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Publication Open Access A benevolent angel with blue eyes(Türk Kütüphaneciler Derneği, 2019) Ergün, Canan; Other; Suna Kıraç LibraryI met Professor Dr. Meral Alpay on my first day at Istanbul University, Department of Librarianship. I tried to tell my memory of this first day that I met with Professor Dr. Meral Alpay. / İstanbul Üniversitesi Kütüphanecilik Bölümünü kazanıp, okula başladığım ilk gün Prof. Dr. Meral Alpay hocam ile tanışma anımı anlatmaya çalıştım.
Publication Metadata only A coarse graining approach in molecular simulations: fuzzy potentials(Istanbul Technical University, 2003) Department of Chemistry; Department of Chemistry; Yurtsever, İsmail Ersin; Eşsiz, Şebnem; Faculty Member; Undergraduated Student; Department of Chemistry; College of Sciences; College of Sciences; 7129; 191615A new representation for interaction potential functions is presented. Unlike the orthodox approaches, the potential function is not a fixed function in terms of internuclear coordinates but a probabilistic one which contains information over a wide range of angular degrees of freedom. It is shown that such approaches can provide practical solutions for bulk systems of high density.Publication Open Access A diagnostic challenge: risk factors and surgical treatment of laryngeal chondroradionecrosis(Aves, 2022) Başaran, Bora; Doruk, Can; Çaytemel, Berkay; Şen, Cömert; Aslan, İsmet; Ünsaler, Selin; School of Medicine; 167909Objectives: thirteen cases of laryngeal chondroradionecrosis unresponsiveto conservative treatment and treated with laryngectomy were presented with an analysis of possible risk factors. Methods: retrospective analysis of 13 patients operated on for chondroradionecrosis was made. Characteristics of the primarytumor, chondroradionecrosis grade, number of biopsies needed to rule out recurrence, and laryngectomy indications were analyzed. The possible predisposing factors such as alcohol and tobacco use and other major chronic diseases were investigated. Results: all of the patients had a history of smoking. The most common comorbidity was hypertension (46.2%), followed by chronic obstructive pulmonary disease (23.1%). The onset of symptoms was documented within the 10 monthsfollowing the radiation therapy in 12 of the patients (93.3%) and 12 years after the primary radiation therapy in 1 patient. Asthe most common symptom, fetor oris was observed in all of the patients, followed by dysphagia (69.2%), hoarseness (61.5%), pain (53.8%), dyspnea (46.2%), and necrotic fistula formation in the anterior neck (15.4%) consecutively. Tumor suspicion (84.6%) was the most common indication for laryngectomy followed by chronic aspiration or feeding disorder (61.5%). Twelve patients were treated with total and 1 with supraglottic laryngectomy. Pectoralis major muscle flap was used in all of the patients for pharyngeal reconstruction or protection against salivary fistula. Conclusion: diagnosis of chondroradionecrosis is challenging, and tumor recurrence should always be kept in mind. Patients must be informed about the possibility of chondroradionecrosis complications including laryngectomy. Introduction: chondroradionecrosis is a rare and the most severe complication of radiation therapy for laryngeal carcinoma.Publication Open Access A nonminimally coupled, conformally extended Einstein-Maxwell theory of pp-waves(TÜBİTAK, 2020) Department of Physics; Dereli, Tekin; Şenikoğlu, Yorgo; Researcher; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; 201358; N/AA nonminimal coupling of Weyl curvatures to electromagnetic fields is considered in Brans-Dicke-Maxwell theory. The gravitational field equations are formulated in a Riemannian spacetime where the spacetime torsion is constrained to zero by the method of Lagrange multipliers in the language of exterior differential forms. The significance and ramifications of nonminimal couplings to gravity are examined in a pp-wave spacetime.Publication Open Access A rabbit model of avascular necrosis of femoral head using surgical trauma and systemic steroids(Galenos Yayınevi, 2020) Özben, Hakan; School of MedicineObjective: avascular necrosis of the femoral head (ANFH) is a disease caused by the diminished circulation of the femoral head. The incidence of the disease is increasing and it has heavy socioeconomical burden. Animal models are indispensable for the development of new treatments for bone avascular necrosis. There is not any reliable animal model for simulating the early stages of femoral head osteonecrosis. The aim of this study is to present an animal model of femoral head osteonecrosis induced by systemic steroid use combined with surgery. Methods: six New Zealand White rabbits were divided into 3 groups. Each group contained 4 femoral heads. For the induction of osteonecrosis, every hip underwent surgical dislocation followed by cauterization of extraperiosteal vessels around the femoral head and ligamentum teres resection. A single dose intramuscular steroid was administered to each rabbit. Rabbits were sacrificed at 2nd, 4th and 6th weeks and femoral heads were sent to histological evaluation. Results: the femoral heads showed typical signs of avascular necrosis at the end of 2nd week. In addition to osteocyte loss and marrow necrosis, there was also new osteoblast formation at the end of 4th week. At the end of 6th week, epiphyseal new bone formation next to large necrotic areas were visible. Conclusion: these results suggest that the single steroid administration combined with hip luxation and cauterization of neck vessels may create femoral head osteonecrosis in rabbits in a repeatable and reliable manner. This model can be presented as an alternative model for the new studies on the treatment of femoral head avascular necrosis in the early stage. / Amaç: femur başı avasküler nekrozu (FBAN), femur başının kanlanmasındaki azalmadan kaynaklanan, görülme sıklığı giderek artan ve ağır sosyo-ekonomik etkileri olan bir hastalıktır. Hayvan modelleri, kemiklerdeki avasküler nekrozlar için yeni tedavi yöntemlerinin oluşturulmasında vazgeçilmezdir. Halen, erken dönem FBAN’yi simüle edebilen güvenilir bir hayvan modeli yoktur. Bu çalışmanın amacı, cerrahi ve sistemik steroid kombinasyonu ile tavşanda FBAN modeli oluşturmaktır. Yöntemler: altı Yeni Zelanda beyaz tavşanı 3 gruba ayrıldı. Her grup 4 femur başı içermekteydi. FBAN oluşturmak için her kalçaya cerrahi olarak dislokasyon, femur boynu periosteal damarların koterizasyonu ve ligamentum teres eksizyonu yapıldı. Sonrasında her tavşana tek doz intramusküler steroid uygulandı. Gruplardaki hayvanlar sırasıyla 2., 4. ve 6. haftalarda sakrifiye edildi ve tüm femur başları rezeke edildi. Femur başları histolojik olarak avasküler nekroz bulguları açısından değerlendirildi. Bulgular: ikinci haftanın sonunda incelenen femur başlarında tipik histolojik avasküler nekroz bulguları mevcut idi. Dördüncü hafta sonunda alınan örneklerin yapılan histolojik değerlendirmelerinde osteosit kaybı ve kemik iliği nekrozuna ek olarak osteoblast oluşumları görüldü. Altıncı hafta sonunda yapılan incelemelerde epifizyel alanlarda geniş kemik iliği nekrozlarına ek olarak yeni kemik oluşumları görüldü. Sonuç: bu sonuçlar, femur başı luksasyonu ve koterizasyonu ile tek doz steroid uygulamasının tavşanlarda güvenilir ve tekrarlanabilir şekilde femur başı nekrozu oluşturduğunu göstermektedir. Bu model, femur başı osteonekrozlarının erken dönem tedavisi araştırmalarında kullanılabilecek bir seçenek olarak sunulabilir.Publication Open Access A systematic and efficient input selection method for artificial neural networks using mixed-integer nonlinear programming(Konya Teknik Üniversitesi, 2022) Şıldır, Hasan; Department of Chemical and Biological Engineering; Aydın, Erdal; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 311745Selection of input variables of the empirical models has vital effect on the prediction performance, reduced overfitting and reduced computational load. Various trials and error and sequential methods in the literature to deal with input selection for artificial neural networks (ANNs). However, these methods are not considered as automatic and systematic. This study proposes a novel and efficient mixed integer nonlinear programming-based approach to handle optimal input selection and the ANN training simultaneously for classification problems. Such selection uses binary (0-1) variables to represent the presence of the input variables and trains traditional continuous network weights simultaneously. Two classification case studies are given to demonstrate the advantages by using widely used data sets and statistical measures. The first data set is related to the characterization of the type of a tumor related to breast cancer, the second data set is about predicting the type of a biotechnological product using different features, the last one is related to heart failure prediction. Results show that better test performance can be achieved with optimally selected inputs, resulting in reduced overfitting. The proposed approach delivers a significant advantage during the design and training of the ANNs and is also applicable to other empirical models. / Ampirik modellerin girdi değişkenlerinin seçimi, tahmin performansı, azaltılmış fazla uydurma ve hesaplama yükünün azaltılması üzerinde önemli etkiye sahiptir. Literatürde yapay sinir ağları (YSA) için girdi seçimi ile ilgili çeşitli deneme yanılma yöntemleri mevcuttur ancak bu metodlar sistematik ve otomatik olarak kabul edilmemektedir. Bu çalışma, sınıflandırma problemleri için optimal girdi seçimi ve YSA eğitimini aynı anda ele almak için yeni ve verimli bir karma tamsayılı doğrusal olmayan programlama tabanlı bir yaklaşım önermektedir. Bu seçim, girdi değişkenlerinin varlığını temsil etmek için ikili (0-1) değişkenleri kullanır ve geleneksel sürekli ağ ağırlıklarını veya parametrelerini aynı anda eğitir. Yaygın olarak kullanılan veri setleri ve istatistiksel ölçümler kullanarak avantajları göstermek amacıyla üç sınıflandırma vaka çalışması sunulmuştur. Birinci veri seti meme kanseri ile ilgili tümörün tipin-in karakterizasyonu ile ilgili olup, ikinci veri seti ise farklı özellikler kullanılarak bir biyoteknolojik ürünün tipinin tahmin edilmesi ile ilgilidir, son veri seti ise kalp sağlığı ile ilgilidir. Sonuçlar, optimal olarak seçilen girdiler ile düşük fazla uydurma sayesinde daha iyi test performansının elde edilebileceğini göstermektedir. Önerilen yaklaşım, YSA'ların tasarımı ve eğitimi sırasında önemli bir avantaj sağlar ve diğer ampirik modellere de uygulanabilir.Publication Metadata only A very rare case of cervicothoracic vertebral synostosis spanning eight adjacent segments: congenital vs acquired(Marmara Univ, Fac Medicine, 2018) Cengiç, İsmet; Altaş, Hilal; Buğdayci, Onur; N/A; Türeli, Derya; Doctor; N/A; Koç University Hospital; N/AAn elderly female presented with acute post-traumatic neck pain. Cervical roentgenogram revealed a long-segment cervicothoracic vertebral fusion spanning 8 adjacent spinal levels. The patient was evaluated with computed tomography (CT) and magnetic resonance (MR) imagings of the spine, electromyography (EMG) and growth differentiation factor 6 (GDF6) gene mutation analysis. Imaging findings were atypical for congenital block vertebrae and there was no GDF6 mutation. A revision of very old medical records and patient's recollections revealed long-term stay in sanatorium for rehabilitation of chronic partially-treated brucella spondylodiscitis during adolescence. Block vertebrae spanning several levels have previously been reported; but, this is the first report of an acquired cervicothoracic fusion spanning 8 adjacent vertebral bodies. / Yaşlı bir kadın hasta travma sonrası akut boyun ağrısı ile başvurdu. Servikal direkt grafisinde 8 ardışık spinal seviyeyi kapsayan uzun segment servikotorakal vertebral füzyon saptandı. Hasta spinal bilgisayarlı tomografi (BT) ve magnetik rezonans (MR) görüntüleme, elektromiyografi (EMG), ve büyüme-farklılaşma faktörü 6 [Growth differentiation factor 6 (GDF6)] gen mutasyonu analizi ile detaylı tetkik edildi. Görüntüleme bulguları konjenital blok vertebra için atipik olan olguda GDF6 gen mutasyonu saptanmadı. Hastanın eski tıbbi raporları ve anamnezinde adolesan dönemde kronik ve kısmen tedavi edilmiş brucella spondilodiskiti rehabilitasyonu amacıyla sanatoryumda uzun dönemli yatış mevcut idi. Birkaç seviyeyi kapsayan blok vertebra olguları daha önceden bildirilmiş olmakla birlikte; bu, 8 ardışık vertebral cismi kapsayan ilk edinsel servikotorakal füzyon olgusudur.Publication Open Access Aberrant methylation profile and microsatellit instability in Turkish sporadic colorectal carcinoma(Galenos Yayınevi, 2019) Ekmekçi, Cumhur Gökhan; Güllüoğlu, Mine; Dizdaroglu, Ferhunde; Özbek, Uğur; N/A; Kapran, Yersu; Faculty Member; School of Medicine; 168101Objective: genomic DNA obtained from paraffin blocks of the intended colorectal cancer cases was evaluated for promoting colorectal cancer by investigating the promoter methylation of 6 different gene promoter regions and microsatellite instability. Methods: DNA was isolated from the paraffin tissue of 76 sporadic colorectal cancer patients by cross sections from the areas determined to be tumorous. The methylation specific PCR (MS-PCR) method was used for these DNA samples fo rmethlylation studies in promoter region of six different APC, hMLH1, p16INK4A, p15, p73 and DAPK1 genes. In the same samples, the presence of microsatellite instability (MSI). Results: the fequencey of methylation was 24% for hMLH1, 31.5% for APC, 19.6% for DAPK1, 42.8% for p16, 30% for p15, 17% for p73. We calculated a methylation index (MI=ratio between the number of genes methylated and the number of genes analyzed). MI was ranged from 0-0.83, with an average of 0.271 corresponding to 1.6 genes/sample and median was 0.225 and there were 15 samples which doesn't methylated in any loci. We analysed MSI in C-kit (21%), hMSH2 (18%) and APC (15%), microsatellite region. Conclusion: we observed APC methylation was common then the other population for Turkish patient. P16 was the most commenest methylated loci among the 6 of gene and it seems storongly related with female patients. P73 was releated with left colorectal cancer and additionally it was related with the MSI.Publication Open Access Abnormal first and second trimester maternal serum marker levels for aneuploidy screening and adverse pregnancy outcomes(Yüzüncü Yıl Üniversitesi Tıp Fakültesi, 2021) Karakış, Lale Susan; Kıyak, Hüseyin; Yücel, Neşe; Türkgeldi, Engin; Faculty Member; School of Medicine; 329649To investigate if there is an association between pregnancy complications and abnormal maternal serum analytes used for first trimester screening (FTS) and second trimester screening (STS) for aneuploidy. More than two hundred three pregnant women who had FTS or STS for Down's syndrome who presented between July 2009 and January 2010 were included. First trimester maternal levels of PAPP-A and free hCG or 2nd trimester maternal levels of AFP, uE3 and hCG were compared between healthy pregnancies and those with preeclampsia, intrauterine growth retardation, intrauterine fetal death or oligohydramnios. PAPP-A levels less than 0.4 MoMs were related with elevated preeclampsia and fetal growth retardation risk. AFP levels over 2.5 MoMs were related with all adverse outcomes evaluated in the study including preeclampsia, fetal growth retardation, intrauterine fetal demise and oligohydramnios. While uE3 levels below 0.5 MoM were found to be related with higher preeclampsia incidence, elevated 2nd trimester hCG levels over 3.0 MoMs were associated with fetal growth retardation. No significant relationship could be established between low 1st trimester free hCG levels (less than 0.5 MoMs) and any of the adverse outcomes. First and 2nd trimester serum analytes for Down syndrome screening are significantly linked with pregnancy complications. However, because their sensitivity and positive predictive values are low, these analytes are not shown to be effective in the screening of pregnancy complications when used alone.Publication Metadata only Acculturation and family relations(Türk Psikologlar Derneği, 2014) Department of Psychology; Kağıtçıbaşı, Çiğdem; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; N/AThis article is an overview of some of the main issues seen in the context of immigration. As an epilogue, it relates to the other articles in this Special Issue, as well. In particular, the European scene is examined on the basis of research conducted over the last decades. There is also an emphasis on family relations and acculturation as well as their interface. Immigration and acculturation over half a century are introduced through a historical perspective noting that multiphasic and multidisciplinary approaches are needed to understand the myriad factors involved. In particular, cultural and developmental viewpoints are promising. Acculturation research has focused on the acculturating migrant, without due attention to the context of acculturation. In particular, prejudice and discrimination are the greatest challenges. This approach leaves something to be desired, since immigration is a very complex human phenomenon involving issues ranging from micro to macro levels of analysis. While the former concerns individual factors, including the family, the latter includes historic, sociological, economic, and legal aspects and applications. Focusing on the acculturating (or non-acculturating) individual or family without a contextual approach can lead to dispositional attributions, even ‘blaming the victim’, that is, social psychological processes not conducive to understanding and promoting the well-being of the immigrant or the host society. In this context, there is a further need for research to address policies and to suggest solutions for improvement. In particular, concerted efforts that prove to be beneficial for the family, women and children are badly needed. Turkish psychologists and social scientists would do well to attend to these very important topics of study. / Bu makale göç olgusunun çeşitli yönlerine eğilen genel bir çalışmadır ve bu özel sayı için bir sonsöz niteliği taşımaktadır. Özellikle son birkaç on yıldaki araştırmalardan yola çıkarak, bu özel sayıdaki makaleler de dahil olmak üzere, Avrupa’daki durumu ele almaktadır. Aynı zamanda kültürleşme ve aile konularını ve bunların etkileşimini inceler. Yarım yüzyıllık bir göç olgusu tarihsel bir perspektifle ele alınıyor. Bu çok faktörlü karmaşık olayı iyi anlayabilmek için çok katmanlı ve çok disiplinli bir yaklaşımın gerekli olduğu da not ediliyor. Özellikle kültürel ve gelişimsel yaklaşımların yararlı olacağı öne sürülüyor. Kültürleşme çalışmaları genellikle kültürleşme ortamını yeterince incelemeden kültürleşen göçmene vurgu yapıyor. Oysa ki baskın toplumdaki önyargı ve ayrımcılık önemli sorunlardır. Bu yaklaşım yetersiz kalıyor çünkü karmaşık göç süreci, mikro yaklaşımlardan, makro yaklaşımları gerekli kılan karmaşık bir olgudur. Mikro düzeyde insan ve aileye yönelik araştırmalar söz konusuyken, makro düzeyde sosyolojik, ekonomik, hukuksal hususların ve uygulamaların incelenmesi önemlidir. Bağlamı dikkate almadan, kültürleşen (ya da kültürleşmeyen) birey ya da aileye vurgu yapmak, içsel atıflara, hatta “mazlumu suçlamaya” kadar gidebilir. Bunlar ise, olayı anlamaya ve gerek göçmenin, gerek baskın toplumun yararına olmayan sosyal psikolojik yaklaşımlardır. Bu noktada araştırmaların göçmen politikalarına yönelik ve çözüm önerici olması çok yararlıdır. Özellikle, göçmen kadın, aile ve çocukların esenliğine katkıda bulunabilecek çabalara ihtiyaç vardır. Türk psikologlar ve sosyal bilimcilerin bu çok önemli araştırma konularına daha fazla eğilmesi çok yararlı olacaktır.