Osman Saracbasi

Is elevated level of soluble endothelial protein C receptor a new risk factor for retinal vein occlusion

Background:  To evaluate the systemic and thrombophilic risk factors for retinal vein occlusion (RVO) and to determine whether the elevated level of soluble endothelial protein C receptor (sEPCR) is a risk factor for thrombosis.

Systemic associations and prevalence of exfoliation syndrome in patients scheduled for cataract surgery.

Purpose To study the frequency of exfoliation syndrome (XFS) and its association with intraocular pressure (IOP) and systemic diseases in patients with age-related cataract scheduled for surgery. Methods All 1480 cataract patients had a comprehensive systemic and eye examination, including slit-lamp biomicroscopy before and after mydriasis, IOP measurement, gonioscopy, and fundus examination. Results The percentage of XFS among patients scheduled for cataract surgery was 16.4, with no gender difference (p=0.833). The mean age of XFS patients (74.3±7.0 years) was significantly higher when compared to the ones without XFS (66.5±10.9 years) (p<0.001). XFS was unilateral in 41.3% of the subjects and bilateral in 58.7%. The number of subjects with XFS increased significantly with aging (p<0.001) (OR=1.093, 95% CI=1.073–1.14) (p<0.001). The most common type of cataract was nuclear in the XFS group (33.5%) and 24.6% of patients with mature cataract had XFS. In the XFS group, 11.2% of the subjects had glaucoma, which was statistically higher than the non-XFS group (4.6%) (p<0.001) (OR=2.67, 95% CI=1.65–4.32). Eighty-four patients had glaucoma and 27 of them (32.1%) had exfoliative glaucoma. The only systemic disease that was found to be associated with XFS was coronary heart disease with an OR of 1.49 (95% CI=1.068–2.072) (p=0.019). Conclusions XFS is a common problem in the aging cataract population of Turkey and increased IOP, glaucomatous optic neuropathy, and coronary heart disease occur more frequently in patients with XFS compared with subjects without XFS.

Fracture resistance of tooth fragment reattachment: effects of different preparation techniques and adhesive materials

The purpose of this study was to evaluate and compare the bond strengths of experimentally fractured human tooth fragments reattached with different adhesive materials and retentive techniques in vitro. Uncomplicated crown fractures were obtained on intact human mandibular permanent incisors by applying perpendicular load to the buccal aspect of tooth crowns. Fractured teeth were randomly assigned into one of three reattachment protocols: (i) Simple reattachment, (ii) Overcontour preparation, and (iii) Internal dentin groove. The first and second groups were divided into 10 subgroups, and the third group into five subgroups (n = 10 per group) with respect to five different adhesive systems (Prime&Bond NT, Adper Single Bond II, Adper Prompt L-Pop, Clearfil S(3) Bond, G Bond) used with or without a hybrid resin composite (Z250). Restored teeth were subjected to thermal cycling, and subsequently to the same loading protocol used for fracturing intact teeth. Fracture strength after reattachment procedures was recorded as a percentage of the original fracture strength. Both type of adhesive material and placement of an intermediate layer of resin composite affected the fracture resistance (P < 0.05). The highest fracture strength recovery was obtained using the internal dentin groove technique (54 +/- 0.58%, P < 0.05), followed by the overcontour and simple reattachment protocols (49 +/- 0.58% and 32 +/- 0.82%, respectively, P < 0.05). Ultramorphological evaluation of bonded specimens revealed voids and microcracks along the adhesive interface, which might contribute to postadhesive failure.

Hip fractures in a developing country: osteoporosis frequency, predisposing factors and treatment costs.

Hip fractures are a burden to both society and the individual. The aim of this study was to describe the frequency of osteoporosis and the in-hospital treatment costs of patients with hip fractures admitted to Hacettepe University Faculty of Medicine Hospital. Patients with a hip fracture who were admitted to the Orthopedics and Traumatology wards between April 2003 and December 2006 were interviewed and 50 of them were enrolled prospectively in the study protocol. Patient characteristics, predisposing factors for fractures and hospital costs were recorded as well as laboratory test results and bone mineral density measurements. The mean age was 74.2 years and 72% of the patients were women. Sixty-four percent of them presented with an intertrochanteric fracture. The patient population was significantly debilitated with a high prevalence of vitamin D insufficiency and secondary hyperparathyroidism. No association was shown with T scores and dietary habits and lifestyle characteristics of patients. In 34% of patients in whom measurements were available, no osteoporosis could be documented. The mean hospital expenditure was

Expression of vascular endothelial growth factor-A, matrix metalloproteinase-9, and extravascular matrix patterns and their correlations with clinicopathologic parameters in posterior uveal melanomas.

5983. Factors affecting the total cost were age and functional status of the patient and the duration of hospital stay, independent of the type of fracture and surgical procedure used.

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation

PurposeTo assess extravascular matrix patterns (EMP) and expression of vascular endothelial growth factor-A (VEGF-A) and matrix metalloproteinase-9 (MMP-9) in posterior uveal melanomas and their correlations with histopathologic parameters and metastasis.MethodsThis study was conducted on 100 consecutive eyes enucleated for posterior uveal melanomas. All tumors were examined by immunohistochemical techniques for VEGF-A and MMP-9 expression, and the presence of EMPs was assessed on routine paraffin sections stained with reticulin. Cell type, tumor localization, degree of pigmentation, necrosis, mitotic index, lymphocytic infiltration, and scleral and optic nerve invasion were analyzed by using light microscopy. No eyes had received prior treatment such as radiotherapy or transpupillary thermotherapy.ResultsIdentified histopathologically, cell types were spindle cells in 60% of the cases, mixed cells in 14%, and epithelioid cells in 26% of tumors. Positive reaction for VEGF-A and MMP-9 was present in 84% and 72% of the tumors, respectively. Microvascular loops and/or networks were seen in 34% of the tumors, with the remaining 16% of the tumors displaying an arc pattern, 21% displaying a parallel pattern, and 29% displaying the normal pattern. The relationships between VEGF-A and MMP-9 expression and necrosis, the degree of lymphocyte infiltration, mitotic rate, and the formation of loop and network patterns were found to be statistically significant (P < 0.05). Metastatic disease developed in 14 patients during follow up.ConclusionsThe incidence of metastatic melanoma increased with the increasing expression of VEGF-A and MMP-9. Our data suggest that increasing VEGF-A and MMP-9 expression and the EMP can be used as independent prognostic factors in the management of posterior uveal melanoma following enucleation. Jpn J Ophthalmol 2007;51:325–331

Quaternary structure evaluation tool for protein assemblies

The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org/).

Diurnal variation of intraocular pressure and its correlation with retinal nerve fiber analysis in Turkish patients with exfoliation syndrome

The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. For example, it makes a difference if the protein is normally a dimer and not a monomer or a trimer or a tetramer or a hexamer in nature. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 86% correct, 9% incorrect, and 5% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org).