Publications by authors named "Bakir I"

Introduction: The evolving landscape of inflammatory bowel disease (IBD) necessitates refining colonoscopic surveillance guidelines. This study outlines methodology adopted by the British Society of Gastroenterology (BSG) Guideline Development Group (GDG) for updating IBD colorectal surveillance guidelines.

Methods And Analysis: The 'Grading of Recommendations, Assessment, Development and Evaluation' (GRADE) approach, as outlined in the GRADE handbook, was employed.

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Article Synopsis
  • Patients with inflammatory bowel disease (IBD) face an increased risk of colorectal cancer (CRC), which is heightened for those with low-grade dysplasia (LGD).
  • A study involving 122 patients revealed that the burden of somatic copy number alterations (CNAs) in LGD lesions can significantly predict future cancer development, outperforming traditional clinical risk factors.
  • The research suggests that measuring CNAs in LGD lesions is a cost-effective method for assessing CRC risk, allowing for better management of high-risk patients while reducing unnecessary treatments for those at low risk.
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  • Colonoscopic surveillance is important for patients with colonic inflammatory bowel disease (IBD) due to their higher risk of colorectal cancer (CRC), and a new prediction model has been developed for assessing this risk.
  • The study analyzed data from 6 cohorts across North America and Europe, including 3731 patients, to create and validate this model using predictive variables and a statistical approach known as Cox proportional hazards modeling.
  • The model showed good accuracy in predicting advanced colorectal neoplasia (aCRN) over 5-10 years, but further research is needed to validate its effectiveness across different populations and to determine how it impacts surveillance strategies.
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Due to their increased cancer risk, patients with longstanding inflammatory bowel disease are offered endoscopic surveillance with concomitant histopathologic assessments, aimed at identifying dysplasia as a precursor lesion of colitis-associated colorectal cancer. However, this strategy is beset with difficulties and limitations. Recently, a novel classification criterion for colitis-associated low-grade dysplasia has been proposed, and an association between nonconventional dysplasia and progression was reported, suggesting the possibility of histology-based stratification of patients with colitis-associated lesions.

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Patients with longstanding extensive colitis are at an increased risk of developing colorectal cancer (CRC), and are therefore enrolled into colonoscopy screening programmes with the aim of detecting pre-cancerous dysplastic change. However, current surveillance programs face multiple limitations relating to low levels of patient enrolment, missed lesions resulting in interval cancers, and uncertainties in the management of dysplasia. Patient counselling regarding the endoscopic and surgical management options of dysplastic lesions can prove particularly challenging, due to the variable risk of progression to cancer.

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Clinical archives of patient material near-exclusively consist of formalin-fixed and paraffin-embedded (FFPE) blocks. The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts.

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Background And Aims: Alterations in body composition are common in inflammatory bowel disease [IBD] and have been associated with differences in patient outcomes. We sought to consolidate knowledge on the impact and importance of body composition in IBD.

Methods: We performed a systematic search of MEDLINE, EMBASE and conference proceedings by combining two key research themes: inflammatory bowel disease and body composition.

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Article Synopsis
  • Patients with ulcerative colitis (UC) and low-grade dysplasia (LGD) are at a higher risk of developing advanced neoplasia (AN), such as high-grade dysplasia or colorectal cancer, highlighting the need for effective risk assessment.
  • A study involving patients diagnosed with LGD from multiple UK centers used clinicopathological data to create a risk prediction model that was validated across additional cohorts, identifying key factors like the size of LGD, resection status, inflammation severity, and multifocality.
  • The model's validated results indicate that patients meeting certain criteria can receive personalized risk assessments through a web tool, aiding in informed treatment decisions to potentially improve outcomes.
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Objective: Genomics and personalised medicine are increasingly relevant for patients with gastroenterological conditions. We aim to capture the current state of genomics training in gastroenterology to review current understanding, clinical experience and long-term educational needs of UK trainees.

Design And Setting: A web-based nationwide survey of all UK gastroenterology specialty trainees was conducted in 2017.

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Mediastinal fat has been suggested to be associated with cardiovascular diseases such as carotid stiffness, atherosclerosis and coronary artery calcification. We investigated the possible role of Ad-36-induced obesity in the pathogenesis of the coronary artery disease (CAD). Ad-36 DNA was investigated in the anterior mediastinal fat tissue samples of obese adults with CAD.

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Whether the nom de guerre is Mathematical Oncology, Computational or Systems Biology, Theoretical Biology, Evolutionary Oncology, Bioinformatics, or simply Basic Science, there is no denying that mathematics continues to play an increasingly prominent role in cancer research. Mathematical Oncology-defined here simply as the use of mathematics in cancer research-complements and overlaps with a number of other fields that rely on mathematics as a core methodology. As a result, Mathematical Oncology has a broad scope, ranging from theoretical studies to clinical trials designed with mathematical models.

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Patients with inflammatory bowel disease have an increased risk of developing colorectal cancer, and this risk is related to disease duration, extent, and cumulative inflammation burden. Carcinogenesis follows the principles of Darwinian evolution, whereby somatic cells acquire genomic alterations that provide them with a survival and/or growth advantage. Colitis represents a unique situation whereby routine surveillance endoscopy provides a serendipitous opportunity to observe somatic evolution over space and time in a human organ.

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Objective: IBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing.

Design: Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods.

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Article Synopsis
  • This study investigates the relationship between the inflammatory burden in ulcerative colitis (UC) and the risk of developing colorectal neoplasia (CRN) over time.
  • It analyzed data from 987 patients with extensive UC over a median of 13 years, concluding that a cumulative inflammatory burden significantly correlates with CRN risk, rather than relying on the severity of inflammation from the most recent colonoscopy alone.
  • The findings suggest that assessing multiple surveillance episodes is crucial for better risk stratification of CRN in patients with UC.
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Small mothers against decapentaplegic (SMAD) proteins are a family of signal transduction molecules in transforming growth factor β (TGFβ) ligand pathways that have been found to have a key role in the pathogenesis of inflammatory bowel disease (IBD). Long standing IBD predisposes individuals to colitis-associated colorectal cancer (CAC), an entity that possess unique characteristics compared to hereditary and sporadic cancer. The ligands of the TGFβ super family along with SMADs have also been implicated in several aspects of colorectal cancer formation.

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Objective: It has been shown that the presence of fragmented QRS (fQRS) is associated with poor prognosis in many cardiovascular diseases and in patients with hypertrophic cardiomyopathy (HCM). However, no study has shown an association with the absolute risk score of sudden cardiac death. The aim of this study was to determine the relationship between QRS and the predicted risk score of sudden cardiac death at 5 years (HCM Risk-SCD) in HCM patients.

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Introduction: Previous studies have demonstrated the predictive value of the neutrophil-to-lymphocyte ratio (NLR) in many cardiovascular disorders. The aim of this study was to assess whether NLR is associated with echocardiographic or electrocardiographic parameters, or with predicted five-year risk of sudden cardiac death (SCD), in patients with hypertrophic cardiomyopathy (HCM).

Methods: This prospective observational study included 74 controls and 97 HCM patients.

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Various factors may be responsible for the development of postoperative atrial fibrillation (POAF) in coronary artery bypass graft (CABG) patients. In our study, we demonstrated the effect of vitamin D deficiency on the development of POAF. In this prospective case control study, patients undergoing elective, isolated CABG were considered.

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Optimizing the management of colorectal cancer (CRC) risk in IBD requires a fundamental understanding of the evolutionary process underpinning tumorigenesis. In IBD, clonal evolution begins long before the development of overt neoplasia, and is probably accelerated by the repeated cycles of epithelial wounding and repair that are characteristic of the condition. Here, we review the biological drivers of mutant clone selection in IBD with particular reference to the unique histological architecture of the intestinal epithelium coupled with the inflammatory microenvironment in IBD, and the unique mutation patterns seen in IBD-driven neoplasia when compared with sporadic adenomas and CRC.

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Kabuki syndrome is a rare congenital malformation syndrome characterized by mental retardation, skeletal deformities, auditory dysfunction, cardiac defects, and distinctive facial appearance. Although complex cardiovascular malformations present in early childhood, rarely, atrioventricular septal defects may also present in young adults. Presently described is case of a 22-year-old female with KS who presented with ostium secundum atrial septal defect with deficient rim and idiopathic thrombocytopenic purpura.

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Mitral valve repair has been one of the widely used applications of robotic surgery. Patients with rheumatic mitral disease usually present at an early age with thickening, retraction, or fusion of the leaflets and subvalvular apparatus. Robotic mitral repair can be feasible among this group of patients, rather than replacement.

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Background: Optimal surgical approach for patients with hemodynamically significant carotid and coronary disease remains controversial. We analyzed our 5-year experience and compared early and long-term outcome following staged and combined carotid and coronary artery bypass.

Methods: 312 consecutive patients undergoing carotid endarterectomy and coronary artery bypass between 2008 and 2013 were prospectively enrolled in the study.

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Optimal hemodynamics in aorta-pulmonary shunt reconstruction is essential for improved post-operative recovery of the newborn congenital heart disease patient. However, prior to in vivo execution, the prediction of post-operative hemodynamics is extremely challenging due to the interplay of multiple confounding physiological factors. It is hypothesized that the post-operative performance of the surgical shunt can be predicted through computational blood flow simulations that consider patient size, shunt configuration, cardiac output and the complex three-dimensional disease anatomy.

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