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Application of deep learning technique in next generation sequence experiments
(Springernature, 2023) Ozgur, Su; Orman, Mehmet
In recent years, the widespread utilization of biological data processing technology has been driven by its cost-effectiveness. Consequently, next-generation sequencing (NGS) has become an integral component of biological research. NGS technologies enable the sequencing of billions of nucleotides in the entire genome, transcriptome, or specific target regions. This sequencing generates vast data matrices. Consequently, there is a growing demand for deep learning (DL) approaches, which employ multilayer artificial neural networks and systems capable of extracting meaningful information from these extensive data structures. In this study, the aim was to obtain optimized parameters and assess the prediction performance of deep learning and machine learning (ML) algorithms for binary classification in real and simulated whole genome data using a cloud-based system. The ART-simulated data and paired-end NGS (whole genome) data of Ch22, which includes ethnicity information, were evaluated using XGBoost, LightGBM, and DL algorithms. When the learning rate was set to 0.01 and 0.001, and the epoch values were updated to 500, 1000, and 2000 in the deep learning model for the ART simulated dataset, the median accuracy values of the ART models were as follows: 0.6320, 0.6800, and 0.7340 for epoch 0.01; and 0.6920, 0.7220, and 0.8020 for epoch 0.001, respectively. In comparison, the median accuracy values of the XGBoost and LightGBM models were 0.6990 and 0.6250 respectively. When the same process is repeated for Chr 22, the results are as follows: the median accuracy values of the DL models were 0.5290, 0.5420 and 0.5820 for epoch 0.01; and 0.5510, 0.5830 and 0.6040 for epoch 0.001, respectively. Additionally, the median accuracy values of the XGBoost and LightGBM models were 0.5760 and 0.5250, respectively. While the best classification estimates were obtained at 2000 epochs and a learning rate (LR) value of 0.001 for both real and simulated data, the XGBoost algorithm showed higher performance when the epoch value was 500 and the LR was 0.01. When dealing with class imbalance, the DL algorithm yielded similar and high Recall and Precision values. Conclusively, this study serves as a timely resource for genomic scientists, providing guidance on why, when, and how to effectively utilize deep learning/machine learning methods for the analysis of human genomic data.
Association between recurrence of stroke and peripheral artery disease after first-ever stroke
(Sage Publications Ltd, 2023) Kumral, Emre; Cetin, Fatma Ece; Ozdemir, Huseyin Nezih; Orman, Mehmet
[No abstract available]
Association of baseline dyslipidemia with stroke recurrence within five-years after ischemic stroke
(Wiley-Blackwell, 2014) Kumral, Emre; Evyapan, Dilek; Gokcay, Figen; Karaman, Bedriye; Orman, Mehmet
Background and purpose The association between dyslipidemia (DL) and stroke recurrence is unclear, but may be influenced by different subtypes of stroke. This study aims to explore whether DL contributes to the recurrence of certain subtypes of ischemic stroke. Methods Data from the Ege Stroke Registry was examined, and five-years follow-up data for stroke recurrence was analyzed. Trial of Org 10172 in Acute Stroke Treatment criteria was used to classify the subtypes of all stroke. Recurrent stroke was defined as a new neurological deficit compatible to ischemic stroke or intracerebral hemorrhage. The association between DL and stroke recurrence in patients with different sroke subtypes was analyzed using univariable and multivariable logistic regression models. Survival curves were estimated with Kaplan-Meier methods, and survival analyses were undertaken using Cox proportional hazards models. Results Of the 9940 patients with ischemic stroke, 5838 (58.7%) had DL and 2202 (22.2%) experienced a stroke recurrence within five-years. The frequency of stroke recurrence of patients with DL was unsignificantly higher than those without at five-years of follow-up (18.0% vs. 17.0%; P = 0.21). After stratification by Trial of Org 10172 in Acute Stroke Treatment subtypes, multivariable analysis revealed a significant association between DL and stroke recurrence in all ischemic stroke at five-years (odds ratio, 1.2; 95% confidence interval, 1.02-1.42), and in the large-artery disease subtype (odds ratio, 1.46; 95% confidence interval, 1.12-1.91), but not in the other stroke subtypes (cardioembolic: odds ratio, 1.18; 95% confidence interval, 0.84-1.65; small-artery disease: odds ratio, 1.24; 95% confidence interval, 0.87-1.76; other subtype: odds ratio, 0.79; 95% confidence interval, 0.48-1.31). The probability of stroke recurrence increased in patients with large-artery disease and DL, compared with other subtypes of stroke [log rank test (Mantel-Cox) P < 0.013]. Conclusions Our results showed that DL is related to the recurrent strokes in patients with ischemic stroke within five-years after ischemic stroke, specifically to the large-artery disease subtype.
Association of Hyperhomocysteinemia with Stroke Recurrence after Initial Stroke
(Elsevier Science Bv, 2016) Kumral, Emre; Saruhan, Gulsum; Aktert, Dilara; Orman, Mehmet
Background and purpose: Homocysteine (Hcy) is closely associated with stroke. Despite the fact that Hcy has consistently been shown to predict development of recurrent stroke, prior studies on the association of Hcy and stroke subtypes have been inconclusive. Methods: Data from the Ege Stroke Registry were examined and 5-year follow-up data were analyzed. Multivariate survival analyses were undertaken using Cox proportional hazards models to determine the prognostic value of Hcy in different ischemic stroke subtypes. Results: Of the 9522 patients with stroke, 307 (27%) with hyperhomocysteinemia (hHcy) had recurrent stroke. Univariate Cox regression model showed that hHcy group was associated with recurrent stroke (crude hazard ratio [HR] 1.16; 95% CI 1.02-1.30). But there was no such association in multivariate regression models (adjusted HR 1.11; 95% CI .97-1.26). hHcy was not associated with any ischemic stroke subtypes at 5 years. Univariate Cox regression model showed that hHcy group was associated with overall cardiovascular events (crude HR 1.44; 95% CI 1.32-1.57). However, this association no longer existed in multivariate regression models (adjusted HR 1.01; 95% CI .93-1.12). Higher plasma Hcy group was significantly associated with higher mortality compared with normal plasma Hcy group (OR 1.83; 95% CI .45-2.32). Conclusions: Our results showed that elevated Hcy is not associated independently with stroke recurrence and overall cardiovascular events in patients with ischemic stroke. There was no association between the hHcy and stroke recurrence in the stroke subtypes within 5 years.
Association of Leukoaraiosis with Stroke Recurrence within 5 Years after Initial Stroke
(Elsevier Science Bv, 2015) Kumral, Emre; Gulluoglu, Halil; Alakbarova, Naila; Karaman, Bedriye; Deveci, Emrah Emre; Bayramov, Aydin; Evyapan, Dilek; Gokcay, Figen; Orman, Mehmet
Background: Leukoaraiosis (LA) is closely associated with stroke. Despite the fact that LA has consistently been shown to predict development of recurrent stroke, prior studies on the association of LA and stroke subtypes have been unsatisfactory. In this study, we sought to identify whether LA contributes to the recurrence of certain subtypes of stroke at long term. Methods: Data from the Ege Stroke Registry were examined, and 5 years follow-up data for LA and stroke recurrence were analyzed. We performed survival curves using the Kaplan-Meier method (unadjusted) and log-rank tests in patients with stroke to determine the relationship between LA and recurrent stroke by stroke subtypes within a time period of 5 years. Multivariate survival analyses were undertaken using Cox proportional hazards models to determine the prognostic value of LA, stroke subtypes, and other vascular risk factors before recurrent stroke. Results: Of 9522 patients with stroke, 1280 (26%) with LA and 901 (19%) without LA experienced a stroke recurrence within 5 years of follow-up (odds ratio, 1.53; 95% confidence interval, 1.39-1.69). After stratification by stroke subtypes, multivariable analysis revealed a significant association between LA and large artery disease (LAD; odds ratio [OR], 1.39; 95% confidence interval [CI], 1.18-1.64), small artery disease (SAD; OR, 1.57; 95% CI, 1.27-1.94), and intracerebral hemorrhage (ICH; OR, 1.88; 95% CI, 1.32-2.66), except cardioembolic stroke and "other'' stroke subtypes at 5 years after stroke onset. The survival analysis showed that stroke recurrence was significantly higher in patients with severe LA compared with those with mild/moderate LA (log-rank test [Mantel-Cox], P < .001). Conclusions: Our results showed that LA is related to the recurrent strokes in patients with stroke within 5 years after stroke, specifically to the LAD, SAD and ICH. (C) 2015 by National Stroke Association
Associations Between Neuroanatomic Patterns of Cerebral Infarctions and Vascular Dementia
(Amer Psychiatric Publishing, Inc, 2021) Kumral, Emre; Bayam, Fatma Ece; Arslan, Hasan; Orman, Mehmet
Objective: A history of multiple cerebral infarctions is generally regarded as an important risk factor for vascular dementia. The authors examined the risk of vascular dementia in patients with multiple acute ischemic lesions. Methods: The authors conducted a hospital-based prospective study of 11,200 patients with first-time stroke who underwent 1.5 or 3-T MRI and a global cognitive assessment. Univariate and multivariate logistic regression analyses estimated the risk of dementia associated with multiple lesions versus a single lesion. Results: Having multiple lesions, compared with having a single lesion, was significantly associated with dementia in patients with stroke (odds ratio=5.83, 95% CI=5.08, 6.70; p<0.001). The apoliproprotein epsilon 4 allele was more frequent in patients with multiple lesions than in those with a single lesion (odds ratio=1.70, 95% CI=1.39, 2.07; p<0.001). Severe leukoaraiosis (odds ratio=15.77, 95% CI=8.38, 29.68; p<0.001) and microbleedings (odds ratio=1.31, 95% CI=1.06, 1.63; p<0.01) were strong confounders for dementia in the multivariate analysis. Multiple logistic regression analysis showed that multiple lesions in one hemisphere versus a single lesion (odds ratio=2.14, 95% CI=1.83, 2.51; p<0.001), involvement of strategic regions (odds ratio=4.73, 95% CI=4.07, 5.49; p<0.001), and stroke lesion volume (odds ratio=1.31, 95% CI=1.03, 1.66; p=0.03) were significantly associated with dementia. Therewas a preponderance of lesions on the left side in patients with dementia (odds ratio=2.56, 95% CI=2.11, 3.11; p<0.001). Conclusions: Multiple spontaneous anterior or posterior circulation lesions after stroke increase a patient's risk of developing dementia. Recognition of multiple ischemic lesions after stroke may allow targeted rapid therapeutic interventions to prevent subsequent cognitive deterioration.
Can using a peel-away sheath in shunt implantation prevent ventricular catheter obstruction?
(Springer, 2011) Camlar, Mahmut; Ersahin, Yusuf; Ozer, Fusun Demircivi; Sen, Fatih; Orman, Mehmet
Shunt obstruction is the most common shunt complication. In 2003, Kehler et al. used peel-away sheath while implanting the ventricular catheter in 20 patients. They found less revision rate in the peel-away sheath group. We aimed to test the efficacy of this technique in cadavers. We used 100 fresh brains obtained from medicolegal autopsies. Posterior parietal and frontal approaches were used to puncture the lateral ventricle in each cerebral hemisphere. The ventricle is punctured with a peel-away sheath system. After the ventricle is reached, the mandarin is retracted and the ventricular catheter is introduced through the opening. The ventricular catheter was removed from the ventricle, the opening at the tip of the ventricular catheter was checked out for obstruction, and the number of patent and plugged openings was recorded. This procedure was repeated four times for each location with and without using peel-away sheath. The control group consisted of the procedures done without using peel-away sheath. The number of the plugged openings in the peel-away sheath group was significantly smaller than the control group. There was no significant difference between the two groups in terms of gender and left and right cerebral hemispheres. The obstruction rate was significantly lower in the posterior parietal approach. Pearson's correlation showed that increasing age was associated with less obstruction rate. Peel-away sheath decreases the number of plugged openings of the ventricular catheter. A clinical cooperative study is needed to prove that a peel-away sheath should be included in the ventricular shunt systems in the market.
Characteristics of Turkish patients with elderly onset psoriatic arthritis A retrospective cohort study
(Lippincott Williams & Wilkins, 2017) Kobak, Senol; Yildiz, Fidan; Karaarslan, Ahmet; Semiz, Huseyin; Orman, Mehmet
Psoriatic arthritis (PsA) is a chronic inflamatory disease characterized with axial and peripheral joints involvement. It rarely affects patients older than 65 years old. The purpose of this study is to compare and evaluate the demographic, clinical and laboratory features of elderly-onset psoriatic arthritis (EOPsA) and young-onset (YOPsA) patients. A total of 180 patients diagnosed with PsA according to CASPAR criteria and followed-up in single center were included in this study. The patients with initial symptoms started after age 65 were accepted as EOPsA. Demographic, clinic, and laboratory data and the medications which the patients received were recorded and retrospectively evaluated. Nineteen (10.5%) of 180 patients were diagnosed as EOPsA, and 161 (89.5%) patients were evaluated as YOPsA. The mean patient age was 42.1years for the YOPsA group and 68.3 years for the elderly onset group. Mean duration of disease was 5.6 years for the early onset group and 1.3 years for the elderly onset group (P=.001). Fourteen (73.3%) of 19 EOPsA patients were female and 5 of them were male. Higher rates of fatique, pain scores, comorbid diseases, and acute phase reactants elevation were detected in EOPsA patients comparing to YOPsA (P=. 000, P=.000, P=.001, and P=.001, respectively). YOPsA patients have more dactilitis, nail involvement, elevated PASI scores, and smoking habitus when compared with EOPsA patients (P=.019, P=.03, P=.005, P=.004, respectively). In terms of the treatment options chosen, there was no significant difference in the use of nonsteroidal antiinflammatory drugs (NSAIDs), corticosteroids (CS), methotrexate (MTX), and sulfasalazine (SSL), but there was a more frequent use of anti-tumor necrosis factor-alpha in the YOPsA group. YOPsA and EOPsA patients may presented with different clinical and laboratory features. EOPsA patients are characterized with higher rates of fatigue, pain scores, comorbid diseases, and acute phase reactants and less dactilitis, nail involvement, and anti-TNFalpha usage.
Cisplatin ototoxicity in children: risk factors and its relationship with polymorphisms of DNA repair genes ERCC1, ERCC2, and XRCC1
(Springer, 2019) Turan, Caner; Kantar, Mehmet; Aktan, Cagdas; Kosova, Buket; Orman, Mehmet; Bilgen, Cem; Kirazli, Tayfun
Purpose We aimed to investigate the cisplatin-related hearing toxicity and its possible relationship with polymorphic variants in DNA repair genes, ERCC1, ERCC2, and XRCC1. Methods Fifty patients treated with cisplatin in the past were included in the study. There were 29 females and 21 males; mean age 13.4 +/- 6.0 years). the polymorphism in DNA repair genes was studied using primer and probes in Light Cycler device after DNA isolation was carried out with PCR technique. the polymorphisms and clinical risk factors were evaluated using Chi square test and logistic regression modelling. Results the patients had hearing loss in 44%. For ERCC1 gene, the patients with hearing loss had 50% of GG (wild type), 40.9% of AG and 9.1% of AA genotypes, while the patients without hearing loss had 28.6% of GG, 53.5% of AG, and 17.9% of AA genotypes. For ERCC2 gene, the patients with hearing loss had 18.2% of GG (wild type), 40.9% of TG, and 40.9% of TT genotypes, while the patients without hearing loss had 10.7% of GG 39.3% of TG, and 50% of TT genotypes. For XRCC1 gene, the patients with hearing loss had 18.2% of CC (wild type), 59.1% of CT, and 22.7% of TT genotypes, while the patients without hearing loss had 35.7% of CC, 50% of CT, and 14.3% of TT genotypes. There was no statistically significant association among the groups (p = 0.24). Conclusion We did not find a relationship between DNA repair gene polymorphisms and hearing toxicity of cisplatin.
The clinical characteristics of sarcoid arthropathy based on a prospective cohort study
(Sage Publications Ltd, 2016) Kobak, Senol; Sever, Fidan; Usluer, Ozan; Goksel, Tuncay; Orman, Mehmet
Background: Sarcoidosis is known as a Th1-mediated disease, which can mimic many primary rheumatologic diseases or sometimes co-exist with them. Clinical characteristics of sarcoid arthropathy are not well described and the studies reported in the literature so far are mostly based on data from referrals. The aim of this study was to evaluate the incidence and clinical characteristics of sarcoid arthropathy. Methods: All our patients were prospectively evaluated in our rheumatology outpatient center from 2011 to 2015. A total of 114 (32 male) patients with sarcoidosis who were admitted to our clinic were included in the study. Clinical, demographical, laboratory, radiological and histological data of these patients obtained during 4-year follow-up and treatment period were compiled and analyzed. Results: The mean patient age was 48.1 years (range, 20-82 years), and the mean disease duration was 40.5 months (range, 1-300 months). Sarcoid arthritis was observed in 71 (62.3%), and arthralgia in 106 (92.9%) patients. Out of the 71 patients with arthritis, 61 (85.9%) had involvement of ankle, 7 (9.8%) knee, 2 (2.8%) wrist, MCP and PIP joints, and 1 (1.4%) had shoulder periarthritis. Oligoarthritis (two to four joints) was the most common pattern followed by monoarthritis and polyarthritis. Arthritis and erytjhema nodosum and arthritis and female sex was found to be correlated (p = 0.03 and p = 0.001). Again, in patients with arthritis, even higher levels of CRP/ESR as well as ANA and RF positivity were observed (p = 0.03, p = 0.01, p = 0.01, and p = 0.02, respectively). A total of 11 patients had another rheumatic pathology concurrent with sarcoidosis. Conclusions: Inflammatory arthritis occurs in a majority of patients with sarcoidosis. Acute arthritis with bilateral ankle involvement is the most common pattern of sarcoid arthropathy. Sarcoidosis can mimic many primary rheumatic diseases or may coexist with them. Sarcoidosis should be considered not only as a mimicker but also as a Th1-mediated primary rheumatologic pathology.
Concomitant Autoimmune Diseases in Patients With Sarcoidosis in Turkey
(2020) Yıldız, Fidan; Kobak, Şenol; Semiz, Hüseyin; Orman, Mehmet
Objectives: This study aims to determine the frequency and characteristics of autoimmune diseases associated with sarcoidosis patients. Patients and methods: The study included 131 sarcoidosis patients (36 males, 95 females; mean age 46.1 years; range, 20 to 82 years). Demographic, clinical, laboratory and radiological data of patients were evaluated retrospectively. The characteristics of autoimmune diseases associated with sarcoidosis (sarcoidosis-overlap group) patients and isolated sarcoidosis (isolated sarcoidosis group) were analyzed and compared. Results: Concomitant autoimmune diseases were detected in 15 (11.5%) (5 males, 10 females; mean age 50.8 years; range, 26 to 58 years) of the 131 patients with sarcoidosis and their mean disease duration was three months (range, 1 to 30 months). When compared with isolated sarcoidosis patients, more hand finger joint involvement, rheumatoid factor (RF) positivity, higher erythrocyte sedimentation rate (ESR) and less nonsteroidal anti-inflammatory drugs (NSAIDs) usage were found in the sarcoidosis-overlap group (p=0.035, p=0.049, p=0.015, p=0.018, respectively). There were no statistically significant differences between the two groups when evaluated for demographic, clinical parameters and disease-modifying antirheumatic drugs usage. Conclusion: Concomitant autoimmune diseases in patients with sarcoidosis may be rarely seen. These patients are characterized with more hand finger joint involvement, RF positivity, higher ESR and less NSAIDs usage. Multicenter, prospective studies involving large numbers of patients are needed to understand whether the association of sarcoidosis-autoimmune diseases is based only on coincidence or on a common etiopathogenesis.
Concomitant Autoimmune Diseases in Patients With Sarcoidosis in Turkey
(2020) Yıldız, Fidan; Kobak, Şenol; Semiz, Hüseyin; Orman, Mehmet
Objectives: This study aims to determine the frequency and characteristics of autoimmune diseases associated with sarcoidosis patients. Patients and methods: the study included 131 sarcoidosis patients (36 males, 95 females; mean age 46.1 years; range, 20 to 82 years). Demographic, clinical, laboratory and radiological data of patients were evaluated retrospectively. the characteristics of autoimmune diseases associated with sarcoidosis (sarcoidosis-overlap group) patients and isolated sarcoidosis (isolated sarcoidosis group) were analyzed and compared. Results: Concomitant autoimmune diseases were detected in 15 (11.5%) (5 males, 10 females; mean age 50.8 years; range, 26 to 58 years) of the 131 patients with sarcoidosis and their mean disease duration was three months (range, 1 to 30 months). When compared with isolated sarcoidosis patients, more hand finger joint involvement, rheumatoid factor (RF) positivity, higher erythrocyte sedimentation rate (ESR) and less nonsteroidal anti-inflammatory drugs (NSAIDs) usage were found in the sarcoidosis-overlap group (p=0.035, p=0.049, p=0.015, p=0.018, respectively). There were no statistically significant differences between the two groups when evaluated for demographic, clinical parameters and disease-modifying antirheumatic drugs usage. Conclusion: Concomitant autoimmune diseases in patients with sarcoidosis may be rarely seen. These patients are characterized with more hand finger joint involvement, RF positivity, higher ESR and less NSAIDs usage. Multicenter, prospective studies involving large numbers of patients are needed to understand whether the association of sarcoidosis-autoimmune diseases is based only on coincidence or on a common etiopathogenesis.
Demographic, clinical, and laboratory features of Turkish patients with late onset ankylosing spondylitis
(Assoc Basic Medical Sci Federation Bosnia & Herzegovina Sarajevo, 2015) Karaarslan, Ahmet; Yilmaz, Hatice; Aycan, Hakan; Orman, Mehmet; Kobak, Senol
Ankylosing spondylitis (AS) is a chronic inflammatory disease, which typically begins in early decades of life with primarily axial joints involvement. This disease rarely affects patients older than 50 years of age. The aim of this study was to compare and evaluate the demographic, clinical, and laboratory features of late onset and early onset AS patients who were followed up in a single rheumatology center. A total of 339 patients who have been diagnosed with AS according to modified New York criteria were included in the study. The patients whose initial symptoms were observed after 50 years of age were accepted as late onset AS. Out of 339 patients, 27 (7.9%) were diagnosed as late onset AS and 312 (92.3%) patients were evaluated as early onset AS. Of 27 late onset patients, 10 were male and 17 were female. Delay in the diagnosis was 5.8 years for early onset AS, while it was 3.8 years for late onset AS (p = 0.001). Higher levels of acute phase reactants and more methotrexate (MTX) use were detected in early onset AS patients compared to late onset AS (p = 0.001, p = 0.007, respectively). Statistically, there was no difference between these two groups, with regard to disease clinical activity indexes, anthropometric measurement parameters, uveitis and peripheral joint involvement. In this study, we showed that early and late onset AS patients may present with different clinical, genetic, and laboratory features. Late onset AS patients are characterized with lower human leukocyte antigen-B27 sequence, less inflammatory sign, delayed diagnosis, and less MTX and anti-tumor necrosis factor alpha drug usage.
Determination of Lymphocyte Cytokinesis-Block Micronucleus Values in Apparently Healthy Children by means of Age and Sex
(Hindawi Ltd, 2019) Durmaz, Burak; Taslidere, Hasan; Koturoglu, Guldane; Gunduz, Cumhur; Orman, Mehmet; Cogulu, Ozgur
The cytokinesis-block micronucleus (MN) assay on blood lymphocytes is one of the most important tests implemented in cytogenetics for the measurement of genotoxicity. For the purpose of biological dosing, it is crucial to know the spontaneous frequency of MN and its normal values in general population, especially in children, which are used for the population databases. in this study, MN levels were investigated in cytokinesis-blocked lymphocytes of 150 apparently healthy children aged 1 to 15. Our aim was to assess the variability of MN values according to age and sex. the mean MN frequency among boys was 3.69 +/- 1.747 parts per thousand and 4.12 +/- 1.867 parts per thousand in girls where there was no significant difference in relation to age and sex. However, when we separated age groups as 0-2 years, 3-5 years, 6-10 years, and 11-15 years, one-way ANOVA test showed significant association. Significance was obvious in the 0-2 years age group with the 3-5 years age group and 6-10 years age group. When we grouped our study population as 0-2 years and 3-15 years, the mean MN frequency among the 0-2 years age group was 2.85 +/- 1.599 parts per thousand and 4.07 +/- 1.867 parts per thousand in the 3-15 years age group which was also statistically significant. This difference may be attributed to age-related increase of close contact with environmental hazardous agents. in conclusion, normal values of MN obtained in this study will add valuable information in regard to update the current childhood population data and will act as a reference for further genotoxicity studies.
Effect of Coronary Thrombus Aspiration in Patients With Non-ST-Segment Elevation Acute Coronary Syndrome on 3-Year Survival: Does It Add Any Benefit?
(Elsevier Science Inc, 2021) Cetin, Nurullah; Orman, Mehmet; Yildiz, Bekir
[No Abstract Available]
Effect of Tibial Plateau Leveling Osteotomy on Mechanical Tibial Axis Shift in Dogs: Two-Dimensional Bone Study in Sagittal Plane
(2022) Orman, Mehmet; Sabancı, Seyyid Said; Kilimci, Figen Sevil
To determine the tibial axis shift (TAS), change in tibial plateau angle (TPA), and the position of the tibial articular surface after tibial plateau leveling osteotomy (TPLO) simulation in the tibiae of dogs, tibias of 91 dogs from 23 dif- ferent breeds were used. The TPA, tibial length, midshaft width, medial tibial condyle length, and distances between the tibial axis (TA) and cranial-most point of the medial condyle were measured on the tibial images. After simulated TPLO, all measurements were retaken. Paired t-tests were used to compare pre- and postoperative variables. Pear- son correlation analysis was conducted to assess whether the difference between pre- and postoperative TAS was re- lated to tibial length, tibial width, medial condyle length, and/or the degree of TPA rotation. The results showed that TPLO shifted the cranial-most point of the medial condyle caudally and distally, and the caudal-most point caudally and proximally. These shifts resulted in significant differences between pre- and postoperative distances between the TA and the cranial-most point and its percentage to the medial condyle length. It is concluded that the TPLO led to caudal TAS and altered the position of the articular surface of the medial condyle with respect to the distal part of the tibia.
Efficacy of citalopram on stroke recurrence: A randomized clinical trial
(Elsevier Sci Ltd, 2022) Cetin, Fatma Ece; Kumral, Emre; Gonul, Ali Saffet; Ozdemir, Hueseyin Nezih; Orman, Mehmet
Post-stroke depression is one of the main causes of cerebrovascular and cardiovascular diseases. The aim of the present study was to investigate the efficacy of citalopram on stroke recurrence. A 52-week, randomized, double-blind, study involved 440 ischemic stroke patients with depression. Patients with depression who met depression criteria of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV and V) and Hamilton Depression Rating Scale >= 8 (HAM-DRS) were dichotomized into patients receiving citalopram (225 patients), titrated according to clinical response, and patients with placebo (215 patients) for 52 weeks. The primary outcome measure was stroke recurrence and the secondary outcome measures were cardiovascular events and mortality. Stroke recurrence (66% vs 34%; P = 0.001) and cardiovascular events (76% vs. 24%; P = o.oo1) were significantly higher in the placebo group compared to those treated with citalopram. Multivariable analysis showed that hypertension, atrial fibrillation, and large-artery disease were significantly associated with stroke recurrence. Executive processing disorder was more associated with stroke recurrence than other neuropsychological disorders (OR, 1.74; CI95%, 1.04-2.89; P = 0.035). Survival analysis showed that treatment for depression interacted with time to reduce stroke recurrence by nearly half (39% vs. 61%; P = 0.05). The current study supports the importance of depression treatment in protecting the patients from recurrent strokes. This result warrants further studies to demonstrate the efficacy of depression treatment on stroke recurrence.
Elderly - Onset Sarcoidosis: a Single Center Comparative Study
(Wiley, 2017) Kobak, Senol; Yildiz, Fidan; Semiz, Huseyin; Orman, Mehmet
Elderly-onset sarcoidosis: A single center comparative study
(Elsevier Espana Slu, 2020) Kobak, Senol; Yildiz, Fidan; Semiz, Huseyin; Orman, Mehmet
Objectives: Sarcoidosis rarely affect patients older than 65 years old. the purpose of this study is to compare and evaluate the demographic, clinical and laboratory features of elderly-onset (EOS) and young-onset sarcoidosis (YOS) patients. Methods: One hundred and thirty one patients diagnosed with sarcoidosis according to clinical, radiologic and histopathological evaluation were included in this study. the patients with initial symptoms started after age 65 were accepted as EOS. Results: Twenty (15.3%) of 131 patients were diagnosed as EOS, and 111 (84.7%) patients were evaluated as YOS. Fifteen of 20 EOS patients were female and 5 of them were male. Average duration of the disease was determined as 38.4 months for YOS and 22.5 months for EOS (p = 0.556). Delay of the diagnosis was 12 months for YOS while it was 3 months for EOS (p = 0.001). Higher rates of fatigue, comorbid diseases and more hydroxychloroquine (HQ) use were detected in EOS patients comparing to YOS (p=0.010, p = 0.003 and p = 0.039 respectively). Conclusions: EOS patients are characterized with higher rates of fatigue and comorbid diseases, less inflammatory sign and delayed diagnosis, and less DMARDs use. (C) 2018 Elsevier Espana, S.L.U. and Sociedad Espanola de Reumatologia y Colegio Mexicano de Reumatologia. All rights reserved.
EVALUATION OF IMMUNOBLOT-BASED ASSAY FOR DETECTING EPSTEIN-BARR VIRUS VIRAL CAPSID ANTIBODIES
(Ankara Microbiology Soc, 2010) Altuglu, Imre; Aksoy, Aysegul; Zeytinoglu, Aysin; Orman, Mehmet
Various attempts have been made to improve Epstein-Barr virus (EBV) serodiagnosis by developing more practical and objective methods than immunofluorescence-based assays In the present study, the performance of immunoblot-based assays were evaluated by comparing the results obtained by the gold standard immunofluorescence antibody (IFA) test for the detection of IgM and IgG antibodies against EBV viral capsid antigen (anti-VCA) Serum samples of 277 patients admitted to Ege University Hospital for routine EBV diagnosis were included in the study The age range of the patients was 3 months-89 years (mean 28 years) and 104 of them were females and 173 were males. All the samples were assayed by commercial immunoblot (Euro line IgM and IgG, Euroimmun, Germany) and IFA (EBV-CA IgG and IgM, Euroimmun, Germany) methods. Crosstabulation, chi-square test and phi (Phi) measures in SPSS 16 0 statistical package programme were used for data analysis Of the 216 samples that were interpreted as positive with immunoblot-based IgM assay, only 34 (15 7%) were confirmed as positive with IFA, whereas 162 (75%) were negative, and 20 (9 3%) were equivocal (Phi = 0 167, low correlation) Of the 85 samples that were anti-VCA IgG positive with immunoblot assay, 82 (96 5%) were positive, 2 (2 3%) were negative and 1 (1 2%) were equivocal with IFA (Phi = 0441, significant correlation) When the indeterminate results obtained by IFA test were excluded from the evaluation, the correlation between immunoblot VCA IgG and IFA IgG was 85 4% (88/103) and between immunoblot VCA IgM and IFA IgM was 27 3% (69/253). When the intensities of bands were evaluated for IgM testing, it was noted that as the intensity of the bands increased (1+ to 3+), IFA VGA IgM reactivity rates increased (from 9 9% to 29 5% for p19 band, from 24% to 85.7% for gp125 band) For immunoblot VCA IgM testing, 165 samples were found to be positive only for VCA p19 band Of these samples, 135 (81.8%) were negative, 15 (9.1%) were positive and 15 (9.1%) were equivocal with IFA It is observed that even though immunoblot assays with automated blotting and scanning systems can be a convenient alternative to immunofluorescence assay, the rate of false positivity obtained for VCA IgM was high (75%) It was concluded that in laboratories which apply immunoblotting as a primary screening test for EBV serodiagnosis, the positive VGA IgM results (particularly isolated p19 band positivity) and the presence of low intensity bands, should be confirmed by IFA testing.

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