a singl...
2014 IEEE 22nd Annual International Symposium on Field-Programmable Custom Computing Machines, 2014
ABSTRACT Nelder-Mead algorithm (NMA) is the best-known algorithm for multidimensional optimizatio... more ABSTRACT Nelder-Mead algorithm (NMA) is the best-known algorithm for multidimensional optimization without involving derivative computations. Due to the simplicity in implementation and the fast convergent property of NMA, it is widely used in the fields of statistics, engineering, physics and medical sciences. In practice, when objective function is complicated, the optimization procedure requires a lot of computation efforts, leading to a time-consuming process. This work introduces a NMA solver engine fully implemented on FPGA hardware and performs design space exploration to provide various solutions suitable for FPGA device.
Our laboratory is credited for the discovery of enzymatic acetylation of protein, a phenomenon un... more Our laboratory is credited for the discovery of enzymatic acetylation of protein, a phenomenon unknown till we identified an enzyme termed acetoxy drug: protein transacetylase (TAase), catalyzing the transfer of acetyl group from polyphenolic acetates to receptor proteins (RP). Later, TAase was identified as calreticulin (CR), an endoplasmic reticulum luminal protein. CR was termed calreticulin transacetylase (CRTAase). Our persistent study revealed that CR like other families of histone acetyltransferases (HATs) such as p300, Rtt109, PCAF, and ESA1, undergoes autoacetylation. The autoacetylated CR was characterized as a stable intermediate in CRTAase catalyzed protein acetylation, and similar was the case with ESA1. The autoacetylation of CR like that of HATs was found to enhance protein-protein interaction. CR like HAT-1, CBP, and p300 mediated the acylation of RP utilizing acetyl CoA and propionyl CoA as the substrates. The similarities between CRTAase and HATs in mediating prote...
... methods for which the external excitation is excluded and considered, respectively, in theper... more ... methods for which the external excitation is excluded and considered, respectively, in theperformance index (cf ... Optimal vibration control of a smart rotor blade ... where Qij and Eij are transformed reduced stiffnesses and reduced piezoelectric coefficients of the composite blade ...
We report a male patient who presented with pyrexia, generalized lymphadenopathy, hepatosplenomeg... more We report a male patient who presented with pyrexia, generalized lymphadenopathy, hepatosplenomegaly, and pleural effusion with no cutaneous or musculoskeletal symptoms. Despite extensive investigation, no cause was detected. His initial serology was also negative for autoantibodies. The patient was placed on a trial of antitubercular treatment in view of a positive Mantoux test. His disease evolved into the full clinical picture of systemic lupus erythematosus with nephritis (World Health Organisation class IV) and strongly positive antinuclear antibody and dsDNA over a period of months. He was treated successfully with intravenous cyclophosphamide pulses along with oral prednisolone, and the disease was still in remission after 3 years of follow-up.
Proceedings of the National Academy of Sciences, 2011
To catalog protein-altering mutations that may drive the development of prostate cancers and thei... more To catalog protein-altering mutations that may drive the development of prostate cancers and their progression to metastatic disease systematically, we performed whole-exome sequencing of 23 prostate cancers derived from 16 different lethal metastatic tumors and three high-grade primary carcinomas. All tumors were propagated in mice as xenografts, designated the LuCaP series, to model phenotypic variation, such as responses to cancer-directed therapeutics. Although corresponding normal tissue was not available for most tumors, we were able to take advantage of increasingly deep catalogs of human genetic variation to remove most germline variants. On average, each tumor genome contained ∼200 novel nonsynonymous variants, of which the vast majority was specific to individual carcinomas. A subset of genes was recurrently altered across tumors derived from different individuals, including TP53, DLK2, GPC6, and SDF4. Unexpectedly, three prostate cancer genomes exhibited substantially hig...
Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substan... more Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substantial amino acid identity and together constitute ~50 % of the total penicillin-binding proteins of E. coli. PBP5 helps maintain intrinsic β-lactam resistance within the cell. To test if PBP6 and DacD play simlar roles, we deleted dacC and dacD individually, and dacC in combination with dacA, from E. coli 2443 and compared β-lactam sensitivity of the mutants and the parent strain. β-Lactam resistance was complemented by wild-type, but not dd-carboxypeptidase-deficient PBP5, confirming that enzymic activity of PBP5 is essential for β-lactam resistance. Deletion of dacC and expression of PBP6 during exponential or stationary phase did not alter β-lactam resistance of a dacA mutant. Expression of DacD during mid-exponential phase partially restored β-lactam resistance of the dacA mutant. Therefore, PBP5 dd-carboxypeptidase activity is essential for intrinsic β-lactam resistance of E. coli an...
International Journal of Environmental Research, 2014
The extent of groundwater arsenic (As) contamination and associated health-risks were studiedin t... more The extent of groundwater arsenic (As) contamination and associated health-risks were studiedin the four villages: Chaukia and Terahrasiya (Vaishali); Mamalkha and Masharu (Bhagalpur) in Bihar, India.Groundwater samples were tested using the standard Silverdiethyledithiocarbamate method at 520nm byThermo UV-1 spectrophotometer. The As levels in both the districts exceeded the WHO standard of 10μg/Lfor drinking water with a maximum value of 20μg/L in Vaishali and 143μg/L in Bhagalpur. However, the FAOstandard of 100μg/L of As for irrigation water was only exceeded in Bhagalpur. The calculated range of thehazard index (HI) for Vaishali was 0.9 to 10, and for Bhagalpur was 10.40 to 40.47. Both ranges exceed theaccepted normal toxic HI of 1.00. The cancer risk was derived as 1-5/1000 people to 5-16/10,000 people inVaishali, and 7-21/1000 and 5-16/1000 people in Bhagalpur. Prevalence of skin pigmentation was double inVaishali in comparison to Bhagalpur. The analysis of principal componen...
Eighty patients with primary carcinoma of the gallbladder were studied by ultrasonography. Two br... more Eighty patients with primary carcinoma of the gallbladder were studied by ultrasonography. Two broad groups were defined. In group I (72.5%), the gallbladder lumen was identified along with a mass lesion, and in group II (27.5%), a large mass totally replacing the gallbladder was seen. Group I was further categorized into three subtypes according to the morphology of the lesion: type 1—a mass almost filling the lumen; type 2—a polypoidal mass projecting into the lumen; and type 3—an infiltrating mass. Associated findings of infiltration of the liver, presence of calculi, biliary tree obstruction, liver metastasis, and lymphadenopathy further supported the diagnosis.Ultrasonography was found to be highly reliable in the diagnosis of carcinoma of the gallbladder. In addition, it provided guidance for biopsy/aspiration of nonpalpable tumors. Its shortcomings appear to be its inability to assess peritoneal and bowel involvement, as well as that of the omentum and posterior rectus sheath.
Weldment characteristics like bead width, bead height, penetration and weldment cross-sectional a... more Weldment characteristics like bead width, bead height, penetration and weldment cross-sectional areas are the factors that contribute the weld quality. Submerged arc welding (SAW) is mostly used to join the heavy structures around the world because of its high deposition rate and good weld quality. The present investigation deals with single pass double side full penetration SAW butt joints with process parameters for minimizing the welding distortions. The plates were without having any edge preparation and welded from both the sides using full factorial design of experiments with process parameters such that full penetration was achieved. The shrinkage forces from both the sides of the joints acted in opposite direction to minimize distortions. The process was modelled using adaptive neuro – fuzzy inference system (ANFIS) technique to predict the effects of process parameters on weldment characteristics and angular distortion of SAW butt joint. The ANFIS model has been developed o...
Two hundred and three multi-transfused children with thalassemia attending the Thalassemia Clinic... more Two hundred and three multi-transfused children with thalassemia attending the Thalassemia Clinic of the Charak Palika Hospital, New Delhi were screened for human immunodeficiency virus (HIV) antibodies by ELISA and all positive cases were confirmed by Western Blot. Of the 203 children screened, 18 (8.9%) were HIV positive, and in these children a detailed immunological work up was done and compared to 18 age-matched HIV negative thalassemics as controls. The tests included absolute lymphocyte counts (ALC), absolute and percentages of CD4+ and CD8+ cells and their ratios (CD4/CD8), immunoglobulin levels (IgG, IgM and IgA) and delayed cutaneous hypersensitivity (DCH) test by Multitest CMI in all the cases and the controls. Of the 18 HIV positive children, 6 were diagnosed to have clinical AIDS as per the WHO criteria. After immunological testing, the children were further classified according to the CDC criteria. By these criteria, 11 children were classified as P1 A (asymptomatic in...
Even in cases where there is no obvious family history of disease, genome sequencing may contribu... more Even in cases where there is no obvious family history of disease, genome sequencing may contribute to clinical diagnosis and management. Clinical application of the genome has not yet become routine, however, in part because physicians are still learning how best to utilize such information. As an educational research exercise performed in conjunction with our medical school human anatomy course, we explored the potential utility of determining the whole genome sequence of a patient who had died following a clinical diagnosis of idiopathic pulmonary fibrosis (IPF). Medical students performed dissection and whole genome sequencing of the cadaver. Gross and microscopic findings were more consistent with the fibrosing variant of nonspecific interstitial pneumonia (NSIP), as opposed to IPF per se. Variants in genes causing Mendelian disorders predisposing to IPF were not detected. However, whole genome sequencing identified several common variants associated with IPF, including a singl...
2014 IEEE 22nd Annual International Symposium on Field-Programmable Custom Computing Machines, 2014
ABSTRACT Nelder-Mead algorithm (NMA) is the best-known algorithm for multidimensional optimizatio... more ABSTRACT Nelder-Mead algorithm (NMA) is the best-known algorithm for multidimensional optimization without involving derivative computations. Due to the simplicity in implementation and the fast convergent property of NMA, it is widely used in the fields of statistics, engineering, physics and medical sciences. In practice, when objective function is complicated, the optimization procedure requires a lot of computation efforts, leading to a time-consuming process. This work introduces a NMA solver engine fully implemented on FPGA hardware and performs design space exploration to provide various solutions suitable for FPGA device.
Our laboratory is credited for the discovery of enzymatic acetylation of protein, a phenomenon un... more Our laboratory is credited for the discovery of enzymatic acetylation of protein, a phenomenon unknown till we identified an enzyme termed acetoxy drug: protein transacetylase (TAase), catalyzing the transfer of acetyl group from polyphenolic acetates to receptor proteins (RP). Later, TAase was identified as calreticulin (CR), an endoplasmic reticulum luminal protein. CR was termed calreticulin transacetylase (CRTAase). Our persistent study revealed that CR like other families of histone acetyltransferases (HATs) such as p300, Rtt109, PCAF, and ESA1, undergoes autoacetylation. The autoacetylated CR was characterized as a stable intermediate in CRTAase catalyzed protein acetylation, and similar was the case with ESA1. The autoacetylation of CR like that of HATs was found to enhance protein-protein interaction. CR like HAT-1, CBP, and p300 mediated the acylation of RP utilizing acetyl CoA and propionyl CoA as the substrates. The similarities between CRTAase and HATs in mediating prote...
... methods for which the external excitation is excluded and considered, respectively, in theper... more ... methods for which the external excitation is excluded and considered, respectively, in theperformance index (cf ... Optimal vibration control of a smart rotor blade ... where Qij and Eij are transformed reduced stiffnesses and reduced piezoelectric coefficients of the composite blade ...
We report a male patient who presented with pyrexia, generalized lymphadenopathy, hepatosplenomeg... more We report a male patient who presented with pyrexia, generalized lymphadenopathy, hepatosplenomegaly, and pleural effusion with no cutaneous or musculoskeletal symptoms. Despite extensive investigation, no cause was detected. His initial serology was also negative for autoantibodies. The patient was placed on a trial of antitubercular treatment in view of a positive Mantoux test. His disease evolved into the full clinical picture of systemic lupus erythematosus with nephritis (World Health Organisation class IV) and strongly positive antinuclear antibody and dsDNA over a period of months. He was treated successfully with intravenous cyclophosphamide pulses along with oral prednisolone, and the disease was still in remission after 3 years of follow-up.
Proceedings of the National Academy of Sciences, 2011
To catalog protein-altering mutations that may drive the development of prostate cancers and thei... more To catalog protein-altering mutations that may drive the development of prostate cancers and their progression to metastatic disease systematically, we performed whole-exome sequencing of 23 prostate cancers derived from 16 different lethal metastatic tumors and three high-grade primary carcinomas. All tumors were propagated in mice as xenografts, designated the LuCaP series, to model phenotypic variation, such as responses to cancer-directed therapeutics. Although corresponding normal tissue was not available for most tumors, we were able to take advantage of increasingly deep catalogs of human genetic variation to remove most germline variants. On average, each tumor genome contained ∼200 novel nonsynonymous variants, of which the vast majority was specific to individual carcinomas. A subset of genes was recurrently altered across tumors derived from different individuals, including TP53, DLK2, GPC6, and SDF4. Unexpectedly, three prostate cancer genomes exhibited substantially hig...
Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substan... more Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substantial amino acid identity and together constitute ~50 % of the total penicillin-binding proteins of E. coli. PBP5 helps maintain intrinsic β-lactam resistance within the cell. To test if PBP6 and DacD play simlar roles, we deleted dacC and dacD individually, and dacC in combination with dacA, from E. coli 2443 and compared β-lactam sensitivity of the mutants and the parent strain. β-Lactam resistance was complemented by wild-type, but not dd-carboxypeptidase-deficient PBP5, confirming that enzymic activity of PBP5 is essential for β-lactam resistance. Deletion of dacC and expression of PBP6 during exponential or stationary phase did not alter β-lactam resistance of a dacA mutant. Expression of DacD during mid-exponential phase partially restored β-lactam resistance of the dacA mutant. Therefore, PBP5 dd-carboxypeptidase activity is essential for intrinsic β-lactam resistance of E. coli an...
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