Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

Ubiquitin and neurogenerative diseases

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N-terminal heterogenicity of amyloid protein examined in Alzheimer's disease

PubMedID: 14660069Alzheimer's disease is the major cause of dementia in humans. The affected brain shows characteristic abnormal filamentous proteins that accumulate intracellularly as neurofibrillary tangles, and extracellularly as senile plaques, as well as in cerebral blood vessels. The extracellular deposits are an amyloid protein, which is highly insoluble. In our study, we intended to show that the N-terminus of amyloid A4 protein can change in length and sequence in Alzheimer's disease, and possibly in other dementias

Evaluation of symptoms and clinical features associated with fibromyalgia syndrome

Objective: Fibromyalgia syndrome is clinical state that is common with symptoms and signs may affect quality of life. In this study, we aimed to investigate symptoms and findings associated with fibromyalgia. Method: Patients who admitted to Pain Clinic between 2003-2004 previously diagnosed fibromyalgia were evaluated prospectively for physical examination, anxiety, depression and clinical complaints. The Hamilton depression scale and state anxiety scale were used. Results: A total of 86 patients admitted to clinic, but 8 patients were out and study was completed with 80 patients. Seventy-seven patients were female (96.3%), 3 were male (3.7%). All but one of patients had generalized pain complaints, 63% had regular analgesics (78.7%). Fourteen patients had antidepressant use. Anxiety score was measured 50.07±10.19 in patients using antidepressants, 52.79±12.1 in not taking. The anxiety score was measured 55.8±12.7 in patients using analgesics, 51.35±11.4 in patients without analgesics. The highest anxiety scores were observed in 60-69 age. The severity of common pain increased with anxiety scores. There was no depression was observed in 42 patients (42.5%). Mild depression was found in 29 patients (36.2%), moderate in 8 (10%), severe in 1 (1.2%). Conclusion: Fibromyalgia is a common syndrome characterized by pain and associated with anxiety and depression. © 2018 Anestezi Dergisi. All rights reserved

Evaluation of Epithelial Chimerism After Bone Marrow Mesenchymal Stromal Cell Infusion in Intestinal Transplant Patients

Intestinal transplantation is the most effective treatment for patients with short bowel syndrome and small bowel insufficiencies. We evaluated epithelial chimerism after infusion of autologous bone marrow mesenchymal stromal cells (BMSCs) in patients undergoing cadaveric donor isolated intestinal transplantation (I-ITx). BMSCs were isolated from patients' bone marrow via iliac puncture and expanded in vitro prior to infusion. Two out of the 3 patients were infused with autologous BMSCs, and small intestine tissue biopsies collected post-operatively were analyzed for epithelial chimerism using XY fluorescent in situ hybridization and short tandem repeat polymerase chain reaction. We observed epithelial chimeric effect in conditions both with and without BMSC infusion. Although our results suggest a higher epithelial chimerism effect with autologous BMSC infusion in I-ITx, the measurements in multiple biopsies at different time points that demonstrate the reproducibility of this finding and its stability or changes in the level over time would be beneficial. BMSC infusion may have potential implications for improved graft survival, lower immunosuppressant doses, superior engraftment of the transplanted tissue, and higher success rates in I-ITx