Araştırmacılar(2)

• Demir, Abdussamed Yasin
• Polat, Seher

• ArticleAçık Erişim2026/r/ebyu/19209
  Comprehensive MEFV Variant Spectrum in Pediatric Patients with Suspected Familial Mediterranean Fever: A Whole-Gene Sequencing Study

  Gunay, Murat; Demir, Abdussamed Yasin; Yeter, Bahtinur

  Objective: To determine the Mediterranean Fever (MEFV) variant spectrum using whole-gene next-generation sequencing (NGS) in pediatric cases with suspected Familial Mediterranean Fever (FMF). Methods: This retrospective cross-sectional study included 471 pediatric cases referred for MEFV analysis. All exons were analyzed using NGS, and variants were classified according to American College of Medical Genetics and Genomics criteria. Results: At least one MEFV variant was detected in 59.4% of cases. A total of 23 variants were identified, predominantly in exon 10 (43.5%) and exon 2 (34.8%). The most frequent variants were R202Q (43.3%), E148Q (16.3%), and M694V (13.7%). A low-frequency variants of uncertain significance, G150R, was detected in one case. Heterozygous genotypes were the most common (59.6%). Conclusion: Whole-gene sequencing enables the detection of both common and rare MEFV variants that may be missed by limited mutation panels. However, frequently detected variants, such as R202Q, require careful interpretation because of their high population frequency and controversial pathogenicity.

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• ArticleYalnız künye2026/r/ebyu/10828
  Variant-specific contributions of CYP21A2 and CYP11B1 to the clinical and hormonal heterogeneity of polyendocrine metabolic ovarian syndrome phenotypes

  Polat, Seher; Simsek, Yasin

  Background: Polyendocrine Metabolic Ovarian Syndrome (PMOS) formerly known as Polycystic Ovary Syndrome (PCOS), characterized by hyperandrogenism, affects approximately 7.1–15.1% of women of reproductive age. While disease-causing CYP21A2 and CYP11B1 variants are well-studied, the contribution of synonymous variants to clinical and hormonal variations remains unclear. This study investigated whether synonymous and non-synonymous variants associated with phenotypic heterogeneity. Methods and results: A total of 275 premenopausal women (110 PMOS women and 165 healthy controls) underwent comprehensive clinical-biochemical evaluation. All exons and exon–intron boundaries of CYP21A2 and CYP11B1 were analyzed using direct sequencing. Genotype–phenotype associations were evaluated using non-parametric statistical tests and genetic model–based logistic regression analyses. Genotype and allele frequencies were similar between PMOS patients and controls; however, several variants showed distinct genotype–phenotype associations. Following false-discovery rate correction within predefined biological blocks, p.Val282Leu and non-classic congenital adrenal hyperplasia (NCAH)-related CYP21A2 variants remained significantly associated with elevated adrenocorticotropic-hormone(ACTH), while combined p.Leu9_Leu10insLeu/p.Arg103Lys/p.Ser269Thr/ p.Ser494Asn variants was linked to reduced ACTH. Carriers of NCAH-associated CYP21A2 allele exhibited significantly reduced sex hormone-binding globulin (SHBG) and higher modified Ferriman-Gallwey(FGS) levels. CYP21A2 synonymous p.Leu40=/p.Pro46 = variant associated with lower BMI. Additionally, combined CYP11B1 p.Leu75=/p.Asp82 = genotype remained significantly associated with reduced SHBG, while p.Arg43Gln/p.Ala386Val was associated with reduced FGS. Conclusion: The findings underscore the variant-specific and cumulative impact of CYP21A2 and CYP11B1 alterations on the adrenal axis and systemic androgen bioavailability. These results suggest that synonymous variants may actively modulate hormonal and clinical traits, contributing to the inter-individual variability of PMOS-related phenotypes independently of overt PMOS risk.

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• ArticleYayıncıda açık erişim2026/r/ebyu/10739
  Phytochemical evaluation via GC-MS and LC-MS/MS: a comprehensive study of antidiabetic, antimicrobial, antioxidant, and genotoxic activities of extracts from endemic species Centaurea amanicola Hub.-Mor. and C. antitauri Hayek (Asteraceae)

  Nobarirezaeyeh, Mohaddeseh; Yuca, Hafize; Aydın, Bilge; Civaş, Ayşe; Karakaya, Songül; Karadayı, Mehmet; Demir, Abdussamed Yasin; Bona, Mehmet; Yılmaz, Bilal; Göger, Gamze

  The study investigated the antidiabetic, antimicrobial, antioxidant, and genotoxic activities of extracts from Centaurea amanicola and C. antitauri (Asteraceae). Methanol extracts were analysed for phenolic and fatty oil contents. Major components of fatty oils were identified, including methyl hexadecanoate (48.30%) and heptacosane (22.13%) in C. antitauri, and methyl hexadecanoate (16.29%) and methyl linoleate (13.55%) in C. amanicola. The highest α-amylase inhibition was observed in hexane extracts of both species with 55.53% and 41.57% inhibition values, respectively. Antioxidant activity, measured by ABTS•+ and DPPH• scavenging, varied among extracts, with notable efficacy in C. antitauri dichloromethane extract and C. amanicola ethyl acetate extract. The dichloromethane extract of C. antitauri demonstrated effectiveness against Candida albicans with MIC= 156.25 µg/mL. Importantly, all extracts were found to be genotoxicity-safe. Overall, the findings highlight the potential of these extracts for various medicinal applications, particularly in managing diabetes and combating microbial infections.

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• ArticleYalnız künye2026/r/ebyu/10199
  Clinical decision support system for detecting right ventricular dysfunction in acute pulmonary embolism: Explainable a new Binary Rule Search (BRS) ensembles and robustness evaluation

  Huyut, Mehmet Tahir; Velichko, Andrei; Belyaev, Maksim; Izotov, Yuriy; Tosun, Mustafa; Sertoğullarından, Bünyamin; Karaoğlanoğlu, Şebnem; Demir, Abdussamed Yasin; Korzun, Dmitry

  Background Right-ventricular dysfunction (RVD) in acute pulmonary embolism (PE) carries excess short-term mortality; fast, transparent risk stratification is needed. Objective To develop and evaluate an interpretable Binary Rule Search (BRS) framework for RVD detection on a fully binarized clinical dataset, emphasizing conservative robustness. Methods We analyzed a single-center cohort ( N = 363; development = 250, external validation = 113) recoded into 0/1 predictors. For subset sizes k = 1–5, a Rust BRS searched bit-mask rules maximizing Matthews correlation coefficient (MCC) on development data and was assessed over 500 stratified 250/113 hold-out repeats. We report MCC with bootstrap 95 % CIs plus sensitivity, specificity, precision, F1, and AUC-ROC. Robustness was summarized by the Stability-Bound Rule Score (SBRS). Results Performance increased with k; triplets offered the best parsimony–robustness balance, with modest conservative gains for quintets. The strongest quintet by point estimate was S{Age65_79; ThromMain; ThromBilat; DVTuni; Malig} (MCC = 0.326; 95 % CI 0.152–0.498). A balanced k = 4 rule, S{SexMale; ThromMain; Hypertens; HeartFail}, achieved Sensitivity 0.791, Specificity 0.557, F1 0.630, AUC-ROC 0.674 on external validation. Decision-tree checks yielded high lower-bound performance (e.g., L95 = 0.302 for S{ThromMain; DVTdist; COPD}), whereas LogNNet often matched mean MCC but showed consistently lower L95, indicating greater dispersion. PFI highlighted a thrombus-centric signal (ThromMain/ThromBilat/DVT) with meaningful secondary contributions from heart failure and hypertension. Conclusions Interpretable BRS ensembles deliver clinically acceptable, conservatively bounded performance using few binary predictors and transparent logic, supporting clinician-facing decision support in resource-constrained settings. We provide rule masks, uncertainty summaries, and an offline CDSS prototype; prospective multicenter validation is warranted.

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• ArticleYalnız künye2025/r/ebyu/11737
  Association between ACE (rs4343 and rs1799752), AGTR1 (rs5186), and PAI-1 (rs2227631) polymorphisms in the host and the severity of Covid-19 infection

  Polat, Seher; Şimşek, Zühal Özer

  Objective: It is necessary to identify appropriate clinical, biochemical, epidemiological and genetic biomarkers to elucidate the underlying mechanisms of the coronavirus disease-2019 (COVID-19) disease. The study focused on not only the link between disease severity (non-intense unit care (non-ICU) versus intensive unit care (ICU) and genetic susceptibility in COVID-19 patients but also the connection between comorbidity and genetic susceptibility affecting the severity of COVID-19. Subject and methods: One hundred and sixty-two COVID-19 patients treated in the non-ICU and ICU in Kayseri City Hospital were included. All volunteers underwent a physical examination and biochemical evaluation. Angiotensin-converting enzyme (ACE p.T776T G > A(rs4343) and g.16471_16472delinsALU (also referred to as I/D polymorphism; rs1799752), angiotensin II receptor type-1 (AGTR1) c.*86A > C (also referred to as A1166C; rs5186), and plasminogen activator inhibitor-1 (PAI-1-844 G > A (rs2227631) polymorphisms were analysed as well. Results: To have ACE “ID” genotype did not change the severity of the disease (OR: 0.92, 95% CI: 0.41–2.1, p = 0.84), but decreased the mortality risk 2.9-fold (OR: 2.9, 95% CI: 1.1–7.0, p = 0.03). In PAI-1-844 G > A, having the “AA” genotype in the “A” recessive model increased the risk of the diabetes mellitus (DM) 2.3-fold (OR: 2.3 95%, CI: 1.16–4.66, p = 0.018). In the “G” recessive model, to have the GG genotype increased the risk of chronic kidney disease (CKD) 4.8-fold (OR:4.8, 95% CI: 1.5–15.5, p = 0.008). “GG” genotype in the DM group had a higher fibrinogen level compared to those with the “AG” genotype (AG:4847.2 mg/L (1704.3) versus GG:6444.67 mg/L (1861.62) p = 0.019) and “AA” genotype in the CKD group had lower platelet levels and those with “GG” had higher platelet levels (AA:149 µL (18–159) versus GG: 228 µL (146–357) p = 0.022). Conclusion: This study was shown that genetic predispositions that causes comorbidities were also likely to affect the prognosis of COVID-19.

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• ArticleYalnız künye2025/r/ebyu/11687
  Phytochemical analysis and biological evaluation of essential oils and extracts from Heracleum pastinacifolium subsp. incanum (Boiss. & A.Huet) P.H.Davis, an endemic plant from Turkey

  Yuca, Hafize; Sefalı, Abdurrahman; Aydın, Bilge; Karadayı, Mehmet; Gülşahin, Yusuf; Yazıcı, Ayşenur; Karakaya, Songül; Demirci, Betül; Çoban, Furkan; Özdemir, Erkan

  Essential oil content of and phenolic compounds flower-fruit, root, and aerial parts of Heracleum pastinacifolium subsp. incanum were analysed by GC/MS and LC/MS methods, respectively. Antidiabetic, anticholinesterase, and antioxidant activities of flower-fruit, root, aerial parts methanol extracts were evaluated. Apiole (35.0%), myristicine (72.2%), and myristicine (15.1%) were found as major compounds of fruit-flower mixture, root, aerial part essential oils, respectively. Hesperidin was found the highest amount in aerial part and flower-fruit extracts with 8904.2621 ng/mL and 11558.3634 ng/mL values, respectively. Fruit-flower extract showed the highest activity against α-glucosidase (24%). Root extract demonstrating the highest activity (18%) against AChE enzyme. Flowers-fruits mixture methanol extract had a higher % inhibition value on ABTS·+ and DPPH•. Flowers-fruits mixture methanol extract was rich in total phenol, total tannin, and protein content. All the extracts were determined as genetoxically safe according to the results of Ames/Salmonella, Escherichia coli WP2 and Allium cepa assays.

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• ArticleYayıncıda açık erişim2024/r/ebyu/19777
  Ailesel Akdeniz Ateşi Hastalarında MEFV Gen Mutasyonları: Erzincan Deneyimi

  Admış, Özlem; Demir, Abdussamed Yasin

  Ailesel Akdeniz Ateşi, MEFV geninde meydana gelen mutasyonların yol açtığı otozomal resesif geçişli otoinflumatuar multisistemik genetik bir hastalıktır. Ülkemizde sık görülen bir hastalık olmakla birlikte hastalığa sebep olan mutasyonların tipi ve sıklıkları bölgesel olarak farklılık göstermektedir. Bu çalışmada, ilimizde Ailesel Akdeniz Ateşi ön tanısı alan hastalarda MEFV gen mutasyonlarının tiplerinin ve sıklıklarının belirlenmesi amaçlanmıştır. Ailesel Akdeniz Ateşi ön tanısı ile laboratuvarımıza yönlendirilen 303 hasta çalışmaya dahil edildi. Real-Time PCR yöntemi ile MEFV geninde sık görülen mutasyonlar açısından analiz edilen hastaların bulguları retrospektif olarak değerlendirildi. Çalışmaya dahil edilen hastaların %44.8’inde MEFV geninde mutasyon saptanırken %55.2’sinde ise araştırılan bölgelere ilişkin mutasyon saptanmadı. Mutasyon tespit edilen hastalarda en sık saptanan genotiplerin frekans yüzdeleri; M694V/- (%36.4), E148Q/- (%18.3), M694V/M694V (%7.3); alellerin frekans yüzdeleri ise M694V (%48.3), E148Q (%22.2), M680I (%10.8), V726A (%10.3) olarak tespit edildi. Çalışmanın sonuçları Ailesel Akdeniz Ateşi hastalarında görülen MEFV gen mutasyonlarındaki heterojeniteyi desteklemektedir. MEFV geninde saptanan mutasyon tipleri ve sıklıkları bakımından minör farklılıklar gözlense de elde edilen bulgular Türk popülasyonunda gerçekleştirilen diğer çalışmaların sonuçları ile uyumludur. İlimizdeki Ailesel Akdeniz Ateşi hastalarının genotip dağılımlarının güncel verileri literatüre katkı sağlayacaktır.

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• ArticleYayıncıda açık erişim2024/r/ebyu/12805
  Host Genetic Polymorphisms and Disease Severity in Pregnant Women with COVID-19 in Türkiye

  Polat, Seher; Kiremitli, Sevil; Kiremitli, Tunay; Kirkinci, Ahmet; Kurnuç, Fatma Zehra; Arslan, Yusuf Kemal

  Objective: The study aimed to analyze the association between coronavirus disease-2019 (COVID-19) disease severity and genetic susceptibility in pregnant women. Material and Methods: The research included 54 pregnant women with confirmed COVID-19 diagnosis. All volunteers were evaluated physically and biochemically. Angiotensin-converting enzyme (ACE)2 (p.T27A A>G, p.G326E G>A, p.K419T A>C, ACE (p.T776T A>G, and g.16471_16472delinsALU (I/D), AGTR1 c.*86A>C, methylenetetrahydrofolate-reductase (MTHFR) p.A222V C>T and PAI-1-844 G>A were analyzed. Results: The allele frequency was also compared with control groups of the different studies made on Turkish women. MTHFR “CT” genotype compared to “CC” had lower platelet counts (p=0.015). In ACE “ID” genotype, there was a lower D-dimer level compared to “DD” genotype (p=0.02). In PAI-1-844G>A, the AA vs. AG+GG genotype and AA vs. GG genotype elevate the risk of hospitalization 6.4-fold (OR: 6.4 95% (Cl): 1.6-25.8 p=0.009), and 4.6-fold (OR: 4.6 95% CI:1.0-21.6 p=0.049), respectively. In MTHFR p.A222V, to have CC vs. CT genotype increased the risk of enoxaparin and antibiotic use 4.1-fold and 3.2-fold at the borderline significance (OR: 4.1 95% Cl: 0.99-16.9 p=0.052 and OR: 3.2 95% Cl: 0.98-10.5 p=0.053), respectively. An allele frequency difference wasn't found between the patient and the healthy women related to the investigated polymorphisms. Conclusion: PAI-1-844G>A, MTHFR p.A222V, and ACE (I/D) associated with a poor COVID-19 outcome, the risk of enoxaparin and antibiotic use, and also increased risk of hospitalization. Allele frequencies of the genes were not different between healthy control women and women with COVID-19; genetic variation may not influence the risk of infection but disease severity.

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• ArticleYayıncıda açık erişim2024/r/ebyu/12296
  Detection of Right Ventricular Dysfunction Using LogNNet Neural Network Model Based on Pulmonary Embolism Data Set

  Huyut, Mehmet Tahir; Velichko, Andrei; Belyaev, Maksim; Karaoğlanoğlu, Şebnem; Sertogullarindan, Bunyamin; Demir, Abdussamed Yasin

  The high association of right ventricular dysfunction (RVD) with mortality in patients with acute pulmonary embolism (PE) remains an important health problem. In this respect, rapid, economical and highly-accurate detection of risk factors for early diagnosis of RVD in patients with PE is expected to greatly benefit the diagnosis and treatment of the disease and contribute significantly to the reduction of mortality. The aim of this study is to identify the most effective features from the PE dataset for RVD diagnosis, using a special-algorithm for the LogNNet reservoir neural-network. The cohort of patients diagnosed with acute PE in the last five years in our hospital was retrospectively analyzed and the data in accordance with our criteria were recorded. A total of 163 patients' data were acces sed and the patients had 20 characteristics. RVD was diagnosed in 27 of these patients. 78-79 years of age was found to be an important threshold for the diagnosis of RVD. The LogNNet model revealed that older age, comorbidities and coronary-heart disease greatly increased the risk of RVD. The model also found that individuals with diabetes and COPD were at higher risk of RVD, while individuals with malignancies were at lower risk of RVD. However, the model found that unilateral-thrombus increased the risk of RVD more than bilateral-thrombus. The risk of RVD is high in PE patients with unilateral-thrombus. In addition, PE patients with comorbidities such as coronary heart disease, diabetes and COPD are at high-risk for RVD and should be followed closely.

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• ArticleYayıncıda açık erişim2023/r/ebyu/20078
  Sivas’taki ailesel akdeniz ateşi hastalarının mefv gen mutasyonları bakımından değerlendirilmesi

  Demir, Abdussamed Yasin; Yakar, Ömer

  Amaç: Ailesel Akdeniz Ateşi, MEFV genindeki mutasyonların yol açtığı otozomal resesif geçişli otoinflumatuar multisistemik genetik bir hastalıktır. Ülkemizde sık görülen bir hastalık olmakla birlikte hastalığa sebep olan mutasyonların tipi ve sıklıkları bölgesel olarak farklılık göstermektedir. Bu çalışmada, ilimizde Ailesel Akdeniz Ateşi ön tanısı alan hastalarda MEFV geni mutasyonlarının tiplerinin ve sıklıklarının belirlenmesi amaçlanmıştır. Gereç ve Yöntemler: Ailesel Akdeniz Ateşi ön tanısı ile Tıbbi Genetik kliniğimize yönlendirilen 495 hasta çalışmaya dahil edildi. Real-Time PCR yöntemi ile MEFV geninde sık görülen mutasyonlar açısından analiz edilen hastaların bulguları retrospektif olarak değerlendirildi. Bulgular: Çalışmaya dahil edilen hastaların %44.4’ünde MEFV geninde mutasyon saptanırken %55.6’sında ise araştırılan bölgelere ilişkin mutasyon saptanmadı. En sık saptanan genotiplerin frekans yüzdeleri incelendiğinde; M694V/- (%47.40), V726A/- (%15.90), M680I(C)/- (%9.99); alellerin frekans yüzdeleri ise  M694V (%52.8), V726A (%16.8), M680I(C) (%13.6) olarak tespit edildi. Sonuç: Çalışmanın sonuçları Ailesel Akdeniz Ateşi hastalarında görülen MEFV geni mutasyonlarındaki heterojeniteyi desteklemektedir. MEFV geninde saptanan mutasyon tipleri ve sıklıkları bakımından minör farklılıklar gözlense de elde edilen bulgular Türk popülasyonunda gerçekleştirilen diğer çalışmaların sonuçları ile uyumludur. İlimizdeki Ailesel Akdeniz Ateşi hastalarının genotip dağılımlarının güncel verileri literatüre katkı sağlayacaktır.

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