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Peiffer-Smadja N, Rawson TM, Ahmad R, Buchard A, Georgiou P, Lescure FX, Birgand G, Holmes AH. Machine learning for clinical decision support in infectious diseases: a narrative review of current applications. Clin Microbiol Infect 2019; 26:584-595. [PMID: 31539636 DOI: 10.1016/j.cmi.2019.09.009] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Machine learning (ML) is a growing field in medicine. This narrative review describes the current body of literature on ML for clinical decision support in infectious diseases (ID). OBJECTIVES We aim to inform clinicians about the use of ML for diagnosis, classification, outcome prediction and antimicrobial management in ID. SOURCES References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, biorXiv, ACM Digital Library, arXiV and IEEE Xplore Digital Library up to July 2019. CONTENT We found 60 unique ML-clinical decision support systems (ML-CDSS) aiming to assist ID clinicians. Overall, 37 (62%) focused on bacterial infections, 10 (17%) on viral infections, nine (15%) on tuberculosis and four (7%) on any kind of infection. Among them, 20 (33%) addressed the diagnosis of infection, 18 (30%) the prediction, early detection or stratification of sepsis, 13 (22%) the prediction of treatment response, four (7%) the prediction of antibiotic resistance, three (5%) the choice of antibiotic regimen and two (3%) the choice of a combination antiretroviral therapy. The ML-CDSS were developed for intensive care units (n = 24, 40%), ID consultation (n = 15, 25%), medical or surgical wards (n = 13, 20%), emergency department (n = 4, 7%), primary care (n = 3, 5%) and antimicrobial stewardship (n = 1, 2%). Fifty-three ML-CDSS (88%) were developed using data from high-income countries and seven (12%) with data from low- and middle-income countries (LMIC). The evaluation of ML-CDSS was limited to measures of performance (e.g. sensitivity, specificity) for 57 ML-CDSS (95%) and included data in clinical practice for three (5%). IMPLICATIONS Considering comprehensive patient data from socioeconomically diverse healthcare settings, including primary care and LMICs, may improve the ability of ML-CDSS to suggest decisions adapted to various clinical contexts. Currents gaps identified in the evaluation of ML-CDSS must also be addressed in order to know the potential impact of such tools for clinicians and patients.
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Review |
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Arakawa H, Ahmad R, Naoui M, Tajmir-Riahi HA. A comparative study of calf thymus DNA binding to Cr(III) and Cr(VI) ions. Evidence for the guanine N-7-chromium-phosphate chelate formation. J Biol Chem 2000; 275:10150-3. [PMID: 10744697 DOI: 10.1074/jbc.275.14.10150] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromium(VI) salts are well known to be mutagens and carcinogens and to easily cross the cell membranes. Because they are powerful oxidizing agents, Cr(VI) reacts with intracellular materials to reduce to trivalent form, which binds DNA. This study was designed to investigate the interaction of calf thymus DNA with Cr(VI) and Cr(III) in aqueous solution at pH 6.5-7.5, using Cr(VI)/DNA(P) molar ratios (r) of 1:20 to 2:1 and Cr(III)/DNA(P) molar ratios (r) of 1:80 to 1:2. UV-visible and Fourier transform infrared (FTIR) difference spectroscopic methods were used to determine the metal ion-binding sites, binding constants, and the effect of cation complexation on DNA secondary structure. Spectroscopic results showed no interaction of Cr(VI) with DNA at low anion concentrations (r = 1:20 to 1:1), whereas some perturbations of DNA bases and backbone phosphate were observed at very high Cr(VI) contents (r > 1) with overall binding constant of K = 508 M(-1). Cr(III) chelates DNA via guanine N-7 and the nearest PO(2) group with overall binding constant of K = 3.15 x 10(3) M(-1). Evidence for cation chelate formation comes from major shiftings and intensity variations of the guanine band at 1717 and the phosphate asymmetric stretching vibration at 1222 cm(-1). At low Cr(III) concentration (r = 1:40), the number of Cr(III) ions bound to DNA were 6-7 cations/500 base pairs, and this increased to 30-35 cations/500 base pairs at high metal ion content (r = 1:4). DNA condensation occurred at high cation concentration (r = 1:10). No major alteration of DNA conformation was observed, and the biopolymer remained in the B family structure upon chromium complexation.
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Comparative Study |
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Ahmad R, Sorrell MF, Batra SK, Dhawan P, Singh AB. Gut permeability and mucosal inflammation: bad, good or context dependent. Mucosal Immunol 2017; 10:307-317. [PMID: 28120842 PMCID: PMC6171348 DOI: 10.1038/mi.2016.128] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/29/2016] [Indexed: 02/04/2023]
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease. A breach in the mucosal barrier, otherwise known as "leaky gut," is alleged to promote mucosal inflammation by intensifying immune activation. However, interaction between the luminal antigen and mucosal immune system is necessary to maintain mucosal homeostasis. Furthermore, manipulations leading to deregulated gut permeability have resulted in susceptibility in mice to colitis as well as to creating adaptive immunity. These findings implicate a complex but dynamic association between mucosal permeability and immune homeostasis; however, they also emphasize that compromised gut permeability alone may not be sufficient to induce colitis. Emerging evidence further supports the role(s) of proteins associated with the mucosal barrier in epithelial injury and repair: manipulations of associated proteins also modified epithelial differentiation, proliferation, and apoptosis. Taken together, the role of gut permeability and proteins associated in regulating mucosal inflammatory diseases appears to be more complex than previously thought. Herein, we review outcomes from recent mouse models where gut permeability was altered by direct and indirect effects of manipulating mucosal barrier-associated proteins, to highlight the significance of mucosal permeability and the non-barrier-related roles of these proteins in regulating chronic mucosal inflammatory conditions.
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Ajmal M, Rao RA, Ahmad R, Ahmad J. Adsorption studies on Citrus reticulata (fruit peel of orange): removal and recovery of Ni(II) from electroplating wastewater. JOURNAL OF HAZARDOUS MATERIALS 2000; 79:117-131. [PMID: 11040390 DOI: 10.1016/s0304-3894(00)00234-x] [Citation(s) in RCA: 162] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The ability of fruit peel of orange to remove Zn, Ni, Cu, Pb and Cr from aqueous solution by adsorption was studied. The adsorption was in the order of Ni(II)>Cu(II)>Pb(II)>Zn(II)>Cr(II). The extent of removal of Ni(II) was found to be dependent on sorbent dose, initial concentration, pH and temperature. The adsorption follows first-order kinetics. The process is endothermic showing monolayer adsorption of Ni(II), with a maximum adsorption of 96% at 50 degrees C for an initial concentration of 50 mg l(-1) at pH 6. Thermodynamic parameters were also evaluated. Desorption was possible with 0.05 M HCl and was found to be 95.83% in column and 76% in batch process, respectively. The spent adsorbent was regenerated and recycled thrice. The removal and recovery was also done in wastewater and was found to be 89% and 93.33%, respectively.
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Ahmad R, Kookana RS, Alston AM, Skjemstad JO. The nature of soil organic matter affects sorption of pesticides. 1. Relationships with carbon chemistry as determined by 13C CPMAS NMR spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2001; 35:878-884. [PMID: 11351530 DOI: 10.1021/es001446i] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The structural composition of soil organic matter (SOM) was determined in twenty-seven soils with different vegetation from several ecological zones of Australia and Pakistan using solid-state CPMAS 13C NMR. The SOM was characterized using carbon types derived from the NMR spectra. Relationships were determined between Koc (sorption per unit organic C) of carbaryl(1-naphthylmethylcarbamate) and phosalone (S-6-chloro-2,3-dihydro-2-oxobenzoxazol-3-ylmethyl O,O-diethyl phosphorodithioate) and the nature of organic matter in the soils. Substantial variations were revealed in the structural composition of organic matter in the soils studied. The variations in Koc values of the pesticides observed for the soils could be explained only when variations in the aromatic components of SOM were taken into consideration. The highly significant positive correlations of aromaticity of SOM and Koc values of carbaryl and phosalone revealed that the aromatic component of SOM is a good predictor of a soil's ability to bind such nonionic pesticides.
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Waraich E, Ahmad R, Halim A, Aziz T. Alleviation of temperature stress by nutrient management in crop plants: a review. JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION 2012; 12:221-244. [PMID: 0 DOI: 10.4067/s0718-95162012000200003] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
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123 |
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Ahmad R, Sindhu ST, Toma E, Morisset R, Vincelette J, Menezes J, Ahmad A. Evidence for a correlation between antibody-dependent cellular cytotoxicity-mediating anti-HIV-1 antibodies and prognostic predictors of HIV infection. J Clin Immunol 2001; 21:227-33. [PMID: 11403230 DOI: 10.1023/a:1011087132180] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using our gp120/41-expressing, NK cell activity-resistant CEM.NKR cell clones as targets in HIV-1-specific antibody-dependent cellular cytotoxicity (ADCC) assays, we demonstrate here that the serum titers of anti-HIV-1 ADCC antibodies bear a significant (P < 0.05) positive correlation with the peripheral blood CD4+ T cell counts and a negative one with the number of copies of HIV-1 RNA in the plasma of HIV-infected individuals. These findings underscore the importance of these antibodies as a protective immune parameter in these infections.
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Charani E, Ahmad R, Rawson TM, Castro-Sanchèz E, Tarrant C, Holmes AH. The Differences in Antibiotic Decision-making Between Acute Surgical and Acute Medical Teams: An Ethnographic Study of Culture and Team Dynamics. Clin Infect Dis 2019; 69:12-20. [PMID: 30445453 PMCID: PMC6579961 DOI: 10.1093/cid/ciy844] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/28/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Cultural and social determinants influence antibiotic decision-making in hospitals. We investigated and compared cultural determinants of antibiotic decision-making in acute medical and surgical specialties. METHODS An ethnographic observational study of antibiotic decision-making in acute medical and surgical teams at a London teaching hospital was conducted (August 2015-May 2017). Data collection included 500 hours of direct observations, and face-to-face interviews with 23 key informants. A grounded theory approach, aided by Nvivo 11 software, analyzed the emerging themes. An iterative and recursive process of analysis ensured saturation of the themes. The multiple modes of enquiry enabled cross-validation and triangulation of the findings. RESULTS In medicine, accepted norms of the decision-making process are characterized as collectivist (input from pharmacists, infectious disease, and medical microbiology teams), rationalized, and policy-informed, with emphasis on de-escalation of therapy. The gaps in antibiotic decision-making in acute medicine occur chiefly in the transition between the emergency department and inpatient teams, where ownership of the antibiotic prescription is lost. In surgery, team priorities are split between 3 settings: operating room, outpatient clinic, and ward. Senior surgeons are often absent from the ward, leaving junior staff to make complex medical decisions. This results in defensive antibiotic decision-making, leading to prolonged and inappropriate antibiotic use. CONCLUSIONS In medicine, the legacy of infection diagnosis made in the emergency department determines antibiotic decision-making. In surgery, antibiotic decision-making is perceived as a nonsurgical intervention that can be delegated to junior staff or other specialties. Different, bespoke approaches to optimize antibiotic prescribing are therefore needed to address these specific challenges.
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Comparative Study |
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Ren J, Bharti A, Raina D, Chen W, Ahmad R, Kufe D. MUC1 oncoprotein is targeted to mitochondria by heregulin-induced activation of c-Src and the molecular chaperone HSP90. Oncogene 2005; 25:20-31. [PMID: 16158055 DOI: 10.1038/sj.onc.1209012] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The MUC1 heterodimeric transmembrane glycoprotein is aberrantly overexpressed by most human carcinomas. The MUC1 C-terminal subunit localizes to mitochondria and blocks stress-induced activation of the intrinsic apoptotic pathway. How MUC1 is delivered to mitochondria is not known. The present studies demonstrate that MUC1 forms intracellular complexes with HSP70 and HSP90. We show that the MUC1 cytoplasmic domain binds directly to HSP70 in vitro. By contrast, binding of MUC1 to HSP90 in vitro is induced by c-Src-mediated phosphorylation of the MUC1 cytoplasmic domain. c-Src also increases binding of MUC1 to HSP90 in cells. In concert with these results, we show that heregulin (HRG), a ligand for ErbB receptors, activates c-Src and, in turn, stimulates binding of MUC1 to HSP90. We also show that inhibitors of c-Src or HSP90 block HRG-induced targeting of MUC1 to mitochondria and integration of MUC1 into the mitochondrial outer membrane. These findings indicate that MUC1 is delivered to mitochondria by a mechanism involving activation of the ErbB receptor-->c-Src pathway and transport by the molecular chaperone HSP70/HSP90 complex.
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Rajabi H, Alam M, Takahashi H, Kharbanda A, Guha M, Ahmad R, Kufe D. MUC1-C oncoprotein activates the ZEB1/miR-200c regulatory loop and epithelial-mesenchymal transition. Oncogene 2013; 33:1680-9. [PMID: 23584475 DOI: 10.1038/onc.2013.114] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 12/18/2012] [Accepted: 02/18/2013] [Indexed: 02/07/2023]
Abstract
The epithelial-mesenchymal transition (EMT) is activated in cancer cells by ZEB1, a member of the zinc finger/homeodomain family of transcriptional repressors. The mucin 1 (MUC1) heterodimeric protein is aberrantly overexpressed in human carcinoma cells. The present studies in breast cancer cells demonstrate that the oncogenic MUC1-C subunit induces expression of ZEB1 by a NF-κB (nuclear factor kappa B) p65-dependent mechanism. MUC1-C occupies the ZEB1 promoter with NF-κB p65 and thereby promotes ZEB1 transcription. In turn, ZEB1 associates with MUC1-C and the ZEB1/MUC1-C complex contributes to the transcriptional suppression of miR-200c, an inducer of epithelial differentiation. The co-ordinate upregulation of ZEB1 and suppression of miR-200c has been linked to the induction of EMT. In concert with the effects of MUC1-C on ZEB1 and miR-200c, we show that MUC1-C induces EMT and cellular invasion by a ZEB1-mediated mechanism. These findings indicate that (i) MUC1-C activates ZEB1 and suppresses miR-200c with the induction of EMT and (ii) targeting MUC1-C could be an effective approach for the treatment of breast and possibly other types of cancers that develop EMT properties.
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Research Support, N.I.H., Extramural |
12 |
98 |
11
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Ahmad R, Kumar B, Chen Z, Chen X, Müller D, Lele SM, Washington MK, Batra SK, Dhawan P, Singh AB. Loss of claudin-3 expression induces IL6/gp130/Stat3 signaling to promote colon cancer malignancy by hyperactivating Wnt/β-catenin signaling. Oncogene 2017; 36:6592-6604. [PMID: 28783170 PMCID: PMC6512312 DOI: 10.1038/onc.2017.259] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/28/2017] [Accepted: 06/19/2017] [Indexed: 12/12/2022]
Abstract
The Hyperactivated Wnt/β-catenin signaling acts as a switch to induce EMT and promote colorectal cancer. However, due to its essential role in gut homeostasis, therapeutic targeting of this pathway has proven challenging. Additionally, IL-6/Stat-3 signaling, activated by microbial translocation through the dysregulated mucosal barrier in colon adenomas, facilitates the adenoma to adenocarcinomas transition. However, inter-dependence between these signaling pathways and key mucosal barrier components in regulating colon tumorigenesis and cancer progression remains unclear. In current study, we have discovered, using a comprehensive investigative regimen, a novel and tissue specific role of claudin-3, a tight junction integral protein, in inhibiting colon cancer progression by serving as the common rheostat of Stat-3 and Wnt-signaling activation. Loss of claudin-3 also predicted poor patient survival. These findings however contrasted an upregulated claudin-3 expression in other cancer types and implicated role of the epigenetic regulation. Claudin-3−/− mice revealed dedifferentiated and leaky colonic epithelium, and developed invasive adenocarcinoma when subjected to colon cancer. Wnt-signaling hyperactivation, albeit in GSK-3β independent manner, differentiated colon cancer in claudin-3−/− mice versus WT-mice. Claudin-3 loss also upregulated the gp130/IL6/Stat3 signaling in colonic epithelium potentially assisted by infiltrating immune components. Genetic and pharmacological studies confirmed that claudin-3 loss induces Wnt/β-catenin activation, which is further exacerbated by Stat-3-activation and help promote colon cancer. Overall, these novel findings identify claudin-3 as a therapeutic target for inhibiting overactivation of Wnt-signaling to prevent CRC malignancy.
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Research Support, U.S. Gov't, Non-P.H.S. |
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96 |
12
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Takahashi H, Jin C, Rajabi H, Pitroda S, Alam M, Ahmad R, Raina D, Hasegawa M, Suzuki Y, Tagde A, Bronson RT, Weichselbaum R, Kufe D. MUC1-C activates the TAK1 inflammatory pathway in colon cancer. Oncogene 2015; 34:5187-97. [PMID: 25659581 PMCID: PMC4530107 DOI: 10.1038/onc.2014.442] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/31/2014] [Accepted: 12/12/2014] [Indexed: 02/08/2023]
Abstract
The mucin 1 (MUC1) oncoprotein has been linked to the inflammatory response by promoting cytokine-mediated activation of the NF-κB pathway. The TGF-β-activated kinase 1 (TAK1) is an essential effector of proinflammatory NF-κB signaling that also regulates cancer cell survival. The present studies demonstrate that the MUC1-C transmembrane subunit induces TAK1 expression in colon cancer cells. MUC1 also induces TAK1 in a MUC1(+/-)/IL-10(-/-) mouse model of colitis and colon tumorigenesis. We show that MUC1-C promotes NF-κB-mediated activation of TAK1 transcription and, in a positive regulatory loop, MUC1-C contributes to TAK1-induced NF-κB signaling. In this way, MUC1-C binds directly to TAK1 and confers the association of TAK1 with TRAF6, which is necessary for TAK1-mediated activation of NF-κB. Targeting MUC1-C thus suppresses the TAK1NF-κB pathway, downregulates BCL-XL and in turn sensitizes colon cancer cells to MEK inhibition. Analysis of colon cancer databases further indicates that MUC1, TAK1 and TRAF6 are upregulated in tumors associated with decreased survival and that MUC1-C-induced gene expression patterns predict poor outcomes in patients. These results support a model in which MUC1-C-induced TAK1NF-κB signaling contributes to intestinal inflammation and colon cancer progression.
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Research Support, U.S. Gov't, Non-P.H.S. |
10 |
86 |
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Mawer GE, Ahmad R, Dobbs SM, McGough JG, Lucas SB, Tooth JA. Prescribing aids for gentamicin. Br J Clin Pharmacol 2012; 1:45-50. [PMID: 22454868 DOI: 10.1111/j.1365-2125.1974.tb00205.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
1 A nomogram and a digital computer program have been developed to calculate dosage schedules of gentamicin for individual patients. The minimum input data consist of the patients' age, sex, body weight and serum creatinine concentration. 2 These prescribing aids have been evaluated in 36 patients with severe Gram negative infections. Renal function ranged from normal to complete anuria. Nomogram dosage schedules gave serum concentrations of gentamicin within the chosen therapeutic limits. Physician dosage schedules gave serum concentrations which sometimes exceeded and sometimes fell below these limits. The validity of the computer program was demonstrated by its ability to predict serum concentrations of gentamicin whatever the dosage schedule. 3 Half the patients recovered from the bacterial infection but seven remained infected and eleven died. Pseudomonas aeruginosa was the most difficult organism to eradicate. 4 Four of the patients who survived developed ataxia and two developed hearing loss at high frequencies. The risk of ototoxicity was a function of mean trough serum gentamicin concentration and duration of treatment. Ototoxicity was only detected in patients with serum creatinine concentrations above 3 mg/100 ml who tended to have higher trough concentrations. When treatment was prolonged beyond 8-10 days the risk of ototoxicity was increased without evidence of further substantial therapeutic benefit.
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Journal Article |
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Nawaz F, Ahmad R, Ashraf MY, Waraich EA, Khan SZ. Effect of selenium foliar spray on physiological and biochemical processes and chemical constituents of wheat under drought stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 113:191-200. [PMID: 25499052 DOI: 10.1016/j.ecoenv.2014.12.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 11/13/2014] [Accepted: 12/01/2014] [Indexed: 05/07/2023]
Abstract
Selenium (Se) is considered an essential micronutrient for humans, animals and plants due to its physiological and antioxidative properties. The positive role of Se in attenuation of drastic effects of various environmental stresses in plants is, however, still unclear and need to be explored. The present study aimed at investigating the physiological and biochemical changes induced by Se foliar spray to improve the drought tolerance potential of wheat. Additionally, we also examined the effect of supplemental Se on uptake of nutrients using detection by ICP-OES. Foliar Se application significantly lowered osmotic potential (13%) that markedly improved turgor by 63%, enhanced transpiration rate (60%), improved accumulation of total soluble sugars (33%) and free amino acids (118%) and activity of antioxidant system which ultimately increased the grain yield by 24%. Supplemental Se also significantly increased Se contents (5.77µgg(-1)DW) and improved Fe (91%) and Na (16%) uptake, whereas it reduced Zn accumulation by 54% and did not affect Ca contents. The results supported our hypothesis that supplemental Se influences nutrients uptake and wheat yield through maintenance of turgor and gas exchange characteristics and enhancement in antioxidant system activity.
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Ahmad R, Arakawa H, Tajmir-Riahi HA. A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: major and minor grooves bindings. Biophys J 2003; 84:2460-6. [PMID: 12668453 PMCID: PMC1302811 DOI: 10.1016/s0006-3495(03)75050-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although structural differences for the Mg-DNA and Ca-DNA complexes are provided in the solid state, such comparative study in aqueous solution has been less investigated. The aim of this study was to examine the bindings of Mg and Ca cations with calf thymus DNA in aqueous solution at physiological pH, using constant concentration of DNA (1.25 or 12.5 mM) and various concentrations of metal ions (2 microM-650 microM). Capillary electrophoresis, UV-visible, and Fourier transform infrared spectroscopic methods were used to determine the cation-binding modes, the binding constants, and DNA structural variations in aqueous solution. Direct Ca-PO(2) binding was evident by major spectral changes (shifting and splitting) of the backbone PO(2) asymmetric stretching at 1222 cm(-1) with K = 4.80 x 10(5) M(-1), whereas an indirect Mg-phosphate interaction occurred (due to the lack of shifting and splitting of the phosphate band at 1222 cm(-1)) with K = 5.6 x 10(4) M(-1). The metal-base bindings were directly for the Mg with K = 3.20 x 10(5) M(-1) and indirectly for the Ca cation with K = 3.0 x 10(4) M(-1). Both major and minor groove bindings were observed with no alteration of the B-DNA conformation.
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research-article |
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Bondar M, Hoogeman M, Mens J, Quint S, Ahmad R, Dhawtal G, Heijmen B. Individualized Nonadaptive and Online-Adaptive Intensity-Modulated Radiotherapy Treatment Strategies for Cervical Cancer Patients Based on Pretreatment Acquired Variable Bladder Filling Computed Tomography Scans. Int J Radiat Oncol Biol Phys 2012; 83:1617-23. [DOI: 10.1016/j.ijrobp.2011.10.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 09/05/2011] [Accepted: 10/06/2011] [Indexed: 10/14/2022]
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Rajah SM, Crow MJ, Penny AF, Ahmad R, Watson DA. The effect of dipyridamole on platelet function: correlation with blood levels in man. Br J Clin Pharmacol 1977; 4:129-33. [PMID: 861128 PMCID: PMC1429003 DOI: 10.1111/j.1365-2125.1977.tb00683.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
1 The effect on platelet functions of dipyridamole (a pyrimido-pyrimidine compound) was compared with a control group of patients taking warfarin. 2 Adhesion, aggregation and platelet factor 4 availability showed a significant decrease in the dypyridamole group. 3 Aggregation and platelet factor 4 showed a significant correlation with blood dipyridamole level. 4 Adhesion, aggregation and platelet factor 4 were reduced below the lower limit of normal at blood dipyridamole levels above 3.5 micronmol/1.
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research-article |
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Tajmir-Riahi HA, Naoui M, Ahmad R. The effects of Cu2+ and Pb2+ on the solution structure of calf thymus DNA: DNA condensation and denaturation studied by Fourier transform ir difference spectroscopy. Biopolymers 1993; 33:1819-27. [PMID: 8268408 DOI: 10.1002/bip.360331208] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The interaction of calf thymus DNA with Cu2+ and Pb2+ was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established. Spectroscopic evidence has shown that at low metal/DNA (P) molar ratios 1/80 and 1/40, copper and lead ions bind mainly to the PO2- of the backbone, resulting in increased base-stacking interaction and duplex stability. The major copper ion base binding via G-C base pairs begins at r > 1/40, while the lead ion base binding occurs at r > 1/20 with the A-T base pairs. The denaturation of DNA begins at r = 1/10 and continues up to r = 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r = 1/2). Metal-DNA binding also results in DNA condensation. No major departure from the B-family structure was observed, upon DNA interaction with these metal ions.
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Ahmad R, Bourgeois S, Postnov A, Schmidt ME, Bormans G, Van Laere K, Vandenberghe W. PET imaging shows loss of striatal PDE10A in patients with Huntington disease. Neurology 2013; 82:279-81. [DOI: 10.1212/wnl.0000000000000037] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Tewari N, Tiwari VK, Mishra RC, Tripathi RP, Srivastava AK, Ahmad R, Srivastava R, Srivastava BS. Synthesis and bioevaluation of glycosyl ureas as alpha-glucosidase inhibitors and their effect on mycobacterium. Bioorg Med Chem 2003; 11:2911-22. [PMID: 12788361 DOI: 10.1016/s0968-0896(03)00214-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycosyl amino esters (2-13) on reaction with different isocyanates resulted in quantitative conversion to glycosyl ureas (14--32). Few of the selected ureas (15-20, 22-28, 30 and 32) on cyclative amidation with DBU/TBAB/4 A MS gave respective dihydropyrimidinones in fair to good yields (33-47). The compounds were screened for alpha-glucosidase inhibitory activity and two (19 and 23) of them showed strong inhibition against rat intestinal alpha-glucosidase. The compounds were also screened against Mycobacterium aurum, however, only one (19) of them exhibited marginal antitubercular activity.
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Ouameur AA, Arakawa H, Ahmad R, Naoui M, Tajmir-Riahi HA. A Comparative study of Fe(II) and Fe(III) interactions with DNA duplex: major and minor grooves bindings. DNA Cell Biol 2005; 24:394-401. [PMID: 15941392 DOI: 10.1089/dna.2005.24.394] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The involvement of the Fe cations in autoxidation in cells and tissues is well documented. DNA is a major target in such reaction, and can chelate Fe cation in many ways. The present study was designed to examine the interaction of calf-thymus DNA with Fe(II) and Fe(III), in aqueous solution at pH 6.5 with cation/DNA (P) (P = phosphate) molar ratios (r) of 1:160 to 1:2. Capillary electrophoresis and Fourier transform infrared (FTIR) difference spectroscopic methods were used to determine the cation binding site, the binding constant, helix stability and DNA conformation in Fe-DNA complexes. Structural analysis showed that at low cation concentration (r = 1/80 and 1/40), Fe(II) binds DNA through guanine N-7 and the backbone PO(2) group with specific binding constants of K(G) = 5.40 x 10(4) M(1) and K(P) = 2.40 x 10(4) M(1). At higher cation content, Fe(II) bindings to adenine N-7 and thymine O-2 are included. The Fe(III) cation shows stronger interaction with DNA bases and the backbone phosphate group. At low cation concentration (r = 1:80), Fe(III) binds mainly to the backbone phosphate group, while at higher metal ion content, cation binding to both guanine N-7 atom and the backbone phosphate group is prevailing with specific binding constants of K(G) = 1.36 x 10(5) M(-1) and K(P) = 5.50 x 10(4) M(-1). At r = 1:10, Fe(II) binding causes a minor helix destabilization, whereas Fe(III) induces DNA condensation. No major DNA conformational changes occurred upon iron complexation and DNA remains in the B-family structure.
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Research Support, Non-U.S. Gov't |
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Burgener A, Rahman S, Ahmad R, Lajoie J, Ramdahin S, Mesa C, Brunet S, Wachihi C, Kimani J, Fowke K, Carr S, Plummer F, Ball TB. Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers. J Proteome Res 2011; 10:5139-49. [PMID: 21973077 DOI: 10.1021/pr200596r] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Not all individuals exposed to HIV-1 become infected, and evidence from HIV-1 highly exposed seronegative women (HIV-1-resistant) suggests that mucosal factors in the female genital tract, the first site of contact for the virus, are playing a role. To better understand factors mediating protection from HIV-1, we performed a large clinical study using the tools of systems biology to fully characterize the cervicovaginal mucosa proteome in HIV-1-resistant women. Cervicovaginal lavage fluid was collected from 293 HIV-1-resistant, uninfected, and infected sex workers and analyzed by 2D-LC LTQ-FT-MS. Of the more than 360 unique proteins identified, 41 were differentially abundant (>3-fold cutoff) in HIV-1-resistant women. The majority of over-abundant proteins were antiproteases (>40%), some with described anti-inflammatory and anti-HIV-1 activity. Quantification of specific anti-HIV-1 antiproteases Serpin A1, Serpin A3, and Cystatin B and an epithelial antiprotease A2ML1 found them to be significantly over-abundant in HIV-1-resistant women (p = 0.004; p = 0.046; p = 0.0003; and p = 0.04, respectively). Expression levels were not correlated to sexual practices or other epidemiological factors. Mucosal antiprotease levels correlated with pro-inflammatory cytokine concentration (p = <0.0001), but independently of pro-inflammatory cytokine levels in HIV-1-resistant women including TNF-alpha, IL-1 alpha, IL-1 beta, IL-6, and IL-8. This comprehensive systems biology approach identifies mucosal serpins and cystatins as novel correlates of HIV-1-resistance. This represents the first study characterizing these factors in the female genital tract.
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Ooi LG, Ahmad R, Yuen KH, Liong MT. Lactobacillus gasseri [corrected] CHO-220 and inulin reduced plasma total cholesterol and low-density lipoprotein cholesterol via alteration of lipid transporters. J Dairy Sci 2011; 93:5048-58. [PMID: 20965319 DOI: 10.3168/jds.2010-3311] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 07/18/2010] [Indexed: 12/13/2022]
Abstract
This randomized, double-blind, placebo-controlled, and parallel-designed study was conducted to investigate the effect of a synbiotic product containing Lactobacillus gasseri [corrected] CHO-220 and inulin on lipid profiles of hypercholesterolemic men and women. Thirty-two hypercholesterolemic men and women with initial mean plasma cholesterol levels of 5.7±0.32 mmol/L were recruited for the 12-wk study. The subjects were randomly allocated to 2 groups; namely the treatment group (synbiotic product) and the control group (placebo), and each received 4 capsules of synbiotic or placebo daily. Our results showed that the mean body weight, energy, and nutrient intake of the subjects did not differ between the 2 groups over the study period. The supplementation of synbiotic reduced plasma total cholesterol and low-density lipoprotein (LDL)-cholesterol by 7.84 and 9.27%, respectively, compared with the control over 12 wk. Lipoproteins were subsequently subfractionated and characterized. The synbiotic supplementation resulted in a lower concentration of triglycerides in the very low, intermediate, low, and high-density lipoprotein particles compared with the control over 12 wk. The concentration of triglycerides in lipoproteins is positively correlated with an increased risk of atherosclerosis. Our results showed that the synbiotic might exhibit an atheropreventive characteristic. Cholesteryl ester (CE) in the high-density lipoprotein particles of the synbiotic group was also higher compared with the control, indicating greater transport of cholesterol in the form of CE to the liver for hydrolysis. This may have led to the reduced plasma total cholesterol level of the synbiotic group. The supplementation of synbiotic also reduced the concentration of CE in the LDL particles compared with the control, leading to the formation of smaller and denser particles that are more easily removed from blood. This supported the reduced LDL-cholesterol level of the synbiotic group compared with the control. Our present study showed that the synbiotic product improved plasma total- and LDL-cholesterol levels by modifying the interconnected pathways of lipid transporters. In addition, although Lactobacillus gasseri [corrected] CHO-220 could deconjugate bile, our results showed a statistically insignificant difference in the levels of conjugated, deconjugated, primary, and secondary bile acids between the synbiotic and control groups over 12 wk, indicating safety from bile-related toxicity.
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Sommerville CAM, Limongelli P, Pai M, Ahmad R, Stamp G, Habib NA, Williamson RCN, Jiao LR. Survival analysis after pancreatic resection for ampullary and pancreatic head carcinoma: an analysis of clinicopathological factors. J Surg Oncol 2010; 100:651-6. [PMID: 19722229 DOI: 10.1002/jso.21390] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES Surgery remains the only curative option for the treatment of pancreatic and ampullary carcinomas. To examine the survival differences between ampullary and pancreatic head carcinomas after pancreaticoduodenectomy. METHODS A retrospective review of patients with ampullary or pancreatic head adenocarcinoma undergoing curative resection during a 6-year period prior to 2000. RESULTS A total of 104 patients underwent pancreaticoduodenectomy for pancreatic head and ampullary carcinomas (n = 65 and n = 39, respectively). Histologically, pancreatic cancer was worse, with more lymph node involvement and more positive resection margins and vascular and perineural invasions than found in ampullary carcinoma. The median disease-free and overall survival rates were significantly better for ampullary cancer when compared with pancreatic cancer (17 vs. 9 months [P = 0.001] and 35 vs. 24 months [P = 0.006], respectively). The actuarial 5-year disease-free and overall survival rates were 4.4% and 10.5%, respectively, for pancreatic carcinoma and 27.9% and 31.8%, respectively, for ampullary carcinoma. Multivariate analysis showed that microscopic resection margin involvement (P = 0.02) and involvement of over three nodes (P < 0.001) were significant factors affecting the overall survival for pancreatic and ampullary carcinomas, respectively. CONCLUSIONS In this study, patients with ampullary carcinoma have a better prognosis and survival than those with pancreatic carcinoma.
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Ali A, Nain A, Chand D, Ahmad R. Volumetric, ultrasonic, viscometric and refractive index behavior of binary mixtures of 2,2,4-trimethylpentane with aromatic hydrocarbons: An experimental and theoretical study. J Mol Liq 2006. [DOI: 10.1016/j.molliq.2005.02.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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