14 results on '"Soban M"'
Search Results
2. Enhancing stent length and stability with a novel through-the-scope suturing platform: a case series
- Author
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Ayowumi A. Adekolu, MD, Ethan M. Cohen, MD, Rohit Agrawal, MD, Soban Maan, MBBS, George Obeng, MD, Shyam Thakkar, MD, and Shailendra Singh, MD
- Subjects
Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background and Aims: Fully covered self-expandable metal stents are commonly used for managing GI adverse events like perforations, leaks, fistulas, and strictures. Although effective, stent length and migration can be a limitation when dealing with larger defects. Over-the-scope clips and over-the-scope suturing can be used to mitigate migration risk; however, their role is limited for stent-to-stent suturing to create longer stents. We present a novel application of through-the-scope suturing (TTSS) system for creating longer stents to manage larger GI defects. Methods: We demonstrate using a video case series the applicability of TTSS for fixing multiple coaxially placed stents to create a longer stent and simultaneously anchor them to underlying GI wall to mitigate stent migration. Results: We illustrate our success in managing 3 cases of large esophageal and/or gastric pathologies (stenosis and leak) using the TTSS system to create longer stents through stent-in-stent fixation. Conclusions: TTSS is a novel endoscopic suturing platform that is compatible with most endoscopes and can be navigated to challenging narrow and angulated location, giving it an advantage over over-the-scope suturing/over-the-scope clips. Our case series demonstrates that stent-in-stent fixation of multiple fully covered self-expandable metal stents to create longer stents using the TTSS system is an effective technique when managing larger GI defects.
- Published
- 2024
- Full Text
- View/download PDF
3. Dynamic profiling of the β-coronavirus 3CL Mpro protease ligand binding sites
- Author
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Cho, E, Rosa, M, Anjum, R, Mehmood, S, Soban, M, Mujtaba, M, Bux, K, Moin, S.T., Tanweer, M, Dantu, S, Pandini, A, Yin, J, Ma, H, Ramanathan, A, Islam, B, Mey, A.S.J.S, Bhowmik, D, and Haider, S
- Subjects
body regions ,Coronavirus ,viruses ,fungi ,binding sites ,inhibitors ,protease ,skin and connective tissue diseases ,molecular dynamics ,respiratory tract diseases - Abstract
MD trajectories of SARS-CoV2, SARS-CoV and MERS-CoV 3CL Mpro protease
- Published
- 2021
- Full Text
- View/download PDF
4. Structural dynamics of the β-coronavirus Mpro protease ligand binding sites
- Author
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Debsindhu Bhowmik, Barira Islam, Arvind Ramanathan, Shozeb Haider, Maria J. Rosa, Antonia S. J. S. Mey, Alessandro Pandini, Heng Ma, Ruhi Anjum, Khair Bux, Junqi Yin, Cho E, Mehmood S, Soban M, Mujtaba M, and Sarath Chandra Dantu
- Subjects
State model ,2019-20 coronavirus outbreak ,Viral Components ,Protease ,Viral replication ,medicine.medical_treatment ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,medicine ,Computational biology ,Biology ,medicine.disease_cause ,Beta (finance) ,Coronavirus - Abstract
This article is a preprint and has not been certified by peer review. It was eventually published online on 14 June 2021 by American Chemical Society (ACS Publications) as: Cho, E. et al. (2021) 'Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites', Journal of Chemical Information and Modeling, 61 (6), pp. 3058 - 3073. doi: 10.1021/acs.jcim.1c00449. Data Availability Statement: The trajectories of Mpro simulations and models of the metastable states can be obtained from the corresponding author. Jupyter-notebooks to generate Markov State Models can be downloaded from 10.6084/m9.figshare.14343725 bioRxiv posts many COVID19-related papers. A reminder: they have not been formally peer-reviewed and should not guide health-related behavior or be reported in the press as conclusive. β-coronaviruses alone have been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a back-up against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensible role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all non-redundant ligand-binding sites available for SARS-CoV2, SARS-CoV and MERS-CoV Mpro. Extensive adaptive sampling has been used to explore conformational dynamics employing convolutional variational auto encoder-based deep learning, and investigates structural conservation of the ligand binding sites using Markov state models across β-coronavirus homologs. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-coronavirus homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor. U.S. Department of Energy, Office of Science, through the Advanced Scientific Computing Research (ASCR), under contract number DEAC05-00OR22725 and the Exascale Computing Project (ECP) (17-SC-20-SC). BI would like to acknowledge the COVID-19 pump-priming grant from the University of Huddersfield for funding computing resources for analysis.
- Published
- 2021
5. Endoscopic closure of a recto-pelvic fistula with a cardiac septal occluder device
- Author
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Ayowumi A. Adekolu, MD, Ethan M. Cohen, MD, Sardar Momin Shah-Khan, MD, Soban Maan, MBBS, Joyce Foryoung, MD, Ademola Ajibade, MD, Shyam Thakkar, MD, and Shailendra Singh, MD
- Subjects
Diseases of the digestive system. Gastroenterology ,RC799-869 - Published
- 2024
- Full Text
- View/download PDF
6. Undiagnosed coeliac disease and risk of autoimmune disorders in subjects with Type I diabetes mellitus
- Author
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Not, T., Tommasini, A., Tonini, G., Buratti, E., Pocecco, M., Tortul, C., Valussi, M., Crichiutti, G., Berti, I., Trevisiol, C., Azzoni, E., Neri, E., Torre, G., Martelossi, S., Soban, M., Lenhardt, A., Cattin, L., and Ventura, A.
- Published
- 2001
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7. Curing Asthma with Diet and Lifestyle Modification
- Author
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Waqas Ali, Rai, primary, Dar, Umair, additional, Khan, Izzatullah, additional, Farooq, Asim, additional, Soban, M., additional, Wain, Zafeer Naeem, additional, Tahir, Umer, additional, and Bashir, Irfan, additional
- Published
- 2018
- Full Text
- View/download PDF
8. Undiagnosed coeliac disease and risk of autoimmune disorders in subjects with Type I diabetes mellitus
- Author
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M. Pocecco, Elena Neri, Irene Berti, G Crichiutti, A. Lenhardt, Tarcisio Not, Alessandro Ventura, Chiara Trevisiol, C. Tortul, Elisabetta Azzoni, Stefano Martelossi, G. Torre, M Soban, G. Tonini, E Buratti, Luigi Cattin, M Valussi, Alberto Tommasini, Not, Tarcisio, Tommasini, A, Tonini, G, Buratti, E, Pocecco, M, Tortul, C, Valussi, M, Crichiutti, G, Berti, I, Trevisiol, C, Azzoni, E, Neri, E, Torre, G, Martelossi, S, Soban, M, Lenhardt, A, Cattin, Luigi, and Ventura, Alessandro
- Subjects
Adult ,Male ,Parents ,medicine.medical_specialty ,Adolescent ,Glutens ,Endocrinology, Diabetes and Metabolism ,Muscle Fibers, Skeletal ,Preschool, Diabetes Mellitu ,Skeletal, Nuclear Family, Parents, Risk Factors ,Muscle Fibers ,Coeliac disease ,Autoimmune Diseases ,Nuclear Family ,Adolescent, Adult, Aged, Autoantibodies, Autoimmune Diseases, Celiac Disease, Child, Child ,Preschool, Diabetes Mellitus ,Type 1, Diet, Female, Glutens, Humans, Male, Middle Aged, Muscle Fibers ,Risk Factors ,Internal medicine ,Immunopathology ,Diabetes mellitus ,Internal Medicine ,medicine ,Diabetes Mellitus ,Humans ,Type 1, Diet, Female, Glutens, Humans, Male, Middle Aged, Muscle Fiber ,Risk factor ,Child ,Preschool ,Aged ,Autoantibodies ,Autoimmune disease ,High prevalence ,biology ,business.industry ,Type i diabetes mellitus ,nutritional and metabolic diseases ,Skeletal ,Middle Aged ,medicine.disease ,Diet ,Celiac Disease ,Endocrinology ,Diabetes Mellitus, Type 1 ,Child, Preschool ,biology.protein ,Female ,Antibody ,business ,Type 1 - Abstract
Aims/hypothesis. We tested the hypothesis that silent coeliac disease is more frequent than expected in both patients with Type I (insulin-dependent) diabetes mellitus and their first-degree relatives. We evaluated how the presence of other autoimmune disorders in diabetic patients and their first-degree relatives is related to silent, unrecognized coeliac disease. Methods. Sera from 491 subjects with Type I diabetes, 824 relatives and 4000 healthy control subjects were screened for anti-endomysial antibodies and all those subjects who tested positive for anti-endomysial antibodies underwent intestinal biopsy. Results. We found that the prevalence of coeliac disease was 5.7 % among the diabetic patients and 1.9 % among the relatives, values significantly higher than those found among the control subjects (p < 0.0001; p < 0.001). The prevalence of autoimmune disorders in diabetic patients with coeliac disease was significantly higher than in subjects with Type I diabetes alone (p < 0.0001). The prevalence of autoimmune disorders in the relatives with coeliac disease was significantly higher than in those who tested negative for anti-endomysial antibodies (p = 0.01). Conclusion/interpretation. This report provides further confirmation of the high prevalence of undiagnosed coeliac disease among diabetic patients and their relatives. This interesting new finding is the increased presence of other autoimmune diseases in these patients, as well as in their relatives with a delayed diagnosis for coeliac disease. Patients newly diagnosed with coeliac disease showed excellent compliance with the gluten-free diet. This should encourage policymakers to consider introducing an easy-to-use screening programme for diabetic patients and their relatives into everyday clinical practice, in order to prevent coeliac-associated symptoms and the onset of additional, more serious auto-immune disorders. [Diabetologia (2001) 44: 151–155]
- Published
- 2001
9. Dynamic Profiling of β-Coronavirus 3CL M pro Protease Ligand-Binding Sites.
- Author
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Cho E, Rosa M, Anjum R, Mehmood S, Soban M, Mujtaba M, Bux K, Moin ST, Tanweer M, Dantu S, Pandini A, Yin J, Ma H, Ramanathan A, Islam B, Mey ASJS, Bhowmik D, and Haider S
- Subjects
- Antiviral Agents, Binding Sites, Humans, Ligands, Protease Inhibitors, RNA, Viral, SARS-CoV-2, COVID-19, Peptide Hydrolases
- Abstract
β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (M
pro ) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro . Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.- Published
- 2021
- Full Text
- View/download PDF
10. A comparison of characteristics and outcomes of patients with community-acquired and hospital-acquired COVID-19 in the United Kingdom: An observational study.
- Author
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Shiwani HA, Bilal M, Shahzad MU, Rodrigues A, Suliman JA, Soban M, Mirza S, Lotca N, Ruslan MR, Memon D, Arshad MA, Fatima K, Kamran A, Egom EE, and Aziz A
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, COVID-19 diagnosis, Community-Acquired Infections diagnosis, Cross Infection diagnosis, Female, Hospital Mortality, Hospitalization, Humans, Male, Middle Aged, Retrospective Studies, Survival Rate, Symptom Assessment, United Kingdom, Young Adult, COVID-19 complications, COVID-19 mortality, Community-Acquired Infections complications, Community-Acquired Infections mortality, Cross Infection complications, Cross Infection mortality
- Abstract
Background and Objectives: Reports comparing the characteristics of patients and their clinical outcomes between community-acquired (CA) and hospital-acquired (HA) COVID-19 have not yet been reported in the literature. We aimed to characterise and compare clinical, biochemical and haematological features, in addition to clinical outcomes, between these patients., Methods: This multi-centre, retrospective, observational study enrolled 488 SARS-CoV-2 positive patients - 339 with CA infection and 149 with HA infection. All patients were admitted to a hospital within the University Hospitals of Morecambe Bay NHS Foundation Trust between March 7th and May 18th
, 2020., Results: The CA cohort comprised of a significantly younger population, median age 75 years, versus 80 years in the HA cohort (P = 0·0002). Significantly less patients in the HA group experienced fever (P = 0·03) and breathlessness (P < 0·0001). Furthermore, significantly more patients had anaemia and hypoalbuminaemia in the HA group, compared to the CA group (P < 0·0001 for both). Hypertension and a lower median BMI were also significantly more pronounced in the HA cohort (P = 0·03 and P = 0·0001, respectively). The mortality rate was not significantly different between the two cohorts (34% in the CA group and 32% in the HA group, P = 0·64). However, the CA group required significantly greater ICU care (10% versus 3% in the HA group, P = 0·009)., Conclusion: Hospital-acquired and community-acquired COVID-19 display similar rates of mortality despite significant differences in baseline characteristics of the respective patient populations. Delineation of community- and hospital-acquired COVID-19 in future studies on COVID-19 may allow for more accurate interpretation of results., (Copyright © 2021 Elsevier Ltd. All rights reserved.)- Published
- 2021
- Full Text
- View/download PDF
11. Role of in silico structural modeling in predicting immunogenic neoepitopes for cancer vaccine development.
- Author
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Zaidi N, Soban M, Chen F, Kinkead H, Mathew J, Yarchoan M, Armstrong TD, Haider S, and Jaffee EM
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- Animals, Antibody Affinity, Antigens, Neoplasm genetics, Antigens, Neoplasm immunology, Cancer Vaccines immunology, Cell Line, Tumor, Cells, Cultured, Epitopes immunology, Histocompatibility Antigens Class I chemistry, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class I immunology, Immunogenicity, Vaccine, Male, Mice, Mice, Inbred C57BL, Mutation, Antigens, Neoplasm chemistry, Cancer Vaccines chemistry, Epitopes chemistry, Molecular Docking Simulation
- Abstract
In prior studies, we delineated the landscape of neoantigens arising from nonsynonymous point mutations in a murine pancreatic cancer model, Panc02. We developed a peptide vaccine by targeting neoantigens predicted using a pipeline that incorporates the MHC binding algorithm NetMHC. The vaccine, when combined with immune checkpoint modulators, elicited a robust neoepitope-specific antitumor immune response and led to tumor clearance. However, only a small fraction of the predicted neoepitopes induced T cell immunity, similarly to that reported for neoantigen vaccines tested in clinical studies. While these studies have used binding affinities to MHC I as surrogates for T cell immunity, this approach does not include spatial information on the mutated residue that is crucial for TCR activation. Here, we investigate conformational alterations in and around the MHC binding groove induced by selected minimal neoepitopes, and we examine the influence of a given mutated residue as a function of its spatial position. We found that structural parameters, including the solvent-accessible surface area (SASA) of the neoepitope and the position and spatial configuration of the mutated residue within the sequence, can be used to improve the prediction of immunogenic neoepitopes for inclusion in cancer vaccines.
- Published
- 2020
- Full Text
- View/download PDF
12. Challenges of training and delivery of pediatric surgical services in developing economies: a perspective from Pakistan.
- Author
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Sohail AH, Maan MHA, Sachal M, and Soban M
- Subjects
- Curriculum, Developing Countries, Humans, Pakistan, Pediatricians education, Surgeons education, Health Workforce statistics & numerical data, Pediatricians supply & distribution, Pediatrics education, Surgeons statistics & numerical data
- Abstract
Background: As the pediatric population requiring health services rises globally, developing countries are struggling to cater to the growing burden of non-communicable diseases - particularly those requiring specialized surgical care., Main Body: Despite the literature supporting specialized pediatric surgical care, the developing world is far from meeting the American Pediatric Surgical Association (APSA) Manpower taskforce recommendation of at least 1 qualified pediatric surgeon per 100,000 patients (0-15 years-old). In Pakistan, there is an unmet surgical need in the pediatric population due to a multitude of short shortcomings, notably in quality and quantity of the training programs on offer, and urgent short- and long-term steps are needed to improve this dire situation., Conclusion: It is crucial for the global surgical community to take steps, especially with regards to pediatric surgical training, to ensure delivery of accessible and quality surgical care to the world's children.
- Published
- 2019
- Full Text
- View/download PDF
13. Primary intracranial extraosseous Ewing's sarcoma.
- Author
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Sohail AH, Sachal M, Maan MAA, Soban M, Khan MS, and Bari ME
- Subjects
- Diagnosis, Differential, Humans, Male, Meningeal Neoplasms diagnosis, Meningioma diagnosis, Sarcoma, Ewing diagnosis, Soft Tissue Neoplasms diagnosis, Young Adult, Dura Mater pathology, Sarcoma, Ewing pathology, Soft Tissue Neoplasms pathology
- Abstract
Introduction: Common sites of occurrence of extraosseous Ewing's sarcoma include the soft tissues and bones of the lower extremity, 12 paravertebral, and retroperitoneal regions. Primary intracranial Ewing's sarcoma/pPNET is usually intraparenchymal located 13 when supratentorially, and an extraaxial epidural tumor radiographically mimicking a meningioma is extremely rare., Case Presentation: A 20-year14 old male presented to the emergency department with a 1-day history of drowsiness, headache, and fever. Neurological exam15 ination revealed decreased muscle strength (4/5) in the left lower limb. Head computed tomography scan showed an epidural 16 space-occupying lesion in the right temporoparietal region, which was assumed to be a meningioma by radiographic criteria. However, the surgical specimen was diagnosed as Ewing's sarcoma., Conclusion: Primary intracranial extraosseous Ewing's sarcoma is a rare condition that may mimic a meningioma on imaging. Physicians must be cognizant of this possibility, particularly in any young individual with a solitary contrast-enhancing dural-based lesion.
- Published
- 2019
- Full Text
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14. Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation.
- Author
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Duran D, Zeng X, Jin SC, Choi J, Nelson-Williams C, Yatsula B, Gaillard J, Furey CG, Lu Q, Timberlake AT, Dong W, Sorscher MA, Loring E, Klein J, Allocco A, Hunt A, Conine S, Karimy JK, Youngblood MW, Zhang J, DiLuna ML, Matouk CC, Mane S, Tikhonova IR, Castaldi C, López-Giráldez F, Knight J, Haider S, Soban M, Alper SL, Komiyama M, Ducruet AF, Zabramski JM, Dardik A, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson E, Smith ER, Orbach DB, Berenstein A, Bilguvar K, Vikkula M, Gunel M, Lifton RP, and Kahle KT
- Subjects
- Ephrins metabolism, Female, Humans, Male, Membrane Glycoproteins genetics, Metalloendopeptidases genetics, Pedigree, Penetrance, Receptor, EphB4 genetics, Signal Transduction, Vein of Galen Malformations pathology, Chromatin Assembly and Disassembly genetics, Mutation, Vein of Galen Malformations genetics
- Abstract
Normal vascular development includes the formation and specification of arteries, veins, and intervening capillaries. Vein of Galen malformations (VOGMs) are among the most common and severe neonatal brain arterio-venous malformations, shunting arterial blood into the brain's deep venous system through aberrant direct connections. Exome sequencing of 55 VOGM probands, including 52 parent-offspring trios, revealed enrichment of rare damaging de novo mutations in chromatin modifier genes that play essential roles in brain and vascular development. Other VOGM probands harbored rare inherited damaging mutations in Ephrin signaling genes, including a genome-wide significant mutation burden in EPHB4. Inherited mutations showed incomplete penetrance and variable expressivity, with mutation carriers often exhibiting cutaneous vascular abnormalities, suggesting a two-hit mechanism. The identified mutations collectively account for ∼30% of studied VOGM cases. These findings provide insight into disease biology and may have clinical implications for risk assessment., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
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