150 results on '"Gardy J"'
Search Results
2. Les inégalités sociales de santé : quelle influence sur l’histoire naturelle du cancer colorectal ?
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Mulliri, A., Gardy, J., Dejardin, O., Bouvier, V., Pocard, M., and Alves, A.
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- 2023
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3. Nanomaterials for solar energy capture and steam generation
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Amjad, Muhammad, primary, Haruna, Maje Alhaji, additional, and Gardy, J., additional
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- 2021
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- View/download PDF
4. List of contributors
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Afrand, Masoud, primary, Ahmed, Ejaz, additional, Ahmed, Waqar, additional, Ali, Hafiz Muhammad, additional, Amjad, Muhammad, additional, Amli, H., additional, Awad, Afrah, additional, Babar, Hamza, additional, Behjani, Mohammadreza Alizadeh, additional, Booth, M., additional, Chamoli, Pankaj, additional, Cheraghian, G. Goshtasp, additional, Dar, Riyaz Ahmad, additional, Dhanak, V., additional, Dondapati, Raja Sekhar, additional, Esmaeili, Hossein, additional, Ferguson, Victoria, additional, Fleck, N., additional, Foroozesh, Jalal, additional, Gardy, J., additional, Haruna, Maje Alhaji, additional, Hassan, Israr Ul, additional, Hassanpour, Ali, additional, Hormozi, Faramarz, additional, Hussain, Syed Asad, additional, Iqbal, T., additional, Ismail, Mohammed S., additional, Karimi, Nader, additional, Khalid, N.R., additional, Khalid, Sadia, additional, Khan, Yaqoob, additional, Kumar, Neeraj, additional, Kumar, Sanjeev, additional, Kumar, Sunil, additional, Magami, Saminu Musa, additional, Malik, Mohammad Azad, additional, Manoj, M.K., additional, Naikoo, Gowhar Ahmad, additional, Nakisa, Mehdi, additional, Nawaz, Saima, additional, Nourafkan, Ehsan, additional, Phani, M. Kalyan, additional, Pourkashanian, Mohamed, additional, Rashidi, Saman, additional, Shah, Tayyab Raza, additional, Sharma, Ashutosh, additional, Silva, S. Ravi P., additional, Srivastava, Ashok Kumar, additional, Sultan, Muhammad, additional, Tahir, M.B., additional, Thadela, Sudheer, additional, Waleed, Muayad, additional, and Zhang, Wei, additional
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- 2021
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5. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
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Sonnenkalb, L, Carter, JJ, Spitaleri, A, Iqbal, Z, Hunt, M, Malone, KM, Utpatel, C, Cirillo, DM, Rodrigues, C, Nilgiriwala, KS, Fowler, PW, Merker, M, Niemann, S, Barilar, I, Battaglia, S, Borroni, E, Brandao, AP, Brankin, A, Cabibbe, AM, Carter, J, Claxton, P, Clifton, DA, Cohen, T, Coronel, J, Crook, DW, Dreyer, V, Earle, SG, Escuyer, V, Ferrazoli, L, Fu Gao, G, Gardy, J, Gharbia, S, Ghisi, KT, Ghodousi, A, Gibertoni Cruz, AL, Grandjean, L, Grazian, C, Groenheit, R, Guthrie, JL, He, W, Hoffmann, H, Hoosdally, SJ, Ismail, NA, Jarrett, L, Joseph, L, Jou, R, Kambli, P, Khot, R, Knaggs, J, Koch, A, Kohlerschmidt, D, Kouchaki, S, Lachapelle, AS, Lalvani, A, Grandjean Lapierre, S, Laurenson, IF, Letcher, B, Lin, W-H, Liu, C, Liu, D, Mandal, A, Mansjö, M, Matias, D, Meintjes, G, De Freitas Mendes, F, Mihalic, M, Millard, J, Miotto, P, Mistry, N, Moore, D, Musser, KA, Ngcamu, D, Hoang, NN, Nimmo, C, Okozi, N, Oliveira, RS, Omar, SV, Paton, N, Peto, TEA, Watanabe Pinhata, JM, Plesnik, S, Puyen, ZM, Rabodoarivelo, MS, Rakotosamimanana, N, Rancoita, PMV, Rathod, P, Rodger, G, Rodwell, TC, Roohi, E, Santos-Lazaro, D, Shah, S, Kohl, TA, Smith, G, Solano, W, Supply, P, Surve, U, Tahseen, S, Thuong, NTT, Thwaites, G, Todt, K, Trovato, A, Van Rie, A, Vijay, S, Walker, TM, Walker, SA, Warren, R, Werngren, J, Wijkander, M, Wilkinson, RJ, Wilson, DJ, Wintringer, P, Yu, XX, Yang, Y, Zhao, Y, Yao, S-Y, Zhu, B, and Consortium, Comprehensive Resistance Prediction for Tuberculosis: an International
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Microbiology (medical) ,Infectious Diseases ,Virology ,Microbiology - Abstract
Background Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis; however, the understanding of resistance mechanisms is poor, which is hampering rapid molecular diagnostics. Some bedaquiline-resistant mutants are also cross-resistant to clofazimine. To decipher bedaquiline and clofazimine resistance determinants, we combined experimental evolution, protein modelling, genome sequencing, and phenotypic data. Methods For this in-vitro and in-silico data analysis, we used a novel in-vitro evolutionary model using subinhibitory drug concentrations to select bedaquiline-resistant and clofazimine-resistant mutants. We determined bedaquiline and clofazimine minimum inhibitory concentrations and did Illumina and PacBio sequencing to characterise selected mutants and establish a mutation catalogue. This catalogue also includes phenotypic and genotypic data of a global collection of more than 14 000 clinical Mycobacterium tuberculosis complex isolates, and publicly available data. We investigated variants implicated in bedaquiline resistance by protein modelling and dynamic simulations. Findings We discerned 265 genomic variants implicated in bedaquiline resistance, with 250 (94%) variants affecting the transcriptional repressor (Rv0678) of the MmpS5–MmpL5 efflux system. We identified 40 new variants in vitro, and a new bedaquiline resistance mechanism caused by a large-scale genomic rearrangement. Additionally, we identified in vitro 15 (7%) of 208 mutations found in clinical bedaquiline-resistant isolates. From our in-vitro work, we detected 14 (16%) of 88 mutations so far identified as being associated with clofazimine resistance and also seen in clinically resistant strains, and catalogued 35 new mutations. Structural modelling of Rv0678 showed four major mechanisms of bedaquiline resistance: impaired DNA binding, reduction in protein stability, disruption of protein dimerisation, and alteration in affinity for its fatty acid ligand. Interpretation Our findings advance the understanding of drug resistance mechanisms in M tuberculosis complex strains. We have established an extended mutation catalogue, comprising variants implicated in resistance and susceptibility to bedaquiline and clofazimine. Our data emphasise that genotypic testing can delineate clinical isolates with borderline phenotypes, which is essential for the design of effective treatments. Funding Leibniz ScienceCampus Evolutionary Medicine of the Lung, Deutsche Forschungsgemeinschaft, Research Training Group 2501 TransEvo, Rhodes Trust, Stanford University Medical Scientist Training Program, National Institute for Health and Care Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Bill & Melinda Gates Foundation, Wellcome Trust, and Marie Skłodowska-Curie Actions.
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- 2023
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- View/download PDF
6. Effect of advanced catalysts on tire waste pyrolysis oil
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Miandad, R., Barakat, M.A., Rehan, M., Aburiazaiza, A.S., Gardy, J., and Nizami, A.S.
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- 2018
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7. Exogenous mineralization of hard tissues using photo-absorptive minerals and femto-second lasers; the case of dental enamel
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Anastasiou, A.D., Strafford, S., Thomson, C.L., Gardy, J., Edwards, T.J., Malinowski, M., Hussain, S.A., Metzger, N.K., Hassanpour, A., Brown, C.T.A., Brown, A.P., Duggal, M.S., and Jha, A.
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- 2018
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8. Waste to biodiesel: A preliminary assessment for Saudi Arabia
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Rehan, M., Gardy, J., Demirbas, A., Rashid, U., Budzianowski, W.M., Pant, Deepak, and Nizami, A.S.
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- 2018
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9. Effect of zeolite catalysts on pyrolysis liquid oil
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Rehan, M., Miandad, R., Barakat, M.A., Ismail, I.M.I., Almeelbi, T., Gardy, J., Hassanpour, A., Khan, M.Z., Demirbas, A., and Nizami, A.S.
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- 2017
- Full Text
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10. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
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Sonnenkalb, Lindsay, Carter, Joshua James, Spitaleri, Andrea, Iqbal, Zamin, Hunt, Martin, Malone, Kerri Marie, Utpatel, Christian, Cirillo, Daniela Maria, Rodrigues, Camilla, Nilgiriwala, Kayzad Soli, Fowler, Philip William, Merker, Matthias, Niemann, Stefan, Consortium, The Comprehensive Resistance Prediction for Tuberculosis: an International, Barilar, I, Battaglia, S, Borroni, E, Brandao, AP, Brankin, A, Cabibbe, AM, Carter, J, Claxton, P, Clifton, DA, Cohen, T, Coronel, J, Crook, DW, Dreyer, V, Earle, SG, Escuyer, V, Ferrazoli, L, Fowler, PW, Gao, G Fu, Gardy, J, Gharbia, S, Ghisi, KT, Ghodousi, A, Cruz, AL Gibertoni, Grandjean, L, Grazian, C, Groenheit, R, Guthrie, JL, He, W, Hoffmann, H, Hoosdally, SJ, Ismail, NA, Jarrett, L, Joseph, L, Jou, R, Kambli, P, Khot, R, Knaggs, J, Koch, A, Kohlerschmidt, D, Kouchaki, S, Lachapelle, AS, Lalvani, A, Lapierre, S Grandjean, Laurenson, IF, Letcher, B, Lin, WH, Liu, C, Liu, D, Malone, KM, Mandal, A, Mansjö, M, Matias, D, Meintjes, G, de Freitas Mendes, F, Mihalic, M, Millard, J, Miotto, P, Mistry, N, Moore, D, Musser, KA, Ngcamu, D, Hoang, NN, Nimmo, C, Okozi, N, Oliveira, RS, Omar, SV, Paton, N, Peto, TE, Pinhata, JM Watanabe, Plesnik, S, Puyen, ZM, Rabodoarivelo, MS, Rakotosamimanana, N, Rancoita, PM, Rathod, P, Rodger, G, Rodwell, TC, Roohi, E, Santos-Lazaro, D, Shah, S, Kohl, TA, Smith, G, Solano, W, Supply, P, Surve, U, Tahseen, S, and Thuong, NTT
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Model organisms ,Human Biology & Physiology ,FOS: Clinical medicine ,Immunology ,Infectious Disease - Abstract
Background: Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis; however, the understanding of resistance mechanisms is poor, which is hampering rapid molecular diagnostics. Some bedaquiline-resistant mutants are also cross-resistant to clofazimine. To decipher bedaquiline and clofazimine resistance determinants, we combined experimental evolution, protein modelling, genome sequencing, and phenotypic data. Methods: For this in-vitro and in-silico data analysis, we used a novel in-vitro evolutionary model using subinhibitory drug concentrations to select bedaquiline-resistant and clofazimine-resistant mutants. We determined bedaquiline and clofazimine minimum inhibitory concentrations and did Illumina and PacBio sequencing to characterise selected mutants and establish a mutation catalogue. This catalogue also includes phenotypic and genotypic data of a global collection of more than 14 000 clinical Mycobacterium tuberculosis complex isolates, and publicly available data. We investigated variants implicated in bedaquiline resistance by protein modelling and dynamic simulations. Findings: We discerned 265 genomic variants implicated in bedaquiline resistance, with 250 (94%) variants affecting the transcriptional repressor (Rv0678) of the MmpS5–MmpL5 efflux system. We identified 40 new variants in vitro, and a new bedaquiline resistance mechanism caused by a large-scale genomic rearrangement. Additionally, we identified in vitro 15 (7%) of 208 mutations found in clinical bedaquiline-resistant isolates. From our in-vitro work, we detected 14 (16%) of 88 mutations so far identified as being associated with clofazimine resistance and also seen in clinically resistant strains, and catalogued 35 new mutations. Structural modelling of Rv0678 showed four major mechanisms of bedaquiline resistance: impaired DNA binding, reduction in protein stability, disruption of protein dimerisation, and alteration in affinity for its fatty acid ligand. Interpretation: Our findings advance the understanding of drug resistance mechanisms in M tuberculosis complex strains. We have established an extended mutation catalogue, comprising variants implicated in resistance and susceptibility to bedaquiline and clofazimine. Our data emphasise that genotypic testing can delineate clinical isolates with borderline phenotypes, which is essential for the design of effective treatments. Funding: Leibniz ScienceCampus Evolutionary Medicine of the Lung, Deutsche Forschungsgemeinschaft, Research Training Group 2501 TransEvo, Rhodes Trust, Stanford University Medical Scientist Training Program, National Institute for Health and Care Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Bill & Melinda Gates Foundation, Wellcome Trust, and Marie Skłodowska-Curie Actions.
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- 2023
- Full Text
- View/download PDF
11. A clonal outbreak of tuberculosis in a homeless population in the interior of British Columbia, Canada, 2008–2015
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CHENG, J. M., HISCOE, L., POLLOCK, S. L., HASSELBACK, P., GARDY, J. L., and PARKER, R.
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- 2015
12. A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates
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Fowler, P.W., Wright, C., Spiers, H., Zhu, T., Baeten, E.M.L., Hoosdally, S.W., Cruz, A.L.G., Roohi, A., Kouchaki, S., Walker, T.M., Peto, T.E.A., Miller, G., Lintott, C., Clifton, D., Crook, D.W., Walker, A.S., Barilar, I., Battaglia, S., Borroni, E., Brandao, A.P., Brankin, A., Cabibbe, A.M., Carter, J., Chetty, D., Cirillo, D.M., Claxton, P., Clifton, D.A., Cohen, T., Coronel, Jorge, Dreyer, V., Earle, S.G., Escuyer, V., Ferrazoli, L., Gao, G.F., Gardy, J., Gharbia, S., Ghisi, K.T., Ghodousi, A., Grandjean, Louis, Grazian, C., Groenheit, R., Guthrie, J.L., He, W., Hoffmann, H., Hoosdally, S.J., Martinhunt, M., Iqbal, Z., Ismail, N.A., Jarrett, L., Joseph, L., Jou, R., Kambli, P., Khot, R., Knaggs, J., Koch, A., Kohlerschmidt, D., Lachapelle, A.S., Lalvani, A., Lapierre, S.G., Laurenson, I.F., Letcher, B., Lin, W.-H., Liu, C., Liu, D., Malone, K.M., Mandal, A., Mansjõ, M., Matias, D., Meintjes, G., Mendes, F.D.F., Merker, M., Mihalic, M., Millard, J., Miotto, P., Mistry, N., Moore, David Alexander James, Musser, K.A., Ngcamu, D., Nhung, H.N., Niemann, S., Nilgiriwala, K.S., Nimmo, C., O’Donnell, M., Okozi, N., Oliveira, R.S., Omar, S.V., Paton, N., Pinhata, J.M.W., Plesnik, S., Puyen, Z.M., Rabodoarivelo, M.S., Rakotosamimanana, N., Rancoita, P.M.V., Rathod, P., Robinson, E., Rodger, G., Rodrigues, C., Rodwell, T.C., Santos-Lazaro, D., Shah, S., Kohl, T.A., Smith, G., Solano, Walter, Spitaleri, A., Supply, P., Steyn, A.J.C., Surve, U., Tahseen, S., Thuong, N.T.T., Thwaites, G., Todt, K., Trovato, A., Utpatel, C., Van Rie, A., Vijay, S., Warren, R., Werngren, J., Wijkander, M., Wilkinson, R.J., Wilson, D.J., Wintringer, P., Xiao, Y.-X., Yang, Y., Yanlin, Z., Yao, S.-Y., Zhu, B., The Zooniverse Volunteer Community, The CRyPTIC Consortium, Community, The Zooniverse Volunteer, Consortium, The CRyPTIC, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), and Wellcome Trust
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Volunteers ,Model organisms ,infectious disease ,[SDV]Life Sciences [q-bio] ,Immunology ,Antitubercular Agents ,Infectious Disease ,Microbial Sensitivity Tests ,Zooniverse Volunteer Community ,0601 Biochemistry and Cell Biology ,antibiotics ,General Biochemistry, Genetics and Molecular Biology ,Imaging ,minimum inhibitory concentrations ,antitubercular drugs ,citizen science ,M. tuberculosis ,Humans ,clinical microbiology ,Human Biology & Physiology ,General Immunology and Microbiology ,CRyPTIC Consortium ,Prevention ,General Neuroscience ,FOS: Clinical medicine ,microbiology ,BashTheBug ,Mycobacterium tuberculosis ,General Medicine ,microdilution plates ,Emerging Infectious Diseases ,Infectious Diseases ,Good Health and Well Being ,tuberculosis ,5.1 Pharmaceuticals ,photographs ,Antimicrobial Resistance ,Biochemistry and Cell Biology ,Development of treatments and therapeutic interventions ,Infection - Abstract
Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally, this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, each being present at a pre-determined concentration, thereby determining if the sample isresistant or susceptible to each sample. The minimum inhibitory concentration (MIC) of a drug is the lowestconcentration that inhibits growth and is a more useful quantity but requires each sample to be tested at a range ofconcentrations for each drug. Using 96-well broth micro dilution plates with each well containing a lyophilised pre-determined amount of an antibiotic is a convenient and cost-effective way to measure the MICs of several drugs at once for a clinical sample. Although accurate, this is still an expensive and slow process that requires highly-skilled and experienced laboratory scientists. Here we show that, through the BashTheBug project hosted on the Zooniverse citizen science platform, a crowd of volunteers can reproducibly and accurately determine the MICs for 13 drugs and that simply taking the median or mode of 11-17 independent classifications is sufficient. There is therefore a potential role for crowds to support (but not supplant) the role of experts in antibiotic susceptibility testing.Tuberculosis is a bacterial respiratory infection that kills about 1.4 million people worldwide each year. While antibiotics can cure the condition, the bacterium responsible for this disease
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- 2022
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13. Deposition and retention of differently shaped micro-particles on textiles during laundry processing
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Manga, MS, Adetomiwa, T, Marks, S, Gardy, J, Blackburn, RS, Russell, SJ, and York, DW
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General Chemical Engineering - Abstract
Particulate additives such as perfume microcapsules are present in detergent formulations to add fragrance to the washed garments. The key challenge is controlling the deposition and retention of such particulates onto textile surfaces, as a large proportion are simply washed down the drain during washing. In this study, the influence of particle shape on the mechanical entrapment of particulates within different fabrics is assessed using a laboratory mixer, which mimics the tumbling action of a washing machine. Using a combination of image analysis and mass balance it is found that with rough, irregular particles, the retention level across all fabric types studied is increased by a factor of up to 3 times when compared to smooth, spherical ones (typically used in industry). The retention rate is also found to be dependent on the tumbling duration, tumbler speed as well as on the fabric characteristics especially when a combination are used.
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- 2022
14. Functionalization of Metallic Powder for Performance Enhancement
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Unnikrishnan, R, Gardy, J, F. Spencer, B, Kurinjimala, R, Dey, A, Nekouie, V, Irukuvarghulaa, S, Hassanpour, A, Eisenmenger-Sittner, C, Francis, JA, and Preuss, M
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History ,Polymers and Plastics ,Mechanics of Materials ,Mechanical Engineering ,General Materials Science ,Business and International Management ,Industrial and Manufacturing Engineering - Abstract
The oxidation state and surface properties of powder particles play a major role in the final properties of powder manufactured components. In the present study, the coating of a non-stainless low alloy (SA508 Grade 3) steel powder was explored to protect it from progressive oxidation while also studying the effects on powder flowability and electrical charging. The protective coating was applied by magnetron sputtering of chromium. The surface chemistries of both as-received and Cr coated powders were studied using X-ray photo electron spectroscopy (XPS). Accelerated oxidation tests were carried out on both uncoated and Cr coated powders to study the effects of coating on oxidation resistance. Hard X-ray photoelectron spectroscopy (HAXPES) analysis was used to measure oxygen pick up near the surface, showing significant reductions for the case of the Cr coated powder. The conductivity of the powder was found to increase with Cr coating. The flowability of the powder was characterised by the tapped density, the angle of repose (AOR) and a powder rheometer, and it was found to improve with a Cr coating, which can be attributed to reduced tribo-electrical charging and reduced cohesivity of the powder particles.
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- 2022
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15. Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of
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Fowler, P.W., Barilar, I., Battaglia, S., Borroni, E., Brandao, A.P., Brankin, A., Cabibbe, A.M., Carter, J., Cirillo, D.M., Claxton, P., Clifton, D.A., Cohen, T., Coronel, Jorge, Crook, D.W., Dreyer, V., Earle, S.G., Escuyer, V., Ferrazoli, L., Gao, G.F., Gardy, J., Gharbia, S., Ghisi, K.T., Ghodousi, A., Cruz, A.L.G., Grandjean, Louis, Grazian, C., Groenheit, R., Guthrie, J.L., He, W., Hoffmann, H., Hoosdally, S.J., Hunt, M., Iqbal, Z., Ismail, N.A., Jarrett, L., Joseph, L., Jou, R., Kambli, P., Khot, R., Knaggs, J., Koch, A., Kohlerschmidt, D., Kouchaki, S., Lachapelle, A.S., Lalvani, A., Lapierre, S.G., Laurenson, I.F., Letcher, B., Lin, W.-H., Liu, C., Liu, D., Malone, K.M., Mandal, A., Mansjö, M., Matias, D., Meintjes, G., de Freitas Mendes, F., Merker, M., Mihalic, M., Millard, J., Miotto, P., Mistry, N., Moore, David Alexander James, Musser, K.A., Ngcamu, D., Nhung, H.N., Niemann, S., Nilgiriwala, K.S., Nimmo, C., Okozi, N., Oliveira, R.S., Omar, S.V., Paton, N., Peto, T.E.A., Pinhata, J.M.W., Plesnik, S., Puyen, Z.M., Rabodoarivelo, M.S., Rakotosamimanana, N., Rancoita, P.M.V., Rathod, P., Robinson, E., Rodger, G., Rodrigues, C., Rodwell, T.C., Roohi, A., Santos-Lazaro, D., Shah, S., Kohl, T.A., Smith, G., Solano, Walter, Spitaleri, A., Supply, P., Surve, U., Tahseen, S., Thuong, N.T.T., Thwaites, G., Todt, K., Trovato, A., Utpatel, C., Van Rie, A., Vijay, S., Walker, T.M., Walker, A.S., Warren, R., Werngren, J., Wijkander, M., Wilkinson, R.J., Wilson, D.J., Wintringer, P., Xiao, Y.-X., Yang, Y., Yanlin, Z., Yao, S.-Y., Zhu, B., Consoritum, CRyPTIC, Walker, AS, and CRyPTIC Consortium
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microdilution ,Pulmonary and Respiratory Medicine ,tuberculosis ,Respiratory ,M. tuberculosis ,Humans ,Tuberculosis ,Human medicine ,infections ,Microbial Sensitivity Tests ,Mycobacterium tuberculosis ,Anti-Bacterial Agents - Abstract
Drug susceptibility testing ofM. tuberculosisis rooted in a binary susceptible/resistant paradigm. While there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, it is necessary to measure the epidemiological cut-off values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-tuberculosis compounds, including bedaquiline and delamanid, derived from 20 637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex, and therefore aphenotypicallywild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined agenotypicallywild-type population and measured the MIC of the 99th percentile by direct measurement andviafitting a Gaussian using interval regression. The proposed ECOFF/ECVs were then validated by comparing with the MIC distributions of high-confidence genetic variants that confer resistance and with qualitative drug susceptibility tests obtainedviathe Mycobacterial Growth Indicator Tube (MGIT) system or Microscopic-Observation Drug Susceptibility (MODS) assay. These ECOFF/ECVs will inform and encourage the more widespread adoption of broth microdilution: this is a cheap culture-based method that tests the susceptibility of 12–14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.
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- 2021
16. Chapter 2 - Nanomaterials for solar energy capture and steam generation
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Amjad, Muhammad, Haruna, Maje Alhaji, and Gardy, J.
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- 2021
- Full Text
- View/download PDF
17. Effect of the loading of di- and tri-valent metal cations on the performance of sulfated silica-titania nano-catalyst in the esterification reaction
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Al-Qaysi, K, Nayebzadeh, H, Saghatoleslami, N, and Gardy, J
- Abstract
In this study, a series of sulfated silica-titania catalysts were modified by metal cations (Al, Co, Zr, Cr, and Zn) to enhance the catalytic activity and stability of sulfated silica-titania in the esterification reaction. The results indicated that the sulfate phases of sulfated silica-titania were mostly changed to TiO(SO4) by the incorporation of support cations. It affected the acidity content of the samples and the bonding strength between the sulfate group and the support surface. Moreover, the mean pore size was drastically increased which had a positive influence on the activity of the sample in the esterification reaction. The results of catalytic activity showed that all the samples had suitable activity at 120°C, whereas the sulfated silica-titania catalyst that was reinforced by Al3+ exhibited less activity reduction by setting the temperature to 90°C. The highest conversion of oleic acid (90.7 ± 2%) was obtained under optimal reaction conditions including the temperature of 90°C, methanol/oleic acid molar ratio of 9:1, 3 wt.% catalyst, and reaction time of 3 h. The sulfated silica-titania modified by Al3+ also exhibited good catalytic stability for six cycles while a high reduction in the activity of sulfated silica-titania catalyst was observed.
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- 2021
18. Supplement to: Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.
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Gardy, J L, Johnston, J C, and Ho Sui, S J
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- 2011
19. Thermogravimetric analysis on the co-combustion of biomass pellets with lignite and bituminous coal
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Guo, F, He, Y, Hassanpour, A, Gardy, J, and Zhong, Z
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This work presents comparative study on the combustion of biomass pellets (BP) with Bituminous coal (BC), and Xiao longtan lignite (XL) using thermogravimetric (TG) analysis. The results show that the combustion process of BP:BC can be divided into the release and combustion of volatile compounds, oxidation of BP char and combustion of BC char. While there are two stages for the blend of XL and BP, which are the combustion of volatile compounds and the char burning of BP and XL. With increasing BP ratio, the maximum combustion rate and combustion index increase, while the burnout temperature decreases, indicating the combustion performance of coal can be improved. In addition, interactions between BP and XL are more significant than that of BP and BC. The maximum deviations are found to be 30% BP with BC and 10% BP with XL. Reaction mechanisms are analysed using Coats–Redfern method. The first order model is found to be suitable for the first stage of biomass burn (stage 1) and coal combustion of BC:BP blends. Diffusion controlled model D3 and D4 are the most effective for the second stage of biomass burn and XL combustion, respectively. The minimum activation energies of biomass blending is obtained with a BP ratio of 30% for BC and 10% for XL.
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- 2020
20. Multi-Label Random Forest Model for Tuberculosis Drug Resistance Classification and Mutation Ranking
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Kouchaki, S, Yang, Y, Lachapelle, A, Walker, T, Walker, SA, Hoosdally, S, Gibertoni Cruz, AL, Carter, J, Grazian, C, Earle, SG, Fowler, P, Iqbal, Z, Hunt, M, Knaggs, J, Smith, GE, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaler, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, Niemann, S, Merker, M, Hoffmann, H, Todt, K, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Thwaites, G, Thuong, TNT, Ngoc, NH, Srinivasan, V, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Liu, C, Ma, A, Zhu, B, Laurenson, I, Claxton, P, Koch, A, Wilkinson, R, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, MH, Lin, WH, Ferrazoli, L, Siqueira de Oliveira, R, Arandjelovic, I, Chaiprasert, A, Comas, I, Roig, CR, Drobniewski, FA, Farhat, MR, Gao, Q, Hee, ROT, Sintchenko, V, Supply, P, van Soolingen, D, Peto, TEA, Crook, D, Clifton, D, Kouchaki, S, Yang, Y, Lachapelle, A, Walker, T, Walker, SA, Hoosdally, S, Gibertoni Cruz, AL, Carter, J, Grazian, C, Earle, SG, Fowler, P, Iqbal, Z, Hunt, M, Knaggs, J, Smith, GE, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaler, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, Niemann, S, Merker, M, Hoffmann, H, Todt, K, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Thwaites, G, Thuong, TNT, Ngoc, NH, Srinivasan, V, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Liu, C, Ma, A, Zhu, B, Laurenson, I, Claxton, P, Koch, A, Wilkinson, R, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, MH, Lin, WH, Ferrazoli, L, Siqueira de Oliveira, R, Arandjelovic, I, Chaiprasert, A, Comas, I, Roig, CR, Drobniewski, FA, Farhat, MR, Gao, Q, Hee, ROT, Sintchenko, V, Supply, P, van Soolingen, D, Peto, TEA, Crook, D, and Clifton, D
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- 2020
21. GenomegaMap: within-species genome-wide d_N/d_S estimation from over 10,000 genomes
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Wilson, D, Crook, DW, Peto, TEA, Walker, AS, Hoosdally, SJ, Gibertoni Cruz, AL, Carter, J, Grazian, C, Earle, SG, Kouchaki, S, Lachapelle, A, Yang, Y, Clifton, DA, Fowler, PW, Iqbal, Z, Hunt, M, Knaggs, J, Smith, EG, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaleri, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, NIemann, S, Kohl, TA, Merker, M, Hoffman, H, Todt, K, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Thwaites, G, Thoung, TNT, Ngoc, NH, Srinivasan, V, Walker, TM, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Liu, C, Ma, A, Zhu, B, Laurenson, I, Claxton, P, Koch, A, Wilkinson, R, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, MH, Lin, WH, Ferrazoli, L, Siqueira de Oliveira, R, Arandjelovic, I, Chaipresert, A, Comas, I, Roig, CJ, Drobniewski, FA, Farhat, MR, Gao, Q, Hee, ROT, Sintchenko, V, Wilson, D, Crook, DW, Peto, TEA, Walker, AS, Hoosdally, SJ, Gibertoni Cruz, AL, Carter, J, Grazian, C, Earle, SG, Kouchaki, S, Lachapelle, A, Yang, Y, Clifton, DA, Fowler, PW, Iqbal, Z, Hunt, M, Knaggs, J, Smith, EG, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaleri, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, NIemann, S, Kohl, TA, Merker, M, Hoffman, H, Todt, K, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Thwaites, G, Thoung, TNT, Ngoc, NH, Srinivasan, V, Walker, TM, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Liu, C, Ma, A, Zhu, B, Laurenson, I, Claxton, P, Koch, A, Wilkinson, R, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, MH, Lin, WH, Ferrazoli, L, Siqueira de Oliveira, R, Arandjelovic, I, Chaipresert, A, Comas, I, Roig, CJ, Drobniewski, FA, Farhat, MR, Gao, Q, Hee, ROT, and Sintchenko, V
- Abstract
The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters such as dN/dS, but analysing very large datasets poses a major statistical challenge. Here I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: (i) it is fast no matter how large the sample size and (ii) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well-estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in M. tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.
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- 2020
22. Influence of carbon quantum dots on the viscosity reduction of polyacrylamide solution
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Haruna, MA, Hu, Z, Gao, H, Gardy, J, Magami, SM, and Wen, D
- Abstract
Viscosity is one of the key factors which influence the application of polyacrylamide (PAM) in enhanced oil recovery (EOR). In this study, we have demonstrated the viscosity reduction of PAM solution by using carbon quantum dots (CQDs) through rheological, spectroscopic and thermal analyses. The stability of PAM, CQDs, and PAM/CQDs composites, and the chemical interactions between PAM and CQDs were investigated. The addition of CQDs into PAM solution decreased its viscosity, demonstrating a phenomenon which contradicts the expression normally derived from the Einstein–Batchelor law for the viscosity of particle suspensions. Consequently, the elastic properties of PAM/CQDs composites were lower than those of the pure PAM solutions. Moreover, the presence of CQDs in the PAM increased its flow activation energy and decreased its yield point, leading to an increased sensitivity to both temperature and shear rate. The mechanism behind the reduced viscosity behaviour of PAM/CQDs composites appears to be the formation of free radicals and the elimination of ammonia molecules, leading to the deterioration of the polymer backbone.
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- 2019
23. Catalytic pyrolysis of plastic waste: Moving towards pyrolysis based biorefineries
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Miandad, R, Rehan, M, Barakat, MA, Aburiazaiza, AS, Khan, H, Ismail, IMI, Dhavamani, J, Gardy, J, Hassanpour, A, and Nizami, A-S
- Abstract
Pyrolysis based biorefineries have great potential to convert wastes such as plastic and biomass waste into energy and other valuable products to achieve maximum economic and environmental benefits. In this study, the catalytic pyrolysis of different types of plastics waste (PS, PE, PP, and PET) as single or mixed in different ratios in the presence of modified natural zeolite (NZ) catalysts in a small pilot scale pyrolysis reactor was carried out. The NZ was modified by thermal activation (TA-NZ) at 550°C and acid activation (AA-NZ) with HNO3 to enhance its catalytic properties. The catalytic pyrolysis of PS produced the highest liquid oil (70 and 60%) than PP (40 and 54%) and PE (40 and 42%) using TA-NZ and AA-NZ catalysts respectively. The gas chromatography-mass spectrometry (GC-MS) analysis of oil showed a mixture of aromatics, aliphatic and other hydrocarbon compounds. The TA-NZ and AA-NZ catalysts showed a different effect on the wt.% of catalytic pyrolysis products and liquid oil chemical composition, with AA-NZ showing higher catalytic activity than TA-NZ. FT-IR results showed clear peaks of aromatic compounds in all liquid oil samples with some peaks of alkanes that further confirmed the GC-MS results. The liquid oil has higher heating values (HHV) range of 41.7-44.2 MJ/kg, close to conventional diesel. Therefore, it has the potential to be used as an alternative source of energy and as transportation fuel after refining/ blending with conventional fuels.
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- 2019
24. DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis
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Yang, Y, Walker, TM, Walker, AS, Wilson, DJ, Peto, TEA, Crook, DW, Shamout, F, Zhu, T, Clifton, DA, Arandjelovic, I, Comas, I, Farhat, MR, Gao, Q, Sintchenko, V, Van Soolingen, D, Hoosdally, S, Cruz, ALG, Carter, J, Grazian, C, Earle, SG, Kouchaki, S, Fowler, PW, Iqbal, Z, Hunt, M, Smith, EG, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaleri, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, Niemann, S, Kohl, T, Merker, M, Hoffmann, H, Molodtsov, N, Plesnik, S, Ismail, N, Omar, SV, Thwaites, G, Thuong, NTT, Nhung, HN, Srinivasan, V, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Ma, A, Liu, C, Zhu, B, Laurenson, I, Claxton, P, Koch, A, Wilkinson, R, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, M-H, Lin, W-H, Ferrazoli, L, De Oliveira, RS, and Wellcome Trust
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DRUG-RESISTANCE ,Technology ,Biochemistry & Molecular Biology ,Science & Technology ,INFORMATION ,MUTATIONS ,CRyPTIC Consortium ,Bioinformatics ,Statistics & Probability ,SUSCEPTIBILITY ,06 Biological Sciences ,GENE ,Biochemical Research Methods ,CLASSIFICATION ,DIMENSIONALITY REDUCTION ,Biotechnology & Applied Microbiology ,Physical Sciences ,Computer Science ,Computer Science, Interdisciplinary Applications ,Mathematical & Computational Biology ,08 Information and Computing Sciences ,Life Sciences & Biomedicine ,Mathematics ,01 Mathematical Sciences - Abstract
Motivation Resistance co-occurrence within first-line anti-tuberculosis (TB) drugs is a common phenomenon. Existing methods based on genetic data analysis of Mycobacterium tuberculosis (MTB) have been able to predict resistance of MTB to individual drugs, but have not considered the resistance co-occurrence and cannot capture latent structure of genomic data that corresponds to lineages. Results We used a large cohort of TB patients from 16 countries across six continents where whole-genome sequences for each isolate and associated phenotype to anti-TB drugs were obtained using drug susceptibility testing recommended by the World Health Organization. We then proposed an end-to-end multi-task model with deep denoising auto-encoder (DeepAMR) for multiple drug classification and developed DeepAMR_cluster, a clustering variant based on DeepAMR, for learning clusters in latent space of the data. The results showed that DeepAMR outperformed baseline model and four machine learning models with mean AUROC from 94.4% to 98.7% for predicting resistance to four first-line drugs [i.e. isoniazid (INH), ethambutol (EMB), rifampicin (RIF), pyrazinamide (PZA)], multi-drug resistant TB (MDR-TB) and pan-susceptible TB (PANS-TB: MTB that is susceptible to all four first-line anti-TB drugs). In the case of INH, EMB, PZA and MDR-TB, DeepAMR achieved its best mean sensitivity of 94.3%, 91.5%, 87.3% and 96.3%, respectively. While in the case of RIF and PANS-TB, it generated 94.2% and 92.2% sensitivity, which were lower than baseline model by 0.7% and 1.9%, respectively. t-SNE visualization shows that DeepAMR_cluster captures lineage-related clusters in the latent space. Availability and implementation The details of source code are provided at http://www.robots.ox.ac.uk/∼davidc/code.php.
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- 2019
25. GenomegaMap: within-species genome-widedN/dSestimation from over 10,000 genomes
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Wilson, DJ, Crook, DW, Peto, TEA, Walker, AS, Hoosdally, SJ, Gibertoni Cruz, AL, Carter, J, Grazian, C, Earle, SG, Kouchaki, S, Lachapelle, A, Yang, Y, Clifton, DA, Fowler, PW, Iqbal, Z, Hunt, M, Knaggs, J, Smith, EG, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaleri, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, Niemann, S, Kohl, TA, Merker, M, Hoffmann, H, Todt, K, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Thwaites, G, Thuong, TNT, Ngoc, NH, Srinivasan, V, Walker, TM, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Liu, C, Ma, A, Zhu, B, Laurenson, I, Claxton, P, Koch, A, Wilkinson, R, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, M-H, Lin, W-H, Ferrazoli, L, De Oliveira, RS, Arandjelovic, I, Chaiprasert, A, Comas, I, Roig, CJ, Drobniewski, FA, Farhat, MR, Gao, Q, Hee, ROT, Sintchenko, V, Supply, P, Van Soolingen, D, University of Oxford, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant no. 101237/Z/13/B) and is a Big Data Institute Robertson Fellow. The CRyPTIC Consortium was supported by grants from the Bill and Melinda Gates Foundation (OPP1133541) and a Wellcome Trust/Newton Fund-MRC Collaborative Award (200205/Z/15/Z). F.A.D. was supported by the Imperial Biomedical Research Centre., Members of the CRyPTIC Consortium : Derrick W. Crook, Timothy E.A. Peto, A. Sarah Walker, Sarah J. Hoosdally, Ana L. Gibertoni Cruz, Joshua Carter, Clara Grazian, Sarah G. Earle, Samaneh Kouchaki, Alexander Lachapelle, Yang Yang, David A. Clifton, and Philip W. Fowler, University of Oxford, Zamin Iqbal, Martin Hunt, and Jeffrey Knaggs, European Bioinformatics Institute, E. Grace Smith, Priti Rathod, Lisa Jarrett, and Daniela Matias, Public Health England, Birmingham, Daniela M. Cirillo, Emanuele Borroni, Simone Battaglia, Arash Ghodousi, Andrea Spitaleri, and Andrea Cabibbe, Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Sabira Tahseen, National Tuberculosis Control Program Pakistan, Islamabad, Kayzad Nilgiriwala and Sanchi Shah, The Foundation for Medical Research, Mumbai, Camilla Rodrigues, Priti Kambli, Utkarsha Surve, and Rukhsar Khot, P.D. Hinduja National Hospital and Medical Research Centre, Mumbai, Stefan Niemann, Thomas A. Kohl, and Matthias Merker, Research Center Borstel, Harald Hoffmann, Katharina Todt, and Sara Plesnik, Institute of Microbiology & Laboratory Medicine, IML Red, Gauting, Nazir Ismail, Shaheed Vally Omar, and Lavania Joseph, National Institute for Communicable Diseases, Johannesburg, Guy Thwaites, Thuong Nguyen Thuy Thuong, Nhung Hoang Ngoc, Vijay Srinivasan, and Timothy M. Walker, Oxford University Clinical Research Unit, Ho Chi Minh City, David Moore, Jorge Coronel and Walter Solano, London School of Hygiene and Tropical Medicine and Universidad Peruana Cayetano Heredá, Lima, George F. Gao, Guangxue He, Yanlin Zhao, and Chunfa Liu, China CDC, Beijing, Aijing Ma, Shenzhen Third People’s Hospital, Shenzhen, Baoli Zhu, Institute of Microbiology, CAS, Beijing, Ian Laurenson and Pauline Claxton, Scottish Mycobacteria Reference Laboratory, Edinburgh, Anastasia Koch, Robert Wilkinson, University of Cape Town, Ajit Lalvani, Imperial College London, James Posey, CDC Atlanta, Jennifer Gardy, University of British Columbia, Jim Werngren, Public Health Agency of Sweden, Nicholas Paton, National University of Singapore, Ruwen Jou, Mei-Hua Wu, Wan-Hsuan Lin, CDC Taiwan, Lucilaine Ferrazoli, Rosangela Siqueira de Oliveira, Institute Adolfo Lutz, São Paulo. Authors contributing to the CRyPTIC Consortium are (in alphabetical order): Irena Arandjelovic (Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia), Angkana Chaiprasert (Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand), Iñaki Comas (Instituto de Biomedicina de Valencia [IBV-CSIC], Calle Jaime Roig, Valencia, Spain, FISABIO Public Health, Valencia, Spain, CIBER in Epidemiology and Public Health, Madrid, Spain), Francis A. Drobniewski (Imperial College, London, UK), Maha R. Farhat (Harvard Medical School, Boston, USA), Qian Gao (Shanghai Medical College, Fudan University, Shanghai, China), Rick Ong Twee Hee (Saw Swee Hock School of Public Health, National University of Singapore, Singapore), Vitali Sintchenko (Centre for Infectious Diseases and Microbiology—Public Health, University of Sydney, Sydney, Australia), Philip Supply (Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 8204—CIIL—Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France), and Dick van Soolingen (National Institute for Public Health and the Environment [RIVM], Bilthoven, The Netherlands)., Supply, Philip, Consortium, CRyPTIC, University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Royal Society (UK), Bill & Melinda Gates Foundation, Newton Fund, Comas, Iñaki [0000-0001-5504-9408], and Comas, Iñaki
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Natural selection ,[SDV]Life Sciences [q-bio] ,Population genetics ,adaptation ,Computational biology ,Biology ,AcademicSubjects/SCI01180 ,0601 Biochemistry and Cell Biology ,Genome ,Coalescent theory ,DEAD-box RNA Helicases ,Big data ,03 medical and health sciences ,0603 Evolutionary Biology ,big data ,Parent-dependent mutation ,Genetics ,dN/dS ,Adaptation ,Selection, Genetic ,Molecular Biology ,Allele frequency ,Ecology, Evolution, Behavior and Systematics ,Silent Mutation ,Selection (genetic algorithm) ,030304 developmental biology ,Evolutionary Biology ,0604 Genetics ,0303 health sciences ,Models, Genetic ,Phylogenetic tree ,030306 microbiology ,AcademicSubjects/SCI01130 ,natural selection ,Mycobacterium tuberculosis ,Recombination ,Resources ,recombination ,3. Good health ,[SDV] Life Sciences [q-bio] ,Genetic Techniques ,Mutation (genetic algorithm) ,parent-dependent mutation ,Genome, Bacterial - Abstract
11 págs, 4 figuras y fórmulas matemáticas. Material suplementario en: http://dx.doi.org/10.1093/molbev/msaa069, The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap's simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species., D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant no. 101237/Z/13/B) and is a Big Data Institute Robertson Fellow. The CRyPTIC Consortium was supported by grants from the Bill and Melinda Gates Foundation (OPP1133541) and a Wellcome Trust/Newton Fund-MRC Collaborative Award (200205/Z/15/Z). F.A.D. was supported by the Imperial Biomedical Research Centre
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- 2019
- Full Text
- View/download PDF
26. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
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Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A, European Research Council, National Institutes of Health (US), University of British Columbia, German Center for Infection Research, German Research Foundation, Research Foundation - Flanders, Comas, Iñaki, and Goig, Galo A.
- Abstract
13 páginas, 4 figuras. Contiene material suplementario., Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting., C.J.M., B.O.-A., L.R. and B.C.d.J. are supported by a European Research Council grant (INTERRUPTB; no. 311725). I.C. and G.A.G. are supported by a European Research Council grant (TB-ACCELERATE; no. 638553). T.C.R. receives salary support from the not-for-profit organization Foundation for Innovative New Diagnostics (the terms of this arrangement have been reviewed and approved by the University of California, San Diego). T.M.W. is an NIHR Academic Clinical Lecturer. J.L.G. and J.G. receive funding from the University of British Columbia, Vancouver, Canada. T.A.K., C.U., V.D. and S.N. receive funding from the German Center for Infection Research (DZIF) and are funded by the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy (EXC 22167–390884018). L.V., T.H.H. and A.V.R. are funded by FWO Odysseus G0F8316N. M.R.F. is supported by the US National Institutes of Health BD2K K01 (MRF ES026835). P.S. is supported by the Agence Nationale de la Recherche (ANR-16-CE35-0009).
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- 2019
27. PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
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Gardy, J. L., Laird, M. R., Chen, F., Rey, S., Walsh, C. J., Ester, M., and Brinkman, F. S. L.
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- 2005
28. Application of machine learning techniques to tuberculosis drug resistance analysis
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Kouchaki, S, Yang, YY, Walker, TM, Walker, AS, Wilson, DJ, Peto, TEA, Crook, DW, Clifton, DA, Hoosdally, SJ, Gibertoni Cruz, AL, Carter, J, Grazian, C, Fowler, PW, Iqbal, Z, Hunt, M, Smith, EG, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaleri, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, Niemann, S, Kohl, T, Merker, M, Hoffmann, H, Molodtsov, N, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Marubini, E, Thwaites, G, Thuong, TNT, Ngoc, NH, Srinivasan, V, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Ma, A, Liu, C, Zhu, B, Laurenson, I, Claxton, P, Wilkinson, RJ, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, MH, Lin, WH, Ferrazoli, L, De Oliveira, RS, Arandjelovic, I, Comas, I, Drobniewski, F, Gao, Q, Sintchenko, V, Supply, P, Van Soolingen, D, Kouchaki, S, Yang, YY, Walker, TM, Walker, AS, Wilson, DJ, Peto, TEA, Crook, DW, Clifton, DA, Hoosdally, SJ, Gibertoni Cruz, AL, Carter, J, Grazian, C, Fowler, PW, Iqbal, Z, Hunt, M, Smith, EG, Rathod, P, Jarrett, L, Matias, D, Cirillo, DM, Borroni, E, Battaglia, S, Ghodousi, A, Spitaleri, A, Cabibbe, A, Tahseen, S, Nilgiriwala, K, Shah, S, Rodrigues, C, Kambli, P, Surve, U, Khot, R, Niemann, S, Kohl, T, Merker, M, Hoffmann, H, Molodtsov, N, Plesnik, S, Ismail, N, Omar, SV, Joseph, L, Marubini, E, Thwaites, G, Thuong, TNT, Ngoc, NH, Srinivasan, V, Moore, D, Coronel, J, Solano, W, Gao, GF, He, G, Zhao, Y, Ma, A, Liu, C, Zhu, B, Laurenson, I, Claxton, P, Wilkinson, RJ, Lalvani, A, Posey, J, Gardy, J, Werngren, J, Paton, N, Jou, R, Wu, MH, Lin, WH, Ferrazoli, L, De Oliveira, RS, Arandjelovic, I, Comas, I, Drobniewski, F, Gao, Q, Sintchenko, V, Supply, P, and Van Soolingen, D
- Abstract
Motivation: Timely identification of Mycobacterium tuberculosis (MTB) resistance to existing drugs is vital to decrease mortality and prevent the amplification of existing antibiotic resistance. Machine learning methods have been widely applied for timely predicting resistance of MTB given a specific drug and identifying resistance markers. However, they have been not validated on a large cohort of MTB samples from multi-centers across the world in terms of resistance prediction and resistance marker identification. Several machine learning classifiers and linear dimension reduction techniques were developed and compared for a cohort of 13 402 isolates collected from 16 countries across 6 continents and tested 11 drugs. Results: Compared to conventional molecular diagnostic test, area under curve of the best machine learning classifier increased for all drugs especially by 23.11%, 15.22% and 10.14% for pyrazinamide, ciprofloxacin and ofloxacin, respectively (P < 0.01). Logistic regression and gradient tree boosting found to perform better than other techniques. Moreover, logistic regression/gradient tree boosting with a sparse principal component analysis/non-negative matrix factorization step compared with the classifier alone enhanced the best performance in terms of F1-score by 12.54%, 4.61%, 7.45% and 9.58% for amikacin, moxifloxacin, ofloxacin and capreomycin, respectively, as well increasing area under curve for amikacin and capreomycin. Results provided a comprehensive comparison of various techniques and confirmed the application of machine learning for better prediction of the large diverse tuberculosis data. Furthermore, mutation ranking showed the possibility of finding new resistance/susceptible markers.
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- 2019
29. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.
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Hunt, M, Bradley, P, Lapierre, SG, Heys, S, Thomsit, M, Hall, MB, Malone, KM, Wintringer, P, Walker, TM, Cirillo, DM, Comas, I, Farhat, MR, Fowler, P, Gardy, J, Ismail, N, Kohl, TA, Mathys, V, Merker, M, Niemann, S, Omar, SV, Sintchenko, V, Smith, G, van Soolingen, D, Supply, P, Tahseen, S, Wilcox, M, Arandjelovic, I, Peto, TEA, Crook, DW, Iqbal, Z, Hunt, M, Bradley, P, Lapierre, SG, Heys, S, Thomsit, M, Hall, MB, Malone, KM, Wintringer, P, Walker, TM, Cirillo, DM, Comas, I, Farhat, MR, Fowler, P, Gardy, J, Ismail, N, Kohl, TA, Mathys, V, Merker, M, Niemann, S, Omar, SV, Sintchenko, V, Smith, G, van Soolingen, D, Supply, P, Tahseen, S, Wilcox, M, Arandjelovic, I, Peto, TEA, Crook, DW, and Iqbal, Z
- Abstract
Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations. Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data. We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showi
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- 2019
30. Novel draw solution for forward osmosis based solar desalination
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Amjad, M, Gardy, J, Ali, H, and Wen, D
- Abstract
Forward osmosis (FO) is an emerging technology for water desalination which requires no external force for its operation. The performance of FO for water desalination is dependent on draw solution (DS) that must provide high osmosis pressure, minimum reverse flux and efficient separation of water. This work proposes an innovative concept of energy efficient material as DS having two functions, i.e. high osmotic pressure and efficient absorption of solar energy for the regeneration phase. The potassium functionalised carbon nanofibers (K/CNF) which are highly solar absorptive, are engineered and suspended in triethylene glycol (TEG) aqueous solution with different concentrations to act as a novel DS. The TEG-K/CNF is fully characterised for morphological appearance and thermophysical characteristics before using in FO experiments. It is found that the osmotic pressure and water flux of the novel DS are directly dependent on the concentration of K/CNF and TEG. The draw solution is re-concentrated by evaporating the water aided by the highly solar absorptive K/CNF under simulated solar flux. The vapours are condensed and the quality of product water is found to be comparable with potable water standard. The novel concept proposed in this study has the potential to be used in arid areas where solar energy is abundant to fulfil the potable water needs.
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- 2018
31. A magnetically separable SO₄/Fe-Al-TiO₂ solid acid catalyst for biodiesel production from waste cooking oil
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Gardy, J, Osatiashtiani, A, Céspedes, O, Hassanpour, A, Lai, X, Lee, AF, Wilson, K, and Rehan, M
- Abstract
A novel magnetic SO₄/Fe-Al-TiO₂ solid acid catalyst was synthesized for biodiesel production via the (trans)esterification of waste cooking oil (WCO). The nanocomposite catalyst was prepared by the sequential functionalisation of commercial rutile/anatase mixed phase TiO₂ nanoparticles (NPs) with alumina as a buffer layer, and subsequently hematite to impart magnetic character, prior to sulfation with chlorosulfonic acid to introduce Brønsted acidity. XRD showed that the SO₄/Fe-Al-TiO₂ catalyst comprised titania (rutile and anatase phases), aluminium sulphate, and hematite nanoparticles, while electron microscopy revealed the layer-by-layer assembly of these components within the SO₄/Fe-Al-TiO₂ catalyst. FTIR confirmed the presence of surface sulphate groups SO₄²⁻ and S₂O₇²⁻/S₃O₁₀²⁻, creating a predominantly Brønsted acid catalyst with high acid loading. The catalyst achieved 96 % fatty acid methyl ester (FAME) yield from WCO after 2.5 h of reaction at 90 °C, using 3 wt% of the magnetic catalyst, and a methanol:oil molar ratio of 10:1. SO₄/Fe-Al-TiO₂ was also effective for feedstocks containing up to 20 wt% of free fatty acid (FFA), and showed excellent stability for WCO (trans)esterification over 10 recycles.
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- 2018
32. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing
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CRyPTIC Consortium, 100000 Genomes Project, Allix-Beguec, C, Arandjelovic, I, Bi, L, Beckert, P, Bonnet, M, Bradley, P, Cabibbe, AM, Cancino-Munoz, I, Caulfield, MJ, Chaiprasert, A, Cirillo, DM, Clifton, D, Comas, I, Crook, DW, De Filippo, MR, de Neeling, H, Diel, R, Drobniewski, FA, Faksri, K, Farhat, MR, Fleming, J, Fowler, P, Fowler, TA, Gao, Q, Gardy, J, Gascoyne-Binzi, D, Gibertoni-Cruz, A-L, Gil-Brusola, A, Golubchik, T, Gonzalo, X, Grandjean, L, He, G, Guthrie, JL, Hoosdally, S, Hunt, M, Iqbal, Z, Ismail, N, Johnston, J, Khanzada, FM, Khor, CC, Kohl, TA, Kong, C, Lipworth, S, Liu, Q, Maphalala, G, Martinez, E, Mathys, V, Merker, M, Miotto, P, Mistry, N, Moore, DAJ, Murray, M, Niemann, S, Ong, RT-H, Peto, TEA, Posey, JE, Prammananan, T, Pym, A, Rodrigues, C, Rodrigues, M, Rodwell, T, Rossolini, GM, Padilla, ES, Schito, M, Shen, X, Shendure, J, Sintchenko, V, Sloutsky, A, Smith, EG, Snyder, M, Soetaert, K, Starks, AM, Supply, P, Suriyapol, P, Tahseen, S, Tang, P, Teo, Y-Y, Thuong, TNT, Thwaites, G, Tortoli, E, Omar, SV, van Soolingen, D, Walker, AS, Walker, TM, Wilcox, M, Wilson, DJ, Wyllie, D, Yang, Y, Zhang, H, Zhao, Y, and Zhu, B
- Abstract
Background: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.\ud \ud \ud \ud Methods: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.\ud \ud \ud \ud Results: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.\ud \ud \ud \ud Conclusions: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.)
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- 2018
33. Potential of Saudi natural clay as an effective adsorbent in heavy metals removal from wastewater
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Khan, M.I., primary, Almesfer, M.K., additional, Danish, M., additional, Ali, I.H., additional, Shoukry, H., additional, Patel, R., additional, Gardy, J., additional, Nizami, A.S., additional, and Rehan, M., additional
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- 2019
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34. Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region
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Guthrie, J. L., primary, Strudwick, L., additional, Roberts, B., additional, Allen, M., additional, McFadzen, J., additional, Roth, D., additional, Jorgensen, D., additional, Rodrigues, M., additional, Tang, P., additional, Hanley, B., additional, Johnston, J., additional, Cook, V. J., additional, and Gardy, J. L., additional
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- 2019
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35. Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting.
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Guthrie, J. L., Strudwick, L., Roberts, B., Allen, M., McFadzen, J., Roth, D., Jorgensen, D., Rodrigues, M., Tang, P., Hanley, B., Johnston, J., Cook, V. J., and Gardy, J. L.
- Abstract
Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005– 2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive UnitsVariable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomicbased (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person’s TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation. [ABSTRACT FROM AUTHOR]
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- 2020
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36. Waste to Energy : A Case Study of Madinah City
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Rehan, M., Nizami, A. -S, Asam, Z. -U.-Z., Ouda, O. K. M., Gardy, J., Raza, G., Naqvi, Muhammad, Mohammad Ismail, I., Rehan, M., Nizami, A. -S, Asam, Z. -U.-Z., Ouda, O. K. M., Gardy, J., Raza, G., Naqvi, Muhammad, and Mohammad Ismail, I.
- Abstract
The concept of energy from waste is getting popular nowadays across the globe, as being capable of producing multi fuels and value-added products from different fractions of municipal solid waste (MSW). The energy recovery technologies under this concept are anaerobic digestion (AD), pyrolysis, transesterification, refuse derived fuel (RDF) and incineration. This concept is very relevant to implementation in countries like Saudi Arabia, who wants to cut their dependence on oil. Moreover, the waste to energy becomes the imperative need of the time because of new governmental policy ’Vision 2030’ that firmly said to produce renewable energy from indigenous sources of waste, wind and solar and due to given situations of Hajj and Umrah with massive amounts of waste generation in a short period. This study focused on two waste to energy technologies, AD and pyrolysis for food (40% of MSW) and plastic (20% of MSW) waste streams respectively. The energy potential of 1409.63 and 5619.80 TJ can be produced if all of the food and plastic waste of the Madinah city are processed through AD and pyrolysis respectively. This is equivalent to 15.64 and 58.81 MW from biogas and pyrolytic oil respectively or total 74.45 MW of continuous electricity supply in Madinah city throughout the whole year. It has been estimated that the development of AD and pyrolysis technologies will also benefit the economy with net savings of around US $63.51 and US $53.45 million respectively, totaling to an annual benefit of US $116.96 million. Therefore, in Saudi Arabia and particularly in Holiest cities of Makkah and Madinah the benefits of waste to energy are several, including the development of renewable-energy, solving MSW problems, new businesses, and job creation and improving environmental and public health.
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- 2017
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37. Synthesis of Ti(SO4)O solid acid nano-catalyst and its application for biodiesel production from used cooking oil
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Gardy, J, Hassanpour, A, Lai, X, and Ahmed, MH
- Abstract
A novel solid acid nano-catalyst [Ti(SO4)O] was synthesised and used for the simultaneous esterification and transesterification of free fatty acids in used cooking oil (UCO) to produce biodiesel. The synthesised nano-catalyst was fully characterized by different analytical techniques. The XPS results clearly confirmed that the bidentate sulphate coordinated to the Ti4+ metal in the nano-catalyst product. Obtained d-spacing values from the experimental data of XRD peaks and the SAED pattern of produced nano-catalyst agreed well with the d-spacing values from the JCPDS-ICDD card numbers 04-011-4951 for titanium sulphate oxide or titanium oxysulfate crystal structures.This confirms the sulphate groups were within the crystalline structure rather than on the surface of titania nanoparticles, which has not been previously reported. It has been demonstrated 97.1% yield for the fatty acid methyl ester can be achieved usign the synthetised catalyst under a reaction time of 3 h, catalyst to UCO ration of 1.5 wt% and methanol to UCO ratio of 9:1 at 75 °C reaction temperature. The nano-catalyst showed a good catalytic activity for the feedstock containing ≤6 wt% free fatty acid. Furthermore, the catalytic activity and re-usability of the Ti(SO4)O for the esterification/transesterification of UCO were investigated. XRD results confirmed that the amount of View the MathML source species in the solid acid nano-catalyst slowly decreased with re-use after 8 cycles under optimised conditions, which is higher than the reusability of other functionalised titania reported in the literature. Finally, the biodiesel prodcued from this process satisfied the ASTM and European Norm standards.
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- 2016
38. The potential of Saudi Arabian natural zeolites in energy recovery technologies
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Nizami, AS, Ouda, OKM, Rehan, M, El-Maghraby, AMO, Gardy, J, Hassanpour, A, Kumar, S, and Ismail, IMI
- Abstract
Energy consumption in KSA (kingdom of Saudi Arabia) is growing rapidly due to economic development with raised levels of population, urbanization and living standards. Fossil fuels are currently solely used to meet the energy requirements. The KSA government have planned to double its energy generating capacity (upto 120 GW (gigawatts)) by 2032. About half of the electricity capacity of this targeted energy will come from renewable resources such as nuclear, wind, solar, WTE (waste-to-energy) etc. Natural zeolites are found abundantly in KSA at Jabal Shamah occurrence near Jeddah city, whose characteristics have never been investigated in energy related applications. This research aims to study the physical and chemical characteristics of natural zeolite in KSA and to review its potential utilization in selected WTE technologies and solar energy. The standard zeolite group of alumina–silicate minerals were found with the presence of other elements such as Na, Mg and K etc. A highly crystalline structure and thermal stability of natural zeolites together with unique ion exchange, adsorption properties, high surface area and porosity make them suitable in energy applications such as WTE and solar energy as an additive or catalyst. A simple solid–gas absorption system for storing solar energy in natural zeolites will be a cheap alternative method for KSA. In AD (anaerobic digestion), the dual characteristics of natural zeolite like Mordenite will increase the CH4 production of OFMSW (organic fraction of municipal solid waste). Further investigations are recommended to study the technical, economical, and environmental feasibility of natural zeolite utilization in WTE technologies in KSA.
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- 2016
39. Spatio-temporal analysis of tuberculous infection risk among clients of a homeless shelter during an outbreak
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Crisan, A., primary, Wong, H. Y., additional, Johnston, J. C., additional, Tang, P., additional, Colijn, C., additional, Otterstatter, M., additional, Hiscoe, L., additional, Parker, R., additional, Pollock, S. L., additional, and Gardy, J. L., additional
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- 2015
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40. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak
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Gardy, J., Johnston, J., Ho Sui, S., Cook, V., Shah, L., Brodkin, E., Rempel, S., Moore, R., Zhao, Y., Holt, R., Varhol, Richard, Birol, I., Lem, M., Sharma, M., Elwood, K., Jones, S., Brinkman, F., Brunham, R., Tang, P., Gardy, J., Johnston, J., Ho Sui, S., Cook, V., Shah, L., Brodkin, E., Rempel, S., Moore, R., Zhao, Y., Holt, R., Varhol, Richard, Birol, I., Lem, M., Sharma, M., Elwood, K., Jones, S., Brinkman, F., Brunham, R., and Tang, P.
- Abstract
Background: An outbreak of tuberculosis occurred over a 3-year period in a medium-size community in British Columbia, Canada. The results of mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) genotyping suggested the outbreak was clonal. Traditional contact tracing did not identify a source. We used whole-genome sequencing and social-network analysis in an effort to describe the outbreak dynamics at a higher resolution. Methods: We sequenced the complete genomes of 32 Mycobacterium tuberculosis outbreak isolates and 4 historical isolates (from the same region but sampled before the outbreak) with matching genotypes, using short-read sequencing. Epidemiologic and genomic data were overlaid on a social network constructed by means of interviews with patients to determine the origins and transmission dynamics of the outbreak. Results: Whole-genome data revealed two genetically distinct lineages of M. tuberculosis with identical MIRU-VNTR genotypes, suggesting two concomitant outbreaks. Integration of social-network and phylogenetic analyses revealed several transmission events, including those involving "superspreaders." Both lineages descended from a common ancestor and had been detected in the community before the outbreak, suggesting a social, rather than genetic, trigger. Further epidemiologic investigation revealed that the onset of the outbreak coincided with a recorded increase in crack cocaine use in the community. Conclusions: Through integration of large-scale bacterial whole-genome sequencing and social-network analysis, we show that a socioenvironmental factor - most likely increased crack cocaine use - triggered the simultaneous expansion of two extant lineages of M. tuberculosis that was sustained by key members of a high-risk social network. Genotyping and contact tracing alone did not capture the true dynamics of the outbreak. (Funded by Genome British Columbia and others.) Copyright © 2011 Massachusetts Medical Society
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- 2011
41. Cross-reactive antibody to swine influenza A(H3N2) subtype virus in children and adults before and after immunisation with 2010/11 trivalent inactivated influenza vaccine in Canada, August to November 2010
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Skowronski, D M, primary, De Serres, G, additional, Janjua, N Z, additional, Gardy, J L, additional, Gilca, V, additional, Dionne, M, additional, Hamelin, M E, additional, Rhéaume, C, additional, and Boivin, G, additional
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- 2012
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42. Recommendations on modern contact investigation methods for enhancing tuberculosis control [Review article]
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Cook, V. J., primary, Shah, L., additional, Gardy, J., additional, and Bourgeois, A-C., additional
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- 2011
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43. Immuno-epidemiologic Correlates of Pandemic H1N1 Surveillance Observations: Higher Antibody and Lower Cell-Mediated Immune Responses with Advanced Age
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Skowronski, D. M., primary, Hottes, T. S., additional, McElhaney, J. E., additional, Janjua, N. Z., additional, Sabaiduc, S., additional, Chan, T., additional, Gentleman, B., additional, Purych, D., additional, Gardy, J., additional, Patrick, D. M., additional, Brunham, R. C., additional, De Serres, G., additional, and Petric, M., additional
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- 2010
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44. Prevalence of seroprotection against the pandemic (H1N1) virus after the 2009 pandemic
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Skowronski, D. M., primary, Hottes, T. S., additional, Janjua, N. Z., additional, Purych, D., additional, Sabaiduc, S., additional, Chan, T., additional, De Serres, G., additional, Gardy, J., additional, McElhaney, J. E., additional, Patrick, D. M., additional, and Petric, M., additional
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- 2010
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45. Seasonal influenza vaccine may be associated with increased risk of illness due to the 2009 pandemic A/H1N1 virus
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Skowronski, D.M., primary, De Serres, G., additional, Crowcroft, N., additional, Janjua, N., additional, Boulianne, N., additional, Hottes, T.S., additional, Rosella, L.C., additional, Dickinson, J.A., additional, Rodica, G., additional, Sethi, P., additional, Ouhoummane, N., additional, Willison, D.J., additional, Rouleau, I., additional, Fonseca, K., additional, Drews, S.J., additional, Rebbapragada, A., additional, Charest, H., additional, Hamelin, M.-E., additional, Boivin, G., additional, Gardy, J., additional, Li, Y., additional, and Martin, P., additional
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- 2010
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46. Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context
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Barsky, A., primary, Munzner, T., additional, Gardy, J., additional, and Kincaid, R., additional
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- 2008
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47. PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
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Gardy, J. L., primary, Laird, M. R., additional, Chen, F., additional, Rey, S., additional, Walsh, C. J., additional, Ester, M., additional, and Brinkman, F. S. L., additional
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- 2004
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48. PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
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Gardy, J. L., primary
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- 2003
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49. Immuno-epidemiologic correlates of pandemic H1N1 surveillance observations: higher antibody and lower cell-mediated immune responses with advanced age.
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Skowronski DM, Hottes TS, McElhaney JE, Janjua NZ, Sabaiduc S, Chan T, Gentleman B, Purych D, Gardy J, Patrick DM, Brunham RC, De Serres G, Petric M, Skowronski, Danuta M, Hottes, Travis S, McElhaney, Janet E, Janjua, Naveed Z, Sabaiduc, Suzana, Chan, Tracy, and Gentleman, Beth
- Abstract
Background: Pandemic H1N1 (pH1N1) surveillance data showed lower attack rates but higher risk of severe outcomes with advanced age. We explored immuno-epidemiologic correlates of surveillance findings including humoral and cell-mediated immunity (CMI).Methods: In an age-based design, ∼100 banked/residual sera per 10-year age stratum were assessed by hemagglutination inhibition (HI) and microneutralization (MN) assays for preexisting antibody to pH1N1 and recent seasonal H1N1 and H3N2 strains. In a separate birth cohort design defined by childhood influenza A/subtype priming (1919-1929: H1N1; 1945-1949: H1N1; 1958-1960: H2N2; 1969-1970: H3N2; 1978-1989: H3N2/H1N1), whole blood was collected from up to 50 volunteers per birth cohort. The ratio of Th1(IFN-γ):Th2(IL-10) cytokine responses was evaluated in vitro.Results: Antibody to seasonal viruses was highest in school-age children. Cross-reactive HI/MN antibody to pH1N1 was low among participants <70 years of age (yoa; 6%/4% ≥ 40), but seroprevalence increased at 70-79 yoa (27%/6%), increased even more at 80-89 yoa (65%/47%), and was highest at ≥90 yoa (88%/76%). CMI to pH1N1 was evident in all 5 birth cohorts but was lower compared with seasonal strains. There was little differentiation by subtype priming, but the Th1:Th2 ratio for all viruses dropped significantly in the 2 oldest cohorts.Conclusions: Preexisting antibody may have protected the very old from pH1N1 infection, while diminished CMI may have contributed to greater severity once infected. In the young, cross-reactive pH1N1 antibody was mostly absent, while more intact CMI may have protected against severe outcomes. [ABSTRACT FROM AUTHOR]- Published
- 2011
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50. A novel highly osmotic K/Fe3O4/CNF magnetic draw solution for salty water desalination
- Author
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Aende, A, Gardy, J, Aslam, Z, Rogers, M, Edokali, M, Cespedes, O, Harbottle, D, and Hassanpour, A
- Subjects
Mechanical Engineering ,General Chemical Engineering ,General Materials Science ,General Chemistry ,Water Science and Technology
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