Robustness of Massively Parallel Sequencing Platforms

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications

ODTÜ kampüsündeki iki baştankara türünün (paridae) üreme ekolojisi.

Use of nest boxes is a common method to perform ecological research on hole nesting species. The family Paridae is the subject of longest running studies in the field of avian ecology. Despite the usefulness of such an approach, only a handful studies utilizing next boxes have been completed in Turkey. The aim of this study is to investigate the breeding ecology of Paridae species at METU campus , Ankara, which offers marginal habitat for most tree-dependent species. A total of 50 nest boxes were attached to tree trunks in three forested patches of the campus in early 2013. Data on breeding parameters (laying date, clutch size, breeding success, body measurements, predation rate) were collected with weekly visits during late March until July in 2013- 2015. Two species have used the nest boxes placed: Great Tit (Parus major) and Coal Tit (Parus ater). In total, 40 nest boxes were occupied by either species during the study, and 26 of those were used to calculate breeding parameters. The proportion of occupied next boxes was found to significantly increase further away from buildings or asphalt roads. Both species started nesting in the first week of April. Mean egg laying dates were 21st of April and 4th of May, and average clutch size were 7.5 and 6.8 for Coal Tits and Great Tits, respectively. The fate of nesting attempts pooled over three years were as follows: 42.5% predated, 40.0% successful, 15.0% deserted or predated, and 2.5% unknown. The number of fledglings per nest was 4.0 and 1.4 for Coal Tits and Great Tits, respectively. The main identified predator was magpie (Pica pica) while the other predators were Caspian snake (Dolichophis caspius), fox (Vulpes vulpes) and domestic cat (Felis catus). Although the findings on laying date and clutch size are comparable to other study sites at similar latitudes, predation rates, and hence the overall rate of breeding failure, are among the highest recorded. Very high densities of magpies at METU campus could be the reason. Our study indicates that the introduction of nest boxes might have created an ecological trap, particularly for Great Tits, leading to a sink population that can only persist with immigration from neighboring habitats. However further research, including some on success rates at nests in natural cavities, should be conducted in order to assess the full impact of nest boxes on tit populations at METU campus.M.S. - Master of Scienc

An evaluation of critical approaches to the customs union betwenn turkey and the European union

1963 Ankara Anlasması ile kararlastırılan, 1973 Katma Protokol’le ayrıntıları belirlenen ve 1 Ocak 1996 itibariyle Türkiye ile Avrupa Birligi arasında tam olarak uygulamaya giren Gümrük Birligi, Türkiye ekonomisine sekil veren önemli bir faktördür. Bu nedenledir ki özellikle Türk kamuoyunda yogun olarak tartısılmaktadır. Çalısmanın temel amacı bu elestirilerin dayandırıldıkları temellere göre kategorizasyonu ve degerlendirilmesidir. Sonuç olarak, Gümrük Birligi’ne yöneltilen elestirilerin ekonomik entegrasyona degil, ekonomik entegrasyonun modeli üzerine yogunlastıgı söylenebilir. Baska bir deyisle, AB ile Türkiye arasında gerçeklesecek bir ekonomik birlik, Türkiye ekonomisi için serbest ticaretten sonra en iyi seçenek olarak kabul görmektedir denebilir. Elestiriler dört ana kategoride toplanmıstır. _lk kategoriyi Gümrük Birligi’nin dayandıgı temel üzerine yapılan elestiriler olustururken, ikinci kategoriyi Gümrük Birligi’nin amacı üzerine yapılan elestiriler olusturur. Üçüncü ve dördüncü kategoriler ise sırasıyla Gümrük Birligi’nin Türkiye ekonomisi üzerine etkileri ile Gümrük Birligi’nin isleyisinden kaynaklı aksaklıklar olusmaktadır. ABSTRACT The Customs Union was determined by 1963 Ankara Agreement, detailed by 1973 Additional Protocol and became effective in 1996 between Turkey an the EC. Since it is one of major factors which effect Turkish economy, it has been very criticized in Turkey. The aim of the study is to make a categorization and evaluation of these critics. Although, there have been many arguments about this issue in Turkey, most of them have not criticize the direction. The critics are not generally concentrated on the concept of economic integration itself, but of its modelling. In other words, it can be said that there is a general consensus that Turkey’s economic integration with the EU is the most rational option. There are four basic categories regarding the essence of critics about the current CU in Turkey. The first one is critics on the source of the CU between Turkey and the EU. The second category is constituted by the critics on the aim of the CU. The third category of the critics on the CU are classified according to possible effects of the CU on an economy. The fourth category of the critics on the CU is about the functioning of it

The effects of mortgage loans on economic growth: Aneconometric analysis on Turkish banking sector

Bu çalışmanın amacı Türkiye'de kullandırılan konut kredilerinin ekonomik büyümeye etkisinin olup olmadığı belirlenmesidir. Bu kapsamda, konut kredisi değişkenini temsilen konut kredilerinin toplam kredilere oranı, ekonomik büyüme bağlamında ise GSYİH rakamının bir önceki döneme göre artış hızı dikkate alınmıştır. Ayrıca, söz konusu değişkenlere ait 2005:1-2017:3 dönem aralığındaki 3 aylık veriler incelenmiştir. Öte yandan, bahsi geçen amaca ulaşılabilmek için Engle-Granger eş bütünleşme analizinden faydalanılmıştır. Analiz sürecinde ilk olarak ilgili değişkenler ADF birim kök testine tabi tutulmuş ve her iki değişkenin de birinci sıra farkları alınarak durağan hale geldiği anlaşılmıştır. Bunun ardından, konut kredisi bağımsız değişken, ekonomik büyüme de bağımlı değişken olacak şekilde regresyon analizi yapılmış ve hata terimi serileri elde edilmiştir. İlgili serinin de düzeyde durağan çıkması sonucunda, Türkiye'deki konut kredileri miktarı ve ekonomik büyüme arasında uzun dönemli bir ilişki bulunduğu sonucuna varılmıştır. Elde edilen sonuçlar dikkate alındığında, ekonomik büyümenin arttırılabilmesi amacıyla, Türkiye'de konut kredilerinin teşvik edilmesinin yerinde olacağı düşünülmektedir. Bu bağlamda, devletin konut kredilerini teşvik edilmesi yönünde, vergi avantajı, bankalar üzerinde de bazı uygulamalar yapılması, devlet dairelerinde karşılaşılan masrafların kaldırılması ve faiz oranlarının düşürülmesi yerinde olacaktır. Bu sayede, konut krediler daha cazip hale gelecek ve bu durum da ülkenin ekonomik kalkınmasına katkı sağlayacaktır. Belirtilen süreçte önemli olan bir diğer husus da konut kredisi rakamlarını arttırmaya çalışırken karşılaşılabilecek risklerin minimize edilmeye çalışılmasının gerekliliğidir. Örnek olarak, söz konusu kredilerin finansal durumu düşük kişiler tarafından kullanılmaması amacıyla bankaların kredi kullandıracakları müşteri seçimine ilişkin minimum koşulları belirleyen bir kural setinin kamu otoritesi tarafından bir kanun olarak belirlenmesi yerinde olacaktır.The purpose of this study is to determine whether mortgage loans have an influence on economic growth in Turkey. In this context, as the variable of the mortgage, the ratio of the mortgage loans to the total loans is taken into consideration. Also, the increase ratio in GDP is used as an economic growth variable. In addition to this situation, quarterly data of these variables for the periods between 2005:1 and 2017:3 is examined. On the other hand, Engle-Granger cointegration analysis is considered in this study in order to reach this objective. In the analysis process, firstly, the variables are subjected to the ADF unit root test and it is understood that both variables become stationary by taking first order differences. Moreover, regression analysis is conducted with mortgage loans as the independent variable and economic growth as dependent variable and error series are obtained. Because error term series are stationary on their level values, it is identified that there is a long-term relationship between mortgage loans and economic growth in Turkey. By considering these results, it is recommended to encourage mortgage loans in order to increase economic growth. Within this framework, it is thought that government should take actions to increase mortgage loans, such as tax incentives, implementing some regulations on the banks, removal of costs incurred in government offices and reduction of interest rates. With the help of these actions, mortgage loans become more attractive for the people and it has a contributing influence on the economic growth. Another important issue in the mentioned process is the necessity of taking actions to minimize the risks that may arise while trying to increase the mortgage loans. As an example, it would be appropriate for the public authority to designate a set of rules that sets the minimum requirements fort he banks regarding customer selection. Owing to these conditions, it can be prevented to give loans fort he people who have low credibility

An evaluation of critical approaches to the customs union betwenn turkey and the European union

ÖZET1963 Ankara Anlasması ile kararlastırılan, 1973 Katma Protokol’le ayrıntıları belirlenen ve1 Ocak 1996 itibariyle Türkiye ile Avrupa Birligi arasında tam olarak uygulamaya girenGümrük Birligi, Türkiye ekonomisine sekil veren önemli bir faktördür. Bu nedenledir kiözellikle Türk kamuoyunda yogun olarak tartısılmaktadır. Çalısmanın temel amacı buelestirilerin dayandırıldıkları temellere göre kategorizasyonu ve degerlendirilmesidir. Sonuçolarak, Gümrük Birligi’ne yöneltilen elestirilerin ekonomik entegrasyona degil, ekonomikentegrasyonun modeli üzerine yogunlastıgı söylenebilir. Baska bir deyisle, AB ile Türkiyearasında gerçeklesecek bir ekonomik birlik, Türkiye ekonomisi için serbest ticaretten sonraen iyi seçenek olarak kabul görmektedir denebilir. Elestiriler dört ana kategoride toplanmıstır._lk kategoriyi Gümrük Birligi’nin dayandıgı temel üzerine yapılan elestiriler olustururken,ikinci kategoriyi Gümrük Birligi’nin amacı üzerine yapılan elestiriler olusturur. Üçüncü vedördüncü kategoriler ise sırasıyla Gümrük Birligi’nin Türkiye ekonomisi üzerine etkileri ileGümrük Birligi’nin isleyisinden kaynaklı aksaklıklar olusmaktadır. ABSTRACTThe Customs Union was determined by 1963 Ankara Agreement, detailed by 1973 AdditionalProtocol and became effective in 1996 between Turkey an the EC. Since it is one of majorfactors which effect Turkish economy, it has been very criticized in Turkey. The aim of thestudy is to make a categorization and evaluation of these critics. Although, there have beenmany arguments about this issue in Turkey, most of them have not criticize the direction. Thecritics are not generally concentrated on the concept of economic integration itself, but of itsmodelling. In other words, it can be said that there is a general consensus that Turkey’seconomic integration with the EU is the most rational option. There are four basic categoriesregarding the essence of critics about the current CU in Turkey. The first one is critics on thesource of the CU between Turkey and the EU. The second category is constituted by thecritics on the aim of the CU. The third category of the critics on the CU are classifiedaccording to possible effects of the CU on an economy. The fourth category of the critics onthe CU is about the functioning of it

FEN BİLİMLERİ ENSTİTÜSÜ/LİSANSÜSTÜ TEZ PROJESİ

ODTÜ BÜYÜK BAŞTANKARA POPULASYON BİYOLOJİSİ ÜZERİNE ARAŞTIRMALA