Abacıoğlu, Yusuf Hakan
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YH ABACIOĞLU
Abacioglu, Hakan
Abacioglu, Yusuf Hakan
Abacıoğlu, Y. H.
Abacioglu H.
Abacioglu, Hakan
Abacioglu, Yusuf Hakan
Abacıoğlu, Y. H.
Abacioglu H.
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hakan.abacioglu@ieu.edu.tr
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09.01. Basic Medical Sciences
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12
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7
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14
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2
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15
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11
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42
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690
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269
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11
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11
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49
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52
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3
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3
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4.45
Scopus Citations per Publication
4.73
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7
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0
| Journal | Count |
|---|---|
| Turkısh Journal of Gastroenterology | 2 |
| Mikrobiyoloji Bülteni | 2 |
| Medical Science Educator | 1 |
| Mikrobiyoloji Bulteni | 1 |
| Journal of Basıc And Clınıcal Health Scıences | 1 |
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Article Citation - WoS: 1Determination of a Sample-To Ratio To Predict True-Positivity in Blood Donor Samples Screened for Syphilis by a Chemiluminescent Immunoassay(Aves Press Ltd, 2018) Akcakanat, I. Ebru; Ozbek, Ozgen Alpay; Dogan, Yavuz; Abacioglu, Yusuf HakanPurpose: The use of Architect Syphilis TP (CMIA) in the blood bank raised the number of syphilis positive samples requiring confirmation. The aim of this study is to determine a sample-to-cutoff (s/co) ratio for CMIA predicting >= 95% of true-positive samples to reduce these samples. Methods: CMIA reactive samples (n=177) were evaluated by Western blot (WB) as the reference standard, as well as by Treponema pallidum hemagglutination (TPHA) and Rapid Plasma Reagin (RPR) tests. The s/co ratio predicting >= 95% of true-positive samples was defined as the threshold leaving >= 95% of WB confirmed samples greater than the particular value. The performances of TPHA and RPR tests were also evaluated with respect to s/co ratios of CMIA positive samples. Results: The s/co ratio 15.17 predicted a true-positive result for >= 95% of samples tested (95% confidence interval: 85.9-99.3) and reduced the number of samples requiring confirmation by 29.9%. Higher s/co ratios were correlated with the increasing number of bands on WB strips (p<0.0001, R=0.906). For the samples with s/co ratios between 3 and 15.17, the agreement of TPHA and WB test results were 90%. The lowest s/co ratio where TPHA was positive, was 3.1. Although RPR predicted > 95% of positive samples with s/co ratios > 15, its sensitivity was 47.7%. Conclusion: Higher s/co ratios can be used to define true-positivity and may indicate an active infection. TPHA may replace WB to confirm samples with s/co ratios between 3 and 15. RPR should not be used as a screening test in blood banks as it could miss almost half of the true-positive samples.Article Citation - WoS: 1Citation - Scopus: 1The Impact of Visual Thinking in Medical Education(Walter De Gruyter Gmbh, 2022) Demir, Ayse Banu; Okuyan; van Eck, Alexander; Mura, Gokhan; Gonlugur, Emre; Karaca, Can; Abacioglu, HakanBackground Considering medical humanities, medicine and art are two areas that resemble each other at several features. Clinical diagnosis involves the observation, description and interpretation of information of which visual ones take an important one. The skills described are important skills in the field of visual arts, as well. Underlying a good clinical practice; clinical examination and observation skills constitute an important place. Although in several studies, these skills are shown to be improved by analyzing visual art pieces, courses intended to improve visual thinking skills are not that much common in medical faculty curriculums. Materials and methods In this article, we share our opinion about the use of visual thinking in medical education by providing preliminary reflection results of learners from the second year of medical education about the visual thinking course that we have recently started to apply in Faculty of Medicine in collaboration with Faculty of Fine Arts in Izmir University of Economics in order to improve the observational skills of learners. Results Reflection results of the learners support the view that training art-viewing skill is helpful to improve observational and descriptive skills. Conclusions Increasing interdisciplinary programs on visual thinking in medical curriculums have the potential to overcome several professional development challenges in clinics.Article Hepatit C Virusunun Genomik Varyasyonları ve Kliniğe Etkileri(2015) Abacıoğlu, Yusuf Hakan; Ergünay, KorayHepatit C virusu (HCV), tüm dünyada yaygın olarak bulunan, 110 milyonu aşkın kişiyi enfekte etmiş, ciddi bir halk sağlığı tehdidi oluşturan kronik hepatit etkenidir. Maruziyetin ardından, kronik hastalık riski yüksek olan ve koruyucu bir aşısı bulunmayan HCV; siroz, transplantasyon gerektiren karaciğer yetmezliği ve hepatoselüler karsinomun önde gelen enfeksiyöz etkenleri arasında yer almaktadır. Replikasyon mekanizmaları ve konaktaki enfeksiyon dinamikleri nedeniyle, virus, enfekte kişilerde türümsüler (quasispecies) olarak tanımlanan, birbirine çok benzer genetik varyantları içeren bir popülasyon halinde bulunur. HCV enfeksiyonlarında patogenez ve hastalığın ilerleyişi, virusa ait genetik çeşitlilik ve türümsü kompozisyonlarında izlenen değişikliklerle doğrudan ilgilidir. Virus, yüksek düzey çeşitlilik gösteren varyant havuzundan, iç ya da dış kaynaklı seçici baskıların varlığında replikasyonunu sürdürebilecek mutantların oluşumu ile, hastalık patogenezini devam ettirir. Enfeksiyon süresince, türümsüler birçok değişikliğe uğrar ve konağın hümoral ve hücresel yanıtından kaçan mutantlar, antiviral tedaviye karşı da dirençli mutantların oluşumu için zemin hazırlar. Yeni jenerasyon dizileme tekniklerinin de katkısıyla, HCV'nin kökeni ve epidemiyolojisi, ayrıca hastalık süreçlerinde izlenen genomik çeşitlilik üzerine birçok güncel bilgi elde edilmiştir. Bu derlemede, HCV'nin genetik çeşitliliğini oluşturan temel mekanizmalar ve klinik gidişle bağlantılı olarak konakla olan etkileşimler; virus ve konak yönünden hümoral ve hücresel immün yanıt, enfeksiyonun erken ve geç dönemlerindeki değişiklikler ve kronik enfeksiyona ilerleme süreci açılarından ele alınmaktadır. Ek olarak virus epidemiyolojisi ve moleküler evrimi üzerine güncel bulgular, türler arası ve popülasyon perspektifl erinden yorumlanmaktadır. Doğrudan etkili antivirallere dayalı rejimlerin uygulamaya girdiği günümüzde, genetik varyasyonlar ve tedaviye direnç ile ilişkileri, güncel saptama yöntemleri de özetlenerek tartışılmaktadırArticle Citation - WoS: 14Citation - Scopus: 14Migrants Rescued on the Mediterranean Sea Route: Nutritional, Psychological Status and Infectious Disease Control(J Infection Developing Countries, 2020) Angeletti, Silvia; Ceccarelli, Giancarlo; Bazzardi, Riccardo; Fogolari, Marta; Vita, Serena; Antonelli, Francesca; De Florio, Lucia; Abacıoğlu, Yusuf HakanIntroduction: North Africa has become a key migratory hub where a large number of migrants attempt the journey by sea from the Libyan coastline to the south of Europe. In this humanitarian disaster scenario, the Mediterranean route has been one of the most used by illegal boats. Methodology: In this report, the state of physical and psychological health of a cluster of Eritrean migrants, escaped from Libya and rescued in the Mediterranean Sea after a shipwreck, was described by epidemiological, clinical and laboratory investigations. Results: Data suggest that despite the majority of the migrants being apparently in good health upon a syndromic surveillance approach, most of them suffered a decline in psychological status as well as severe malnutrition. The emergence of infectious diseases, related to poor living conditions during the journey, is not a rare event. Conclusion: The present report highlights the risks of failures of the syndromic medical approach in the setting of the extremely challenging migration route and underlines migrant frailties consequent to a prolonged journey and long period of detention. These stressors, which can degrade the initial health condition of traveling migrants, can lead to a premature exhausted migrant effect that should be carefully investigated in order to avoid the early emergence of diseases related to frailty.Article Citation - WoS: 15Citation - Scopus: 17Identification of the Nucleotide Substitutions in 62 Sars-Cov Sequences From Turkey(Tubitak Scientific & Technical Research Council Turkey, 2020) Demir, Ayse Banu; Benvenuto, Domenico; Abacioglu, Hakan; Angeletti, Silvia; Ciccozzi, MassimoA previously unknown coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to cause coronavirus disease 2019 (COVID-19) pandemic. The first case of COVID-19 in Turkey has been declared in March 11th, 2020 and from there on, more than 150,000 people in the country have been diagnosed with the disease. In this study, 62 viral sequences from Turkey, which have been uploaded to GISAID database, were analyzed by means of their nucleotide substitutions in comparison to the reference SARS-CoV-2 genome from Wuhan. Our results indicate that the viral isolates from Turkey harbor some common mutations with the viral strains from Europe, Oceania, North America and Asia. When the mutations were evaluated, C3037T, C14408T and A23403G were found to be the most common nucleotide substitutions among the viral isolates in Turkey, which are mostly seen as linked mutations and are part of a haplotype observed high in Europe.Article Citation - Scopus: 3Clinical Impact of Hepatitis C Virus Genomic Variations(Ankara Microbiology Society, 2015) Ergünay K.; Abacioglu H.Hepatitis C virus (HCV) is a globally-dispersed agent of chronic hepatitis with a significant public health threat, affecting over 110 million individuals throughout the world. The increased risk for chronicity after exposure and the lack of a protective vaccine make HCV is a leading infectious cause of cirrhosis, liver failure requiring transplantation and hepatocellular carcinoma. The replicative process and infection dynamics in the host enable HCV to generate an array of closely-related but non-identical genetic variants known as quasispecies in the infected individuals. Pathogenesis and outcome in HCV infections are directly affected by the virus genetic heterogeneity, reflected as the emergence of quasispecies in infected individuals. The evolution of these highly-diverse viral populations in the host directly influences the disease course, via providing a pool of variants capable of resuming viral replication under extrinsic and/or intrinsic selective pressures. Viral quasispecies go through several alterations during the course of the infection, and provide a background for the selection of escape mutants from the host humoral and cell-mediated immune responses and antiviral treatment. Supported by the robust next generation sequencing techniques, recent studies have provided significant insights on the genomic diversity and progression as well as on the origin and the epidemiology of HCV. This review provides an overview of the mechanisms of HCV genetic variability, and the interactions with the host, that affects clinical disease, covering viral and host determinants of humoral and cell-mediated immune responses, alterations during the early and late stages of the infection and disease progression leading to chronicity. In addition, current findings in virus evolution and epidemiology were briefly interpreted from the inter-species and population perspectives. The impact of viral genomic heterogeneity on antiviral treatment in the era of direct-acting agents is also discussed, along with an overview of current methods employed for the characterization of viral diversity.Article Citation - WoS: 2Citation - Scopus: 2Optimization of Elisa and Immunoblot Methods for the Detection of Igg Antibodies Against Old World Hantaviruses in Wild Rodents(Ankara Microbiology Soc, 2016) Polat, Ceylan; Karatas, Ahmet; Sozen, Mustafa; Matur, Ferhat; Abacioglu, Hakan; Oktem, Mehmet AliHantaviruses infect humans via inhalation of viral particles in infected rodents' secretions such as saliva, urine and faeces or via direct contact with infected rodents. The rodent species that are known as the carriers of Dobrava (DOBV), Puumala (PUUV), Saaremaa (SAAV), Tula (TULV) and Seoul (SEOV) viruses are found in our country. The presence of specific antibodies against hantaviruses have been demonstrated in rodents collected from Black Sea and Aegean Regions of Turkey in 2004 for the first time. The first hantavirus-related hemorrhagic fever with renal syndrome (HFRS) cases were reported in Black Sea region in 2009. The determination of the hantavirus prevalence in wild life and rodent populations in the field is crucial for the information about hantavirus-related cases and to clarify the state of risk. There is no commercial product optimized for the screening of rodent serum samples in terms of HFRS agents like DOBV and PUUV that are widely seen in Eurasia as well as Turkey. In this study, the antigens belonging to the commercial enzyme-linked immunoassay (ELISA) and immunoblot tests that are produced for the screening of human sera were used for the development of antibody screening tests against hantavirus in rodent sera and were optimized. The most appropriate serum and conjugate dilutions were determined for the optimization of ELISA (Anti-Hantavirus Pool ELISA; Euroimmun, Germany) and immunoblot (Euroline Anti-Hanta Profile 1 strips; Euroimmun, Germany) methods. Optimized ELISA method was used for the screening and optimized immunoblot method was used for the confirmation. A total of 84 wild rodent sera that belonged to Apodemus and Microtus species were evaluated with this procedure and the cut-off value, sensitivity and specificity of optimized ELISA method were determined. For the optimization of ELISA 1/50, 1/100 and 1/200 serum dilutions and 1/10.000, 1/20.000 and 1/40.000 conjugate dilutions were tested. For the optimization of immunoblot, 1/50 and 1/100 serum dilutions and 1/5.000 and 1/10.000 conjugate dilutions were tested. The horseradish peroxidase conjugated goat anti-mouse IgG for ELISA and the alkaline phosphatase conjugated goat anti-mouse IgG for immunoblot were used. We followed the manufacturer's recommendations for the incubation parameters, substrate and the number of washes. 1/50 serum dilution and 1/10.000 conjugate dilution for ELISA and 1/100 serum dilution and 1/5.000 conjugate dilution for immunoblot were determined as optimal concentrations. By using the optimized ELISA, 26.2% (22/84) of rodents were found positive for hantavirus antibodies according the determined cut-off value (OD450/620: 0.325). By using immunoblot as a confirmatory test, 20 out of 22 ELISA positive samples could be studied because of the insufficient amount of sera and 17 of them was found positive in terms of DOBV antibodies. Of these rodents 11 were Apodemus flavicollis, three were Apodemus agrarius, two were Microtus guentheri and one was Apodemus sylvaticus. When the results of ELISA were compared to immunoblot results, the optimized ELISA's sensitivity and specificity were found as 100% and 95%, respectively. In this study, a method that can be used in the screening of rodent sera was constituted which uses commercial antigens that can be provided easily, gives fast and reliable results. Similar serological methods optimized for different types of rodents are of great importance for the realization of active follow-up and monitoring of the studies in the field.Article Citation - WoS: 1Citation - Scopus: 1Healthcare-Related Hcv Genotype 4d Infections in Kayseri, Turkey(Aves, 2022) Gokahmetoglu, Selma; Polat, Ceylan; Atalay, Mustafa Altay; Sezgin, Gulten Can; Ergor, Gul; Aygen, Bilgehan; Gursoy, Sebnem; Abacıoğlu, Yusuf HakanBackground: The frequency of genotype 4 hepatitis C virus infection is significantly higher in a city compared to other provinces in Turkey. In this study, we aimed to investigate the epidemiology and risk factors of hepatitis C virus genotype 4 infection in Kayseri province of Turkey. Methods: A case-control study was conducted with 61 hepatitis C virus genotype 4-infected patients and 71 controls. A questionnaire was administered to the patients and controls, asking for information about the risk factors of hepatitis C virus transmission. Core/E1 and NS5B regions of hepatitis C virus genome were amplified and sequenced by Sanger method. Phylogenetic analysis and molecular clock analysis were performed. The risk was determined by calculating the odds ratio and 95% CI. Logistic regression analysis was performed to determine the effect of risk factors by controlling for confounding variables. Results: Kayseri isolates were closely related to type 4d sequences but formed a separate cluster. According to the molecular clock analysis, hepatitis C virus genotype 4d entered Kayseri province probably between 1941 and 1988. Blood transfusion and surgical intervention were found to be significant risk factors for the infection. Conclusion: Epidemiological data showed that hepatitis C virus genotype 4d infections are significantly associated with unsafe medical procedures.Article Citation - WoS: 15Citation - Scopus: 14Changes on Hepatitis C Virus Genotype Distribution in Western Turkey: Evaluation of Twelve-Year Data(Aves, 2020) Duran, Alev Cetin; Cetinkaya, Ozgul Kaya; Sayiner, Ayca Arzu; Seydaoglu, Gulsah; Ozkaratas, Emre; Abacioglu, HakanBackground/Aims: Hepatitis C virus (HCV) prevalence is 1% in Turkey with genotype 1 being the predominant type traditionally. However unique geographical location of Turkey and increasing human migration in the region influences the epidemiology of the infection. The aim of this study was to determine the changes in distribution of HCV genotypes and risk factors. Materials and Methods: In this retrospective single-center study, HCV genotyping results of 558 patients were evaluated in between 2005 and 2016.Three different HCV genotyping assays were used during the 12-year study period;restriction fragment length polymorphism (RFLP), Abbott Real Time HCV Genotype II and Bosphore HCV genotyping kit. Results: The most prevalent HCV genotype was genotype 1 detected in 88.4% of the patients followed by genotype 3 (5.2%),genotype 4 (2.9%),genotype 2 (2.1%), mixed genotypes (1.1%) and genotype 5 (0.3%). Genotype 1a showed an increasing prevalence. There were 19 patients (3.4%) either of foreign nationalities or Turkish citizens living abroad. Genotype 3 was the most common type among these patients which 10.3% had intravenous drug use history. Syrian migrant population differed in terms of HCV genotypes. Genotype 5 detected in two Syrian patients, which is the first report of HCV type 5 in Western Turkey. Among the HCV genotype 4 infected patients, 31.3% were Syrians. Conclusion: Our study showed that although genotype 1b dominance continues, the distribution and prevalence of HCV genotypes are changing in our region mainly due to migration and increase in the frequency of patients with non-traditional risk factors such as intravenous drug use. Monitoring the epidemiology of HCV genotypes may provide guidance in treatment decisions.Article Yabani Kemiricilerde Eski Dünya Hantavirus Igg Antikorlarının Saptanması için Elısa ve İmmünoblot Yöntemlerinin Optimizasyonu(2016) Sözen, Mustafa; Öktem, İbrahim Mehmet Ali; Polat, Ceylan; Abacıoğlu, Yusuf Hakan; Karataş, Ahmet; Matur, FerhatHantaviruslar, enfekte kemiricilerin salya, dışkı ve idrar gibi salgılarında bulunan virus partiküllerinin solunması ya da enfekte kemiricilerle direkt temas sonucu insanlara bulaşmaktadır. Ülkemizde, hantavirus tiplerinden Dobrava (DOBV), Puumala (PUUV), Saaremaa (SAAV), Tula (TULV) ve Seoul (SEOV) viruslarının taşıyıcısı olan kemirici türleri bulunmaktadır. Türkiye'deki kemiricilerde hantaviruslara özgül antikor varlığı, ilk kez 2004 yılında Karadeniz ve Ege bölgelerinden toplanan kemiricilerde gösterilmiştir. İlk renal sendromlu kanamalı ateş (RSKA) olguları ise 2009 yılında yine Karadeniz bölgesinden bildirilmiştir. Yaban hayatı ve sahadaki kemirici popülasyonlarında hantavirus prevalansının önceden belirlenmesi, hantaviruslara bağlı olguların durumu hakkında bilgi edinilmesi ve sahadaki risk durumunun ortaya konması açısından önem taşımaktadır. Kemiricilere ait örneklerin, DOBV ve PUUV gibi Avrasya'da sık görülen ve ülkemizde de görüldüğü bilinen bazı RSKA etkenleri açısından taranmasında kullanılabilecek şekilde optimize edilmiş bir ticari ürün bulunmamaktadır. Bu çalışmada, insan serumlarının taranması için üretilmiş, ticari enzim temelli immünolojik yöntem (ELISA) ve immünoblot testlerine ait antijenler kullanılarak, kemirici örneklerinde hantavirusa özgül antikorların taranmasına uygun testlerin optimizasyonu sağlanmıştır. ELISA (Anti-Hantavirus Pool ELISA; Euroimmun, Almanya) ve immünoblot (Euroline Anti-Hanta Profi le 1 strips; Euroimmun, Almanya) yöntemlerinin optimizasyonu için, en uygun serum ve konjugat dilüsyonları denenmiş ve ELISA yöntemi tarama, immünoblot yöntemi ise doğrulama amacıyla kullanılmıştır. Belirlenen bu prosedür ile, Apodemus ve Microtus türlerinden 84 kemiriciye ait serum örnekleri değerlendirilmiş ve elde edilen sonuçlar ile optimize edilen ELISA yönteminin eşik değeri, duyarlılık ve özgüllüğü saptanmıştır. ELISA yönteminin optimizasyonu için 1/50, 1/100 ve 1/200 serum dilüsyonları ile 1/10.000, 1/20.000 ve 1/40.000 konjugat dilüsyonları; immünoblot yönteminin optimizasyonu için ise 1/50 ve 1/100 serum dilüsyonları ile 1/5.000 ve 1/10.000 konjugat dilüsyonları değerlendirilmiştir. ELISA için "horseradish" peroksidaz enzimi ile işaretli keçi anti-fare IgG konjugatı, immünoblot için ise alkalen fosfataz ile işaretli keçi anti-fare IgG konjugatı kullanılmıştır. İnkübasyon süresi, yıkama sayısı ve substrat seçimi için üretici fi rmanın protokolü uygulanmıştır. ELISA yöntemi için 1/50 serum dilüsyonu ve 1/10.000 konjugat dilüsyonu, immünoblot için ise 1/100 serum dilüsyonu ve 1/5.000 konjugat dilüsyonu optimal değerler olarak belirlenmiştir. Optimize edilen ELISA yöntemiyle, belirlenen eşik değerine (ODantikor varlığı saptanmıştır. Doğrulama amacıyla kullanılan optimize immünoblot yöntemiyle ise, ELISA ile pozitif bulunan 22 örneğin -serum yetersizliği nedeniyle- 20'si çalışılmış ve 17'sinde DOBV antikor pozitifl iği saptanmıştır. Bu kemiricilerden 11'i Apodemus fl avicollis, üçü Apodemus agrarius, ikisi Microtus guentheri ve biri de Apodemus sylvaticus türlerine aittir. Her iki yöntem ile elde edilen sonuçlar karşılaştırıldığında, optimize ELISA yönteminin %100 duyarlılık ve %95 özgüllükte olduğu belirlenmiştir. Bu çalışma ile kemirici serumlarının taranmasında kullanılabilecek, kolaylıkla ulaşılabilen ticari ürünlerden elde edilen antijenlerin kullanıldığı, hızlı ve güvenilir sonuç veren bir yöntem oluşturulmuştur. Benzer çalışmalar ile farklı türden kemiricilere yönelik olarak optimize edilecek serolojik yöntemler, alanda aktif izlem ve denetleme çalışmalarının gerçekleştirilmesi açısından büyük önem taşımaktadır.