1
|
Imam N, Alam A, Siddiqui MF, Veg A, Bay S, Khan MJI, Ishrat R. Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes. Brief Funct Genomics 2023; 22:250-262. [PMID: 36790356 DOI: 10.1093/bfgp/elac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 02/16/2023] Open
Abstract
Primary hyperparathyroidism is caused by solitary parathyroid adenomas (PTAs) in most cases (⁓85%), and it has been previously reported that PTAs are associated with cardiovascular disease (CVD) and type-2 diabetes (T2D). To understand the molecular basis of PTAs, we have investigated the genetic association amongst PTAs, CVD and T2D through an integrative network-based approach and observed a remarkable resemblance. The current study proposed to compare the PTAs-associated proteins with the overlapping proteins of CVD and T2D to determine the disease relationship. We constructed the protein-protein interaction network by integrating curated and experimentally validated interactions in humans. We found the $11$ highly clustered modules in the network, which contain a total of $13$ hub proteins (TP53, ESR1, EGFR, POTEF, MEN1, FLNA, CDKN2B, ACTB, CTNNB1, CAV1, MAPK1, G6PD and CCND1) that commonly co-exist in PTAs, CDV and T2D and reached to network's hierarchically modular organization. Additionally, we implemented a gene-set over-representation analysis over biological processes and pathways that helped to identify disease-associated pathways and prioritize target disease proteins. Moreover, we identified the respective drugs of these hub proteins. We built a bipartite network that helps decipher the drug-target interaction, highlighting the influential roles of these drugs on apparently unrelated targets and pathways. Targeting these hub proteins by using drug combinations or drug-repurposing approaches will improve the clinical conditions in comorbidity, enhance the potency of a few drugs and give a synergistic effect with better outcomes. This network-based analysis opens a new horizon for more personalized treatment and drug-repurposing opportunities to investigate new targets and multi-drug treatment and may be helpful in further analysis of the mechanisms underlying PTA and associated diseases.
Collapse
Affiliation(s)
- Nikhat Imam
- Institute of Computer Science and Information Technology, Department of Mathematics, Magadh University, Bodh Gaya, Bihar India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi India
| | - Mohd Faizan Siddiqui
- International Medical Faculty, Osh State University, Osh City, 723500, Kyrgyz Republic Kyrgyzstan
| | - Akhtar Veg
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi India
| | - Sadik Bay
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University; Istanbul Türkiye
| | - Md Jawed Ikbal Khan
- Institute of Computer Science and Information Technology, Department of Mathematics, Magadh University, Bodh Gaya, Bihar India.,Department of Mathematics, Mirza Ghalib College, Magadh University, Bodh Gaya, Bihar India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi India
| |
Collapse
|
2
|
Imam N, Bay S, Siddiqui MF, Yildirim O. Network Analysis Based Software Packages, Tools, and Web Servers to Accelerate Bioinformatics Research. Biological Networks in Human Health and Disease 2023:51-64. [DOI: 10.1007/978-981-99-4242-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
|
3
|
Alam A, Yildirim O, Siddiqui F, Imam N, Bay S. Network Medicine: Methods and Applications. Biological Networks in Human Health and Disease 2023:75-90. [DOI: 10.1007/978-981-99-4242-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
|
4
|
Ahmed MM, Tazyeen S, Ali R, Alam A, Imam N, Malik MZ, Ali S, Ishrat R. Network centrality approaches used to uncover and classify most influential nodes with their related miRNAs in cardiovascular diseases. Gene Reports 2022. [DOI: 10.1016/j.genrep.2022.101555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
5
|
Alam A, Abubaker Bagabir H, Sultan A, Siddiqui MF, Imam N, Alkhanani MF, Alsulimani A, Haque S, Ishrat R. An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. Front Pharmacol 2022; 12:770762. [PMID: 35153741 PMCID: PMC8829040 DOI: 10.3389/fphar.2021.770762] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/27/2021] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent. The estimated total global TB deaths in 2019 were 1.4 million. The decline in TB incidence rate is very slow, while the burden of noncommunicable diseases (NCDs) is exponentially increasing in low- and middle-income countries, where the prevention and treatment of TB disease remains a great burden, and there is enough empirical evidence (scientific evidence) to justify a greater research emphasis on the syndemic interaction between TB and NCDs. The current study was proposed to build a disease-gene network based on overlapping TB with NCDs (overlapping means genes involved in TB and other/s NCDs), such as Parkinson’s disease, cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and lung cancer. We compared the TB-associated genes with genes of its overlapping NCDs to determine the gene-disease relationship. Next, we constructed the gene interaction network of disease-genes by integrating curated and experimentally validated interactions in humans and find the 13 highly clustered modules in the network, which contains a total of 86 hub genes that are commonly associated with TB and its overlapping NCDs, which are largely involved in the Inflammatory response, cellular response to cytokine stimulus, response to cytokine, cytokine-mediated signaling pathway, defense response, response to stress and immune system process. Moreover, the identified hub genes and their respective drugs were exploited to build a bipartite network that assists in deciphering the drug-target interaction, highlighting the influential roles of these drugs on apparently unrelated targets and pathways. Targeting these hub proteins by using drugs combination or drug repurposing approaches will improve the clinical conditions in comorbidity, enhance the potency of a few drugs, and give a synergistic effect with better outcomes. Thus, understanding the Mycobacterium tuberculosis (Mtb) infection and associated NCDs is a high priority to contain its short and long-term effects on human health. Our network-based analysis opens a new horizon for more personalized treatment, drug-repurposing opportunities, investigates new targets, multidrug treatment, and can uncover several side effects of unrelated drugs for TB and its overlapping NCDs.
Collapse
Affiliation(s)
- Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Hala Abubaker Bagabir
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Armiya Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Nikhat Imam
- Department of Mathematics, Institute of Computer Science and Information Technology, Magadh University, Bodh Gaya, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
6
|
Ishrat R, Ahmed MM, Tazyeen S, Alam A, Farooqui A, Ali R, Imam N, Tamkeen N, Ali S, Zubbair Malik M, Sultan A. In Silico Integrative Approach Revealed Key MicroRNAs and Associated Target Genes in Cardiorenal Syndrome. Bioinform Biol Insights 2021; 15:11779322211027396. [PMID: 34276211 PMCID: PMC8256246 DOI: 10.1177/11779322211027396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cardiorenal syndromes constellate primary dysfunction of either heart or kidney whereby one organ dysfunction leads to the dysfunction of another. The role of several microRNAs (miRNAs) has been implicated in number of diseases, including hypertension, heart failure, and kidney diseases. Wide range of miRNAs has been identified as ideal candidate biomarkers due to their stable expression. Current study was aimed to identify crucial miRNAs and their target genes associated with cardiorenal syndrome and to explore their interaction analysis. Three differentially expressed microRNAs (DEMs), namely, hsa-miR-4476, hsa-miR-345-3p, and hsa-miR-371a-5p, were obtained from GSE89699 and GSE87885 microRNA data sets, using R/GEO2R tools. Furthermore, literature mining resulted in the retrieval of 15 miRNAs from scientific research and review articles. The miRNAs-gene networks were constructed using miRNet (a Web platform of miRNA-centric network visual analytics). CytoHubba (Cytoscape plugin) was adopted to identify the modules and the top-ranked nodes in the network based on Degree centrality, Closeness centrality, Betweenness centrality, and Stress centrality. The overlapped miRNAs were further used in pathway enrichment analysis. We found that hsa-miR-21-5p was common in 8 pathways out of the top 10. Based on the degree, 5 miRNAs, namely, hsa-mir-122-5p, hsa-mir-222-3p, hsa-mir-21-5p, hsa-mir-146a-5p, and hsa-mir-29b-3p, are considered as key influencing nodes in a network. We suggest that the identified miRNAs and their target genes may have pathological relevance in cardiorenal syndrome (CRS) and may emerge as potential diagnostic biomarkers.
Collapse
Affiliation(s)
- Romana Ishrat
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Mohd Murshad Ahmed
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Aftab Alam
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Anam Farooqui
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Rafat Ali
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Nikhat Imam
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Naaila Tamkeen
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Shahnawaz Ali
- Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi,
India
| | - Md Zubbair Malik
- School of Computational and Integrative
Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Armiya Sultan
- Department of Biosciences, Jamia Millia
Islamia (A Central University), New Delhi, India
| |
Collapse
|
7
|
Alam A, Khan A, Imam N, Siddiqui MF, Waseem M, Malik MZ, Ishrat R. Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach. Brief Bioinform 2021; 22:1309-1323. [PMID: 33285567 PMCID: PMC7799329 DOI: 10.1093/bib/bbaa340] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.
Collapse
Affiliation(s)
- Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia University, New Delhi 110025, India
| | - Arbaaz Khan
- Department of computer science, Jamia Millia Islamia University, New Delhi, India
| | - Nikhat Imam
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia University, New Delhi, India
| | | | - Mohd Waseem
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md Zubbair Malik
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia University, New Delhi, India
| |
Collapse
|
8
|
Ahmed MM, Tazyeen S, Alam A, Farooqui A, Ali R, Imam N, Tamkeen N, Ali S, Malik MZ, Ishrat R. Deciphering key genes in cardio-renal syndrome using network analysis. Bioinformation 2021; 17:86-100. [PMID: 34393423 PMCID: PMC8340714 DOI: 10.6026/97320630017086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 12/23/2022] Open
Abstract
Cardio-renal syndrome (CRS) is a rapidly recognized clinical entity which refers to the inextricably connection between heart and renal impairment, whereby abnormality to one organ directly promotes deterioration of the other one. Biological markers help to gain insight into the pathological processes for early diagnosis with higher accuracy of CRS using known clinical findings. Therefore, it is of interest to identify target genes in associated pathways implicated linked to CRS. Hence, 119 CRS genes were extracted from the literature to construct the PPIN network. We used the MCODE tool to generate modules from network so as to select the top 10 modules from 23 available modules. The modules were further analyzed to identify 12 essential genes in the network. These biomarkers are potential emerging tools for understanding the pathophysiologic mechanisms for the early diagnosis of CRS. Ontological analysis shows that they are rich in MF protease binding and endo-peptidase inhibitor activity. Thus, this data help increase our knowledge on CRS to improve clinical management of the disease.
Collapse
Affiliation(s)
- Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Rafat Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Nikhat Imam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Naaila Tamkeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Shahnawaz Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Md Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-1100067, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| |
Collapse
|
9
|
Alam A, Imam N, Siddiqui MF, Ali MK, Ahmed MM, Ishrat R. Human gene expression profiling identifies key therapeutic targets in tuberculosis infection: A systematic network meta-analysis. Infection, Genetics and Evolution 2021; 87:104649. [DOI: 10.1016/j.meegid.2020.104649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022]
|
10
|
Imam N, Alam A, Siddiqui MF, Ahmed MM, Malik MZ, Ikbal Khan MJ, Ishrat R. Identification of key regulators in parathyroid adenoma using an integrative gene network analysis. Bioinformation 2020; 16:910-922. [PMID: 34803267 PMCID: PMC8573468 DOI: 10.6026/97320630016910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Parathyroid adenoma (PA) is marked by a certain benign outgrowth in the surface of parathyroid glands. The transcriptome analysis of parathyroid adenomas can provide a deep insight into actively expressed genes and transcripts. Hence, we analyzed and compared the gene expression profiles of parathyroid adenomas and healthy parathyroid gland tissues from Gene Expression Omnibus (GEO) database. We identified a total of 280 differentially expressed genes (196 up-regulated, 84 down-regulated), which are involved in a wide array of biological processes. We further constructed a gene interaction network and analyzed its topological properties to know the network structure and its hidden mechanism. This will help to understand the molecular mechanisms underlying parathyroid adenoma development. We thus identified 13 key regulators (PRPF19, SMC3, POSTN, SNIP1, EBF1, MEIS2, PAX9, SCUBE2, WNT4, ARHGAP10, DOCK5, CAV1 and VSIR), which are deep-rooted from top to bottom in the gene interaction network forming a backbone for the network. The structural features of the network are probably maintained by crosstalk between important genes within the network along with associated functional modules.Thus, gene-expression profiling and network approach could be used to provide an independent platform to glen insights from available clinical data.
Collapse
Affiliation(s)
- Nikhat Imam
- Institute of Computer Science and Information Technology, Department of Mathematics, Magadh University, Bodh Gaya-824234, Bihar, India
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Mohd Faizan Siddiqui
- International Medical Faculty, Osh State University, Osh City, 723500, Kyrgyz Republic, Kyrgyzstan
| | - Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Md. Zubbair Malik
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md. Jawed Ikbal Khan
- Institute of Computer Science and Information Technology, Department of Mathematics, Magadh University, Bodh Gaya-824234, Bihar, India
- Department of Mathematics, Mirza Ghalib College, Magadh University, Bodh Gaya-824234, Bihar, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India
| |
Collapse
|
11
|
Abstract
The top priority of any nation is to lead the nation towards prosperity, progress, and economic growth, confronting several challenges and concerns arisen from global situations. The sudden outbreak of any disease defies the health care systems and economy of nations. COVID-19 is one of the viral diseases which broke out in Wuhan city of China in 2019. COVID-19 outbreak intermittently prevailed all over the world. It exposes the fragility of the established health care systems across the world in spite of comprising modern science and technology. Unfortunately, there is no chemotherapeutic agent in the regimen of antiviral drugs or no vaccine available to curb this infectious disease. As a consequence, this deadly infection has prevailed all over the world. The antiviral drugs used for viral diseases excluding COVID-19 infection are Ramdesvir, Favipiravir, and Ribavarin, and antimalarial agents (Chloroquine & Hydroxychloroquine) are being administered to the patients for redemption of this infection. Fortunately, these existing drugs have been found clinically active and are being used. In this review, we present the current scenario and status of epidemiology, diagnosis, treatment, vaccine development for COVID-19, and its impact on the socio-economic structure.
Collapse
Affiliation(s)
- Aftab Alam
- Center for Interdisciplinary Research in Basic Sciences, JMI University, New Delhi India
| | - Mohd Faizan Siddiqui
- International Medical Faculty, Osh State University, Osh City, Kyrgyz Republic Kyrgyzstan
| | - Nikhat Imam
- Institute of Computer Science & Information Technology, Department of Mathematics, Magadh University, Bodh Gaya, Bihar India
| | - Rafat Ali
- Center for Interdisciplinary Research in Basic Sciences, JMI University, New Delhi India
| | - Md Mushtaque
- Department of Chemistry, School of Physical and Molecular Sciences, Al-Falah University, Dhauj, Faridabad, Haryana India
| | - Romana Ishrat
- Center for Interdisciplinary Research in Basic Sciences, JMI University, New Delhi India
| |
Collapse
|
12
|
Alam A, Imam N, Ahmed MM, Tazyeen S, Tamkeen N, Farooqui A, Malik MZ, Ishrat R. Identification and Classification of Differentially Expressed Genes and Network Meta-Analysis Reveals Potential Molecular Signatures Associated With Tuberculosis. Front Genet 2019; 10:932. [PMID: 31749827 PMCID: PMC6844239 DOI: 10.3389/fgene.2019.00932] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is one of deadly transmissible disease that causes death worldwide; however, only 10% of people infected with Mycobacteriumtuberculosis develop disease, indicating that host genetic factors may play key role in determining susceptibility to TB disease. In this way, the analysis of gene expression profiling of TB infected individuals can give us a snapshot of actively expressed genes and transcripts under various conditions. In the present study, we have analyzed microarray data set and compared the gene expression profiles of patients with different datasets of healthy control, latent infection, and active TB. We observed the transition of genes from normal condition to different stages of the TB and identified and annotated those genes/pathways/processes that have important roles in TB disease during its cyclic interventions in the human body. We identified 488 genes that were differentially expressed at various stages of TB and allocated to pathways and gene set enrichment analysis. These pathways as well as GSEA’s importance were evaluated according to the number of DEGs presents in both. In addition, we studied the gene regulatory networks that may help to further understand the molecular mechanism of immune response against the TB infection and provide us a new angle for future biomarker and therapeutic targets. In this study, we identified 26 leading hubs which are deeply rooted from top to bottom in the gene regulatory network and work as the backbone of the network. These leading hubs contains 31 key regulator genes, of which 14 genes were up-regulated and 17 genes were down-regulated. The proposed approach is based on gene-expression profiling, and network analysis approaches predict some unknown TB-associated genes, which can be considered (or can be tested) as reliable candidates for further (in vivo/in vitro) studies.
Collapse
Affiliation(s)
- Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nikhat Imam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.,Department of Mathematics, Institute of Computer Science & Information Technology, Magadh University, Bodh Gaya, India
| | - Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naaila Tamkeen
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Zubbair Malik
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
13
|
Imam N, Alam A, Ali R, Siddiqui MF, Ali S, Malik MZ, Ishrat R. In silico characterization of hypothetical proteins from Orientia tsutsugamushi str. Karp uncovers virulence genes. Heliyon 2019; 5:e02734. [PMID: 31720472 PMCID: PMC6838952 DOI: 10.1016/j.heliyon.2019.e02734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/29/2019] [Accepted: 10/23/2019] [Indexed: 11/20/2022] Open
Abstract
Scrub typhus also known as bush typhus is a disease with symptoms similar to Chikungunya infection. It is caused by a gram-negative bacterium Orientia tsutsugamushi which resides in its vertebrate host, Mites. The genome of Orientia tsutsugamushi str. Karp encodes for 1,563 proteins, of which 344 are characterized as hypothetical ones. In the present study, we tried to identify the probable functions of these 344 hypothetical proteins (HPs). All the characterized hypothetical proteins (HPs) belong to the various protein classes like enzymes, transporters, binding proteins, metabolic process and catalytic activity and kinase activity. These hypothetical proteins (HPs) were further analyzed for virulence factors with 62 proteins identified as the most virulent proteins among these hypothetical proteins (HPs). In addition, we studied the protein sequence similarity network for visualizing functional trends across protein superfamilies from the context of sequence similarity and it shows great potential for generating testable hypotheses about protein structure-function relationships. Furthermore, we calculated toplogical properties of the network and found them to obey network power law distributions showing a fractal nature. We also identifed two highly interconnected modules in the main network which contained five hub proteins (KJV55465, KJV56211, KJV57212, KJV57203 and KJV57216) having 1.0 clustering coefficient. The structural modeling (2D and 3D structure) of these five hub proteins was carried out and the catalytic site essential for its functioning was analyzed. The outcome of the present study may facilitate a better understanding of the mechanism of virulence, pathogenesis, adaptability to host and up-to-date annotations will make unknown genes easy to identify and target for experimentation. The information on the functional attributes and virulence characteristic of these hypothetical proteins (HPs) are envisaged to facilitate effective development of novel antibacterial drug targets of Orientia tsutsugamushi.
Collapse
Affiliation(s)
- Nikhat Imam
- Institute of Computer Science and Information Technology, Magadh University, Bodhgaya, India
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Rafat Ali
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Mohd Faizan Siddiqui
- International Medical Faculty, Osh State University, Osh City, 723500, Kyrgyz Republic (Kyrgyzstan)
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Md. Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, Delhi, 110067, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
14
|
Qureshi S, Saxena HM, Imam N, Kashoo Z, Sharief Banday M, Alam A, Malik MZ, Ishrat R, Bhat B. Isolation and genome analysis of a lytic Pasteurella multocida Bacteriophage PMP-GAD-IND. Lett Appl Microbiol 2018; 67:244-253. [PMID: 29808940 DOI: 10.1111/lam.13010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/10/2018] [Accepted: 04/25/2018] [Indexed: 11/28/2022]
Abstract
Currently used alum precipitated and oil adjuvant vaccines against HS caused by Pasteurella multocida B:2, have side effects and short-lived immunity, leading to regular catastrophic outbreaks in bovines in Asian subcontinent. The need for the development of an improved vaccine with longer immunity and the ability to differentiate between vaccinated and infected is essential. Pasteurella phage isolated in present study belongs to family Siphoviridae. PMP-GAD-IND phage exhibited lytic activity against vaccine strain (P52) as well as several field strains of P. multocida (B:2), and fowl cholera agent (P. multocida A:1).The phage has a double stranded DNA (dsDNA) with a genome of 46 335 bp. The complete genome sequence of the Pasteurella multocida phage has been deposited in Gen Bank with accession no: KY203335. PMP-GAD-IND being a lytic phage with broad activity range has a potential to be used in therapy against multidrug resistant P. multocida infections. SIGNIFICANCE AND IMPACT OF THE STUDY The present work is a part of research for the development of an improved phage lysate marker vaccine and a companion DIVA assay against haemorhagic septicaemia. This study describes the isolation and genome analysis of PMP-GAD-IND a lytic Pasteurella multocida bacteriophage.
Collapse
Affiliation(s)
- S Qureshi
- Division of Veterinary Microbiology & Immunology, FVSc & A.H., Shuhama (Aulesteng), SKUAST-K, Shalimar, India
| | - H M Saxena
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - N Imam
- Department of Mathematics, Institute of Computer Science & Information Technology, Magadh University, Bodh Gaya, Bihar, India
| | - Z Kashoo
- Division of Veterinary Microbiology & Immunology, FVSc & A.H., Shuhama (Aulesteng), SKUAST-K, Shalimar, India
| | - M Sharief Banday
- Department of Pharmacology, Government Medical College, Srinagar, Kashmir, India
| | - A Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Milia Islamia, Jamia Nagar, New Delhi, India
| | - Md Z Malik
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Milia Islamia, Jamia Nagar, New Delhi, India
| | - R Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Milia Islamia, Jamia Nagar, New Delhi, India
| | - B Bhat
- Division of Veterinary Microbiology & Immunology, FVSc & A.H., Shuhama (Aulesteng), SKUAST-K, Shalimar, India.,Division of Animal Genetics and Breeding, FVSc& A.H., Shuhama (Aulesteng), SKUAST-K, Shalimar, India
| |
Collapse
|
15
|
Hoskins AJ, Worth LJ, Imam N, Johnson SA, Bull AL, Richards MJ, Bennett NJ. Validation of healthcare-associated infection surveillance in smaller Australian hospitals. J Hosp Infect 2017; 99:85-88. [PMID: 29031863 DOI: 10.1016/j.jhin.2017.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/09/2017] [Indexed: 11/26/2022]
Abstract
A validation study was conducted in smaller (<100 acute beds) Victorian hospitals to evaluate case detection for Staphylococcus aureus bloodstream (SAB), meticillin-resistant S. aureus (MRSA) and vancomycin-resistant enterococci (VRE) infections. Overall, 142 infections were identified in 20 hospitals. For routine surveillance of SAB events, sensitivity was 74.4% and specificity was 100.0%. For MRSA infections, sensitivity was 47.5% and specificity was 90.9%. All confirmed VRE infections were reported correctly. Of unreported SAB and MRSA infections, 80% (N = 16) and 83.9% (N = 26) were community-associated infections, respectively. Future programme refinements include targeted education to ensure appropriate application of case definitions, particularly those including community onset.
Collapse
Affiliation(s)
- A J Hoskins
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - L J Worth
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - N Imam
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - S A Johnson
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - A L Bull
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - M J Richards
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - N J Bennett
- Victorian Healthcare Associated Infection Surveillance System Coordinating Centre, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|
16
|
Alam A, Imam N, farooqui A, Ali S, Malik MZ, Ishrat R. Recent trends in ZikV research: A step away from cure. Biomed Pharmacother 2017; 91:1152-1159. [DOI: 10.1016/j.biopha.2017.05.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/02/2017] [Accepted: 05/09/2017] [Indexed: 12/23/2022] Open
|
17
|
Abstract
We study memory states of a circuit consisting of a small inductively coupled Josephson junction array and introduce basic (write, read, and reset) memory operations logics of the circuit. The presented memory operation paradigm is fundamentally different from conventional single quantum flux operation logics. We calculate stability diagrams of the zero-voltage states and outline memory states of the circuit. We also calculate access times and access energies for basic memory operations.
Collapse
Affiliation(s)
- Y Braiman
- Computer Science and Mathematics Division, Computing and Computational Science Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.,Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - B Neschke
- Computer Science and Mathematics Division, Computing and Computational Science Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.,Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - N Nair
- Computer Science and Mathematics Division, Computing and Computational Science Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.,Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - N Imam
- Computing and Computational Science Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R Glowinski
- Department of Mathematics, Houston University, Houston, Texas 77204, USA
| |
Collapse
|
18
|
Otsuka-Tanaka Y, Oommen S, Kawasaki M, Kawasaki K, Imam N, Jalani-Ghazani F, Hindges R, Sharpe PT, Ohazama A. Oral lining mucosa development depends on mesenchymal microRNAs. J Dent Res 2012; 92:229-34. [PMID: 23242232 DOI: 10.1177/0022034512470830] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The oral mucosa plays critical roles in protection, sensation, and secretion and can be classified into masticatory, lining, and specialized mucosa that are known to be functionally, histologically, and clinically distinct. Each type of oral mucosa is believed to develop through discrete molecular mechanisms, which remain unclear. MicroRNAs (miRNAs) are 19 to 25nt non-coding small single-stranded RNAs that negatively regulate gene expression by binding target mRNAs. miRNAs are crucial for fine-tuning of molecular mechanisms. To investigate the role of miRNAs in oral mucosa development, we examined mice with mesenchymal (Wnt1Cre;Dicer(fl/fl)) conditional deletion of Dicer. Wnt1Cre;Dicer(fl/fl) mice showed trans-differentiation of lining mucosa into an epithelium with masticatory mucosa/ skin-specific characteristics. Up-regulation of Fgf signaling was found in mutant lining mucosal epithelium that was accompanied by an increase in Fgf7 expression in mutant mesenchyme. Mesenchyme miRNAs thus have an indirect effect on lining mucosal epithelial cell growth/differentiation.
Collapse
Affiliation(s)
- Y Otsuka-Tanaka
- Craniofacial Development and Stem Cell Biology, and Biomedical Research Centre, Dental Institute, King's College London, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Winn AJ, Boccaccini AR, Imam N, Trusty PA. Examination of microhardness indentation‐induced subsurface damage in alumina platelet reinforced borosilicate glass using confocal scanning laser microscopy. J Microsc 2003. [DOI: 10.1046/j.1365-2818.1997.1880751.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- A. J. Winn
- Manchester Materials Science Centre, Grosvenor Street, Manchester M1 7HS, U.K
| | - A. R. Boccaccini
- School of Metallurgy and Materials, The University of Birmingham, Birmingham B15 2TT, U.K
| | - N. Imam
- Manchester Materials Science Centre, Grosvenor Street, Manchester M1 7HS, U.K
| | - P. A. Trusty
- Interdisciplinary Research Centre in Materials for High Performance Applications, The University of Birmingham, Birmingham B15 2TT, U.K
| |
Collapse
|
20
|
Poirier F, Imam N, Pontet M, Joubert-Caron R, Caron M. The BPP (protein biochemistry and proteomics) two-dimensional electrophoresis database. J Chromatogr B Biomed Sci Appl 2001; 753:23-8. [PMID: 11302443 DOI: 10.1016/s0378-4347(00)00459-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The BPP (protein biochemistry and proteomics) two-dimensional electrophoresis (2-DE) database (http://www-smbh.univ-paris13.fr/lbtp/Biochemistry/Biochimie/bque.htm) was established in 1998. The current release contains 11 reference maps from human hematopoietic and lymphoid cell line samples. These reference maps have now 255 identified spots, corresponding to 84 protein entries. The World Wide Web (WWW) presentation is designed to allow public access to the available 2-DE data together with logical connections to databases providing complementary information.
Collapse
Affiliation(s)
- F Poirier
- Biochimie des Protéines et Protéomique, Biochimie Cellulaire des Hémopathies Lymphoïdes (EA 1625), UFR SMBH Léonard de Vinci, Université Paris 13, Bobigny, France
| | | | | | | | | |
Collapse
|
21
|
Joubert-Caron R, Le Caër JP, Montandon F, Poirier F, Pontet M, Imam N, Feuillard J, Bladier D, Rossier J, Caron M. Protein analysis by mass spectrometry and sequence database searching: a proteomic approach to identify human lymphoblastoid cell line proteins. Electrophoresis 2000; 21:2566-75. [PMID: 10939474 DOI: 10.1002/1522-2683(20000701)21:12<2566::aid-elps2566>3.0.co;2-f] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lymphoblastoid cell lines correspond to in vitro EBV-immortalized lymphocyte B-cells. These cells display a suitable model for experiments dealing with changes in protein expression occurring upon B-cell differentiation, after drug treatment, or after inhibition of some transcription factors. For all these reasons we have undertaken an effort aimed at developing a hematopoietic cell line protein two-dimensional electrophoresis (2-DE) database, containing B-lymphoblastoid 2-DE maps. In this work, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) peptide mass fingerprinting analysis was adopted for protein identification. The peptide mass fingerprinting identification and the sequence coverage obtained on colloidal Coomassie blue (CBB) stained gel was close to that obtained using zinc-imidazole staining. Everything considered, CBB being more comfortable for subsequent spot manipulations, CBB staining was chosen for identification of a larger number of polypeptides. The results suggest that reticulation of the gel can interfere preventing the uptake of the enzyme during the in-gel digestion step. Consequently, low molecular mass proteins appear more difficult to identify by mass fingerprinting. Finally, the information provided in this study allows the construction of a new annoted reference map of human lymphoblastoid cell proteins. Among the identified proteins 60% were not yet positioned on 2-DE maps in three of the most important well-documented databases. The annoted map will be accessible via Internet on the LBPP server at URL:http:// www-smbh.univ-paris13.fr/lbtp/index.htm.
Collapse
Affiliation(s)
- R Joubert-Caron
- Biochimie Cellulaire des Hémopathies Lymphoïdes, Université Paris 13, UFR SMBH, Leonard de Vinici, Bibogny, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Rashid H, Smith DA, Bao Z, Chakravarthy RS, Pathan MA, Imam N, Kissa K, Kallman J. Use of radio-frequency-pulse surface acoustic wave profilometry for passband engineering of acousto-optic tunable filters. Opt Lett 1996; 21:342-344. [PMID: 19865399 DOI: 10.1364/ol.21.000342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
One can determine the acoustic profile of an acousto-optic tunable filter (AOTF) either by measuring the intensity of a laser diffracted off the surface of an AOTF by the surface acoustic wave (SAW) or by measuring the optical output power of an AOTF as a short burst of rf energy is launched down the device. This rf-burst technique (also called pulse probing) is compared with the established optical diffraction SAW profilometry technique. We demonstrate the usefulness of rf-burst profilometry to measure the acousto-optic coupling as a function of position along an AOTF interaction region. Such a probe can be used to make adjustments to the acousto-optic coupling in real time to achieve passband shape modification in complex AOTF structures.
Collapse
|
23
|
Abstract
PURPOSE Candida is the most common cause of opportunistic mucosal infections in human immunodeficiency virus (HIV)-positive women. We had observed an apparent correlation between the severity of immunodeficiency and the site of mucosal candida infection. The current study was designed to determine whether significant correlations existed between the sites of mucosal candida infection and the degree of immunodeficiency, as determined by subsets of lymphocyte populations. PATIENTS AND METHODS The subjects in this study are 66 HIV-seropositive women evaluated by members of the Brown University Acquired Immunodeficiency Syndrome (AIDS) Program during the 3-year period, September 1, 1986, through August 30, 1989. All patients had thorough clinical evaluations and relevant laboratory studies at defined intervals. All patients with CD4 lymphocyte counts below 0.2 X 10(9)/L received zidovudine therapy as soon as it became available. After July 1988, all patients with CD4 counts below 0.2 X 10(9)/L received prophylaxis against Pneumocystis carinii pneumonia. All patients were counseled about HIV infection, its modes of transmission, and the early symptoms of opportunistic infections. RESULTS The longitudinal data demonstrated that candida often infected vaginal mucosa when there was no significant reduction in CD4 lymphocyte counts. Candida infection of the oropharyngeal mucosa was associated with highly significant reductions in CD4 lymphocyte counts. Esophageal candidiasis occurred only with advanced immunodeficiency associated with CD4 counts below 0.1 X 10(9)/L. CONCLUSIONS Candida mucosal infections occur in a hierarchical pattern in women with HIV infection. Determination of the basis for the differences in susceptibility to candida of the vaginal, oropharyngeal, and esophageal mucosal surfaces will require further studies.
Collapse
Affiliation(s)
- N Imam
- Brown University AIDS Program, Providence, Rhode Island
| | | | | | | | | | | |
Collapse
|
24
|
Itoh K, Saini S, Hahn PF, Imam N, Ferrucci JT. Differentiation between small hepatic hemangiomas and metastases on MR images: importance of size-specific quantitative criteria. AJR Am J Roentgenol 1990; 155:61-6. [PMID: 2112865 DOI: 10.2214/ajr.155.1.2112865] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We studied the feasibility of using MR imaging at 0.6 T to differentiate small hepatic hemangiomas from small metastases on the basis of quantitative criteria. Ninety-two liver masses up to 5 cm in diameter, including 51 proved hemangiomas (mean, 1.9 +/- 1.1 cm) and 41 proved metastases (mean, 1.9 +/- 1.2 cm) were analyzed. Lesions were divided into three groups on the basis of size (less than or equal to 1 cm, greater than 1- less than or equal to 2 cm, greater than 2- less than or equal to 5 cm). The ability to distinguish hemangiomas from metastases was examined by using differences in lesion/liver signal-intensity ratio (SIR) and contrast-to-noise ratio (CNR) on T2-weighted images (SE 2350/180). Receiver-operating-characteristic analysis for all lesions grouped together showed that differentiation based on SIR was superior to that based on CNR (p less than .05). The mean SIR of hemangioma and the difference between mean SIRs of hemangioma and metastasis decreased with lesion size (greater than 2- less than or equal to 5 cm: 6.11 +/- 2.61 vs 2.30 +/- 1.22; greater than 1- less than or equal to 2 cm: 4.47 +/- 1.56 vs 2.40 +/- 0.73; less than or equal to 1 cm: 3.59 +/- 0.92 vs 2.01 +/- 0.52). However, in each size group, the difference between the mean SIR of hemangioma and metastasis was statistically significant (p less than .0001). These observations suggest that MR imaging is useful in differentiating small hepatic hemangiomas from small metastases and suggest the need for establishing size-specific quantitative criteria for tissue characterization.
Collapse
Affiliation(s)
- K Itoh
- Department of Radiology, Massachusetts General Hospital, Boston
| | | | | | | | | |
Collapse
|