4 results on '"Ammari, M."'
Search Results
2. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
- Author
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Biotechnology and Biological Sciences Research Council (UK), European Commission, Ontario Research Fund, Canada Research Chairs, Fondation pour la Recherche Médicale, British Heart Foundation, European Research Council, Wellcome Trust, National Institutes of Health (US), Sivade (Dumousseau), M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H, Ceol, A., Cesareni, G., Combe, C. W., De Las Rivas, Javier, Toro, N. del, Heimbach, J., Hermjakob, H., Jurisica, I., Koch, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B. H. M., Micklem, G., Panni, S., Porras, P., Ricard-Blum, S., Roechert, B., Salwinski, L., Shrivastava, A., Sullivan, J., Thierry-Mieg, N., Yehudi, Y., Van Roey, K., Orchard, S., Biotechnology and Biological Sciences Research Council (UK), European Commission, Ontario Research Fund, Canada Research Chairs, Fondation pour la Recherche Médicale, British Heart Foundation, European Research Council, Wellcome Trust, National Institutes of Health (US), Sivade (Dumousseau), M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H, Ceol, A., Cesareni, G., Combe, C. W., De Las Rivas, Javier, Toro, N. del, Heimbach, J., Hermjakob, H., Jurisica, I., Koch, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B. H. M., Micklem, G., Panni, S., Porras, P., Ricard-Blum, S., Roechert, B., Salwinski, L., Shrivastava, A., Sullivan, J., Thierry-Mieg, N., Yehudi, Y., Van Roey, K., and Orchard, S.
- Abstract
[Background]: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. [Results]: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. [Conclusions]: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and dow
- Published
- 2018
3. Drug resistant tuberculosis in Saudi Arabia: an analysis of surveillance data 2014-2015.
- Author
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Al Ammari M, Al Turaiki A, Al Essa M, Kashkary AM, Eltigani SA, and Ahmed AE
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- Adult, Age Factors, Ethambutol pharmacology, Female, Humans, Isoniazid pharmacology, Logistic Models, Male, Microbial Sensitivity Tests, Middle Aged, Mycobacterium tuberculosis drug effects, Mycobacterium tuberculosis pathogenicity, Pyrazinamide pharmacology, Regression Analysis, Retrospective Studies, Rifampin pharmacology, Saudi Arabia epidemiology, Sex Factors, Streptomycin pharmacology, Tuberculosis, Multidrug-Resistant prevention & control, World Health Organization, Young Adult, Antitubercular Agents pharmacology, Tuberculosis, Multidrug-Resistant drug therapy, Tuberculosis, Multidrug-Resistant epidemiology
- Abstract
Background: There is limited data that investigates the national rates of drug-resistant tuberculosis (TB) in Saudi Arabia.This study aimed to estimate the rates of multi-drug-resistant tuberculosis (MDR-TB), rifampicin-resistant tuberculosis (RR-TB), and monoresistance (MR) in Saudi Arabia., Methods: A retrospective cohort study was conducted on all TB cases reported to the National TB Control and Prevention Program (NTCPP) registry at the Saudi Ministry of Health between January 1, 2014 and December 31, 2015. A total of 2098 TB patients with positive TB cultures were included in the study. Subgroup analyses and multivariate binary logistic regression models were performed with IBM SPSS 23.0., Results: Of the total TB cases, 4.4% (95% CI: 3.59%-5.40%) were found to have MDR-TB. The rates of MR were 3.8% (95% CI: 2.99%-4.67%) for ethambutol, 5.4% (95% CI: 4.50%-6.49%) for pyrazinamide, 10.2% (95% CI: 5.89%-11.52%) for isoniazid, 11% (95% CI: 9.70%-12.43%) for streptomycin, and 5.9% (95% CI: 4.90%-6.96%) for rifampicin. The high rates of MDR and RR-TB were found among the younger age group, female gender, and those who had a previous history of TB. We also discovered that renal failure tends to increase the risk of rifampicin resistance., Conclusions: National TB data in Saudi Arabia shows that the rate of MDR-TB was similar to the global rate reported by the World Health Organization (WHO). It is a relatively high rate as compared to Western countries. The proportion of MDR/RR-TB patients tends to be higher in the younger age group, female gender, and in patients with a previous history of TB treatment. Effective strategies for prevention of all multi-drug-resistant TB cases are warranted., Competing Interests: The study received ethical approval from the Institutional Review Board (IRB) at Saudi Ministry of Health and King Abdullah International Medical Research Center.Not applicable.The authors declare that they have no competing interests. Open Choice: Yes.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- Published
- 2018
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4. Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences.
- Author
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Ammari M, McCarthy FM, Nanduri B, and Pinchuk LM
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- Animals, Cattle, Cells, Cultured, Diarrhea Viruses, Bovine Viral genetics, Diarrhea Viruses, Bovine Viral immunology, Host-Pathogen Interactions, Molecular Sequence Annotation, Monocytes immunology, Cytopathogenic Effect, Viral genetics, Diarrhea Viruses, Bovine Viral pathogenicity, Monocytes virology
- Abstract
Background: Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune suppression if animals are infected with an ncp biotype during early gestation, followed by a subsequent infection of the cp biotype. The molecular mechanisms that underscore the complex disease etiology leading to immune suppression in cattle caused by BVDV are not well understood., Results: Using proteomics, we evaluated the effect of cp and ncp BVDV infection of bovine monocytes to determine their role in viral immune suppression and uncontrolled inflammation. Proteins were isolated by differential detergent fractionation and identified by 2D-LC ESI MS/MS. We identified 137 and 228 significantly altered bovine proteins due to ncp and cp BVDV infection, respectively. Functional analysis of these proteins using the Gene Ontology (GO) showed multiple under- and over- represented GO functions in molecular function, biological process and cellular component between the two BVDV biotypes. Analysis of the top immunological pathways affected by BVDV infection revealed that pathways representing macropinocytosis signalling, virus entry via endocytic pathway, integrin signalling and primary immunodeficiency signalling were identified only in ncp BVDV-infected monocytes. In contrast, pathways like actin cytoskeleton signalling, RhoA signalling, clathrin-mediated endocytosis signalling and interferon signalling were identified only in cp BDVD-infected cells. Of the six common pathways involved in cp and ncp BVDV infection, acute phase response signalling was the most significant for both BVDV biotypes. Although, most shared altered host proteins between both BVDV biotypes showed the same type of change, integrin alpha 2b (ITGA2B) and integrin beta 3 (ITGB3) were down- regulated by ncp BVDV and up- regulated by cp BVDV infection., Conclusions: This study shows that, as we expected, there are significant functional differences in the host proteins that respond to cp or ncp BVDV infection. The combined use of GO and systems biology network modelling facilitated a better understanding of host-pathogen interactions.
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- 2010
- Full Text
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