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Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets
Get PDFIdentification of microorganisms in a biological sample is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment. While progress has been made in studying larger organisms, there is a need for an efficient and scalable method that can handle thousands of whole genomes for organisms with high mutation rates and genetic diversity such as single stranded viruses. In this study, we developed a novel method to identify subsequences for detection of a given species/subspecies in a (meta)genomic sample using the Polymerase Chain Reaction (PCR) method. Species detection in any analysis depends highly on the measurement method and since thermodynamic interactions are critical in PCR, thermodynamics is the main driving force in the proposed methodology. Our method is parallelized in multiple steps and involves extracting all oligonucleotides from target genomes. We then locate the target sites for each oligonucleotide using the constructed suffix array and local alignment followed by thermodynamic interaction assessment. An important requirement for subspecies identification is to avoid amplifying a non-target set of genomes and our method addresses this. We applied our method to three highly divergent viruses; (1) Hepatitis C virus (HCV), where the subtypes differ in 31–33% of nucleotide sites on average, (2) Human immunodeficiency virus (HIV), for which, 25–35% between-subtype and 15–20% within-subtype variation is observed, and (3) the Dengue virus, whose respective genomes (only DENV 1–4) share 60% sequence identity to each other. Using our method, we were able to select oligonucleotides that can identify in silico 99.9% of 1657 HCV genomes, 99.7% of 11,838 HIV genomes, and 95.4% of 4016 Dengue genomes. We also show subspecies identification on genotypes 1–6 of HCV and genotypes 1–4 of the Dengue virus with more than 99.5% true positive and less than 0.05% false positive rate, on average. None of the state-of-the-art methods can produce oligonucleotides with this specificity and sensitivity on highly divergent viral genomes like the ones studied in this article
VİDEO ARACILI SANAL DEĞİŞİMLERDE KONU YÖNETİMİNDE UYUM VE YAKINLIK KURMA KAYNAKLARINI İNCELEYEN BİR KONUŞMA ÇÖZÜMLEMESI ARAŞTIRMASI
No full textA number of recent studies have explored virtual exchanges in a microanalytic
way, however the ways how alignment and affiliation are built in
online interaction remains underexplored. Addressing this gap, this study
investigates resources for alignment and affiliation within topic management
in video-mediated Virtual Exchange (VE) between tertiary-level second
language (L2) speakers from Türkiye and Tunisia. It specifically explores the
(re)construction of (dis)alignment and (dis)affiliation within topic
management in on-task and off-task talk. The data comes from an Erasmus+
project, in which dyads collaborated for five meetings to complete nine tasks.
Using Multimodal Conversation Analysis, the study analyzes over 30 hours
of screen-recorded spoken data. This is the first study to combine these underresearched
areas, which are essential in both everyday and institutional
interactions. Findings reveal when and how off-task talk occurs in task-based VE.
In the dataset, alignment emerges as central to on-task topic management,
while affiliation is a byproduct of interaction. Alignment is facilitated through
(non)verbal and screen-based resources, with cooperative contributions in
both on-task and off-task talk. In contrast, humor, storytelling, and
collaborative turn construction are more common in off-task-talk, enhancing
mutual understanding and affiliative bonds. Findings show that on-task
interactions are structured and goal-oriented, emphasizing alignment,
whereas off-task VE interactions are flexible and relational, emphasizing
affiliation. The findings highlight the interplay between on-task and off-task
interaction, indicating that both are crucial for building an effective
communication repertoire in VE. The study has implications for research on
topic management, alignment and affiliation, online task-based interaction,
VE, and L2 interactional competence.Son yıllarda yapılan çalışmalar sanal değişimleri mikro düzeyde incelemiş
olsa da, çevrim içi etkileşimlerde uyum ve yakınlık kurma süreçleri yeterince
araştırılmamıştır. Bu çalışma, Türkiye ve Tunus’tan üniversite düzeyinde
ikinci dil konuşucularının katıldığı video aracılı sanal değişim
etkileşimlerinde konu yönetimi bağlamında uyum/uyumsuzluk ve yakınlık
kurabilme/kuramama dinamiklerinin görev içi ve görev dışı konuşmalarda
nasıl (yeniden) inşa edildiğini incelemektedir. Çalışmanın verileri,
katılımcıların Erasmus+ projesi kapsamında beş oturum boyunca ikili gruplar
hâlinde iş birliği yaparak tamamladığı dokuz görevden gelmektedir. Veriler,
Çokkipli Konuşma Çözümlemesi yöntemiyle incelenmiş, toplamda 30 saatten
fazla ekran kaydı analiz edilmiştir. Bu çalışma, hem günlük hem de kurumsal
etkileşimde önemli olan fakat yeterince araştırılmamış alanları bir araya
getiren ilk çalışmadır. Bulgular, görev temelli sanal değişimlerde konu dışı
konuşmaların ne zaman ve nasıl gerçekleştiğini ortaya koymakta; görev içi
etkileşimlerde uyumun merkezi bir rol oynadığını, yakınlığın ise çoğunlukla
görev dışı konuşmalarda ortaya çıktığını göstermektedir. Uyum, sözel,
sözsüz ve ekran temelli kaynaklar ile işbirlikli katkılar aracılığıyla
sağlanmakta; mizah, hikayelendirme, ve işbirlikçi söz sırası inşaası ise daha
çok görev dışı konuşmalarda görülerek karşılıklı anlayış ve yakınlık bağlarını
pekiştirmektedir. Sonuçlar, görev içi etkileşimlerin yapılandırılmış ve hedef
odaklı, görev dışı etkileşimlerin ise daha esnek ve ilişki temelli olduğunu
ortaya koymakta; her iki tür etkileşimin de etkili iletişim açısından
tamamlayıcı nitelikte olduğunu vurgulamaktadır. Bu çalışma, konu, uyum,
yakınlık, çevrimiçi görev temelli etkileşim, sanal değişim ve ikinci dilde
etkileşimsel yeterlilik alanlarına özgün katkılar sunmaktadır.Ph.D. - Doctoral Progra
Kuantum Hesaplamaya Dayanıklı Doğrulanabilir Zamanlı İmza Şemaları
No full textVerifiable Timed Signatures (VTS) are cryptographic constructions that ensure a digital signature can only be obtained at a specific point in the future, while also providing a proof to the verifier that the signature already exists. Existing VTS designs are based on classical signature schemes such as BLS, Schnorr, and ECDSA. However, the security of these schemes relies on the discrete logarithm problem, which can be efficiently solved by Shor's algorithm, rendering them vulnerable to quantum attacks. In this thesis, two novel VTS schemes based on quantum-resistant signature algorithms are proposed: VT-Dilithium and VT-UOV. VT-Dilithium is built upon CRYSTALS-Dilithium, which has been standardized by NIST as a quantum-safe digital signature algorithm. On the other hand, VT-UOV is based on the Unbalanced Oil and Vinegar (UOV) algorithm, one of the leading candidates in NIST’s additional post-quantum signature standardization process. The mathematical complexity inherent in quantum-resistant algorithms poses significant challenges for their integration into VTS frameworks. This thesis presents a comprehensive study on the integration, design, and performance comparison of Dilithium and UOV algorithms within VTS schemes.Doğrulanabilir Zamanlı İmzalar (Verifiable Timed Signatures – VTS), bir dijital imzanın yalnızca belirli bir gelecek zamanda elde edilebilmesini sağlayan, ayrıca doğrulayıcıya bu imzanın var olduğunu da kanıtlayan kriptografik yapılardır. Mevcut VTS tasarımları, BLS, Schnorr ve ECDSA gibi klasik imza algoritmalarına dayanmakta olup, bu algoritmaların güvenliği, Shor algoritması tarafından verimli bir şekilde çözülebilen ayrık logaritma problemini temel aldığı için kuantum hesaplamaya karşı savunmasızdır. Bu tezde, kuantum hesaplamaya dayanıklı imzalama algoritmalarına dayanan iki yeni VTS şeması tanıtılmaktadır: VT-Dilithium ve VT-UOV. VT-Dilithium, NIST tarafından kuantum hesaplamaya dayanıklı imzalama standardı olarak kabul edilen CRYSTALS-Dilithium imza algoritması üzerine inşa edilmiştir. VT-UOV ise, NIST’in ilave kuantum sonrası dijital imza standardizasyon sürecindeki güçlü adaylardan biri olan Unbalanced Oil and Vinegar (UOV) algoritmasına dayanmaktadır. Kuantum hesaplamaya dayanıklı algoritmaların sahip olduğu matematiksel karmaşıklıklar, bu imza algoritmalarının VTS şemalarına entegre edilmesini zor bir problem haline getirmektedir. Bu tezde Dilithium ve UOV algoritmalarının VTS şemalarına entegre edilmesi, tasarımı ve performans karşılaştırmaları kapsamlı bir şekilde sunulmaktadır.Ph.D. - Doctoral Progra
Phosphorylation of SNAP-25 at Ser187 is enhanced following its cleavage by Botulinum Neurotoxin Serotype A, promoting the dominant-negative effect of the resulting fragment
Get PDFBotulinum Neurotoxin Serotype A (BoNT/A), responsible for most human botulism cases, inhibits neurotransmitter release by cleaving the target protein SNAP-25. Previous literature demonstrated that BoNT/A mediated cleavage of a small subset of the SNAP-25 pool, resulting in SNAP-25 (1–197) fragments, is sufficient to block exocytosis. SNAP-25 (1–197) potentially competes against intact SNAP-25 for SNARE complexes and blocks neurotransmission through a dominant-negative mechanism. However, how a tiny fraction of cleaved SNAP-25 efficiently outcompetes a large pool of intact SNAP-25 remains unknown. Here, we examined the importance of SNAP-25 phosphorylation at Ser187 residue, located in the C-terminus SNARE domain, in the context of BoNT action. Our results demonstrated that Ser187-phosphorylated SNAP-25 can be efficiently cleaved in cells. Importantly, BoNT/A-cleaved SNAP-25 fragments in neuronal and non-neuronal cells are heavily phosphorylated at Ser187 and localized on the cell membrane. SNAP-25 (1–197) binds to syntaxin-1A, and the interaction is enhanced by Ser187 phosphorylation. We also found that SNAP-25 (1–197) survives longer than the BoNT/A enzymatic component itself in cells. Molecular modeling suggested that SNAP-25 (1–197), phosphorylated or not, forms stable SNARE complexes; however, Ser187 phosphorylation induces local changes in surface electrostatic potential and dynamics of the complex. This study characterizes the molecular mechanism underlying the dominant-negative effect of SNAP-25 (1–197) on neurotransmission. This research could have implications for the future development of BoNT/A inhibitors and the generation of new BoNT/A clinical formulations by regulating the abundance of Ser187 phosphorylation in cleaved SNAP-25 fragments
An All-Conjugated, PM6-Based Block Copolymer Enables Stable Nanoparticle Dispersions in Methanol
No full textOrganic semiconductors are commonly processed using toxic halogenated or aromatic solvents due to their poor solubility in less harmful alternatives, leading to significant environmental and health concerns. Although there are "green" solvents available, these materials often face limited processing options and challenges in microstructure control. To mitigate this, an emerging approach involves creating dispersions of organic semiconductor nanoparticles in polar, environmentally friendly solvents. However, achieving stable nanoparticle dispersions without ligands remains a significant challenge. This study introduces a novel method for enhancing the stability of these ligand-free dispersions by developing an amphiphilic conjugated polymer, PM6-FNT, designed to form stable nanoparticles in alcohol-based dispersions. PM6-FNT is synthesized via a one-pot, stepwise Stille cross-coupling polymerization, where an amino group-functionalized fluorene-thiophene copolymer (FNT) chain is grown in situ on preformed PM6 chains. Nanoparticles of PM6-FNT, prepared by nanoprecipitation in polar solvents like alcohols, exhibited exceptional colloidal stability due to the high zeta potential of around 35 mV and controllable particle sizes in the range of 35-200 nm. In contrast, nanoparticle dispersions of PM6 could not be formed under the same conditions. This research highlights the potential of PM6-FNT to address existing challenges in organic semiconductor processing. Using nanoparticles instead of solutions enables enhanced layer-by-layer processing capabilities, morphology control, and higher crystallinity, further optimizing performance and paving the way for the eco-friendly, large-scale production of organic semiconductor devices
Tarihsel Entropi ve Çağın Ruhu: 20. Yüzyıl Faşizmi ve 21. Yüzyıl Aşırı-Sağın Karşılaştırmalı bir Analizi
No full textThis study investigates the political, economic, and social conditions that facilitated
the rise of fascism in the interwar period and systematically compares them with the
contemporary dynamics shaping populist far-right movements. It argues that despite
profound contextual differences, striking parallels—ranging from socioeconomic
precarity and intensified social fragmentation to crises of political legitimacy—
continue to structure both historical moments. These resonances suggest not a direct
recurrence of fascism but the re-emergence of deeper structural logics that recur
across historically transformed settings. the study employs entropy as a metaphorical
and analytic lens to conceptualize the growing uncertainty, institutional
destabilization, and ideological diffusion characterizing today’s global political
environment. This approach demonstrates that structural conditions resembling those
that enabled fascism to persist, yet they operate within a far more complex, digitally
mediated, and globally interdependent system. The study concludes that
contemporary far-right movements should be understood as historically inflected
phenomena shaped by both enduring structural pressures and the high-entropy
dynamics of the twenty-first century.Bu çalışma, 20. yüzyılın ilk yarısında faşizmin yükselişini mümkün kılan siyasi,
ekonomik ve sosyal koşulları incelemekte ve bunları günümüz popülist aşırı sağ
hareketlerinin dinamikleriyle sistematik olarak karşılaştırmaktadır. Çalışma,
bağlamsal farklılıkların derin olmasına rağmen, ekonomik güvencesizlik, artan
sosyal parçalanma ve siyasi meşruiyet krizleri gibi çarpıcı paralelliklerin her iki
tarihi dönemi de şekillendirmeye devam ettiğini ileri sürmektedir. Bu benzerlikler,
faşizmin doğrudan tekrarı değil, tarihsel olarak dönüştürülmüş bağlamlarda yeniden
ortaya çıkan daha derin yapısal mantıkların varlığını göstermektedir. Çalışma,
günümüzün küresel siyasi ortamını karakterize eden artan belirsizlik, kurumsal
istikrarsızlık ve ideolojik yayılmayı kavramsallaştırmak için entropiyi metaforik ve
analitik bir mercek olarak kullanmaktadır. Bu yaklaşım, faşizmi mümkün kılan
yapısal koşulların devam ettiğini göstermekte, ancak artık çok daha karmaşık, dijital
olarak aracılı ve küresel ölçekte birbirine bağımlı bir sistem içinde işlediğini ortaya
koymaktadır. Son olarak, çalışma, çağdaş aşırı sağ hareketlerin hem kalıcı yapısal
baskılar hem de yirmi birinci yüzyılın yüksek entropik dinamikleri tarafından şekillenen
tarihsel olarak etkilenmiş olgular olarak anlaşılması gerektiğini sonucuna vardırmaktadır.M.S. - Master of Scienc
Driver dysfunctional impulsivity dominates over others in anger expression
No full textThe aim of this study is to examine whether driver impulsivity predicts aggressive driver behavior and to compare the predictive power of driver impulsivity and general impulsivity towards aggressive driver behavior. A total of 312 drivers, 113 women and 199 men, participated in the study and completed the Demographic Information Form, Driver Anger Expression Inventory, Barrat Impulsivity Scale-Short Form and Impulsive Driver Scale by way of an online link. The hierarchical regression analyses showed that driver dysfunctional impulsivity positively predicted physical anger expression, verbal anger expression and the use of a vehicle to express anger whereas it negatively predicted the adaptive anger expression. Driver functional impulsivity positively predicted physical anger expression, the use of a vehicle to express anger and the adaptive anger expression. The dominance analyses results show that driver dysfunctional impulsivity completely dominates all other driver impulsivity and general impulsivity dimensions for both adaptive and non-adaptive anger expression of drivers. The results of the study emphasize the importance of conceptually addressing impulsivity in future studies and the impact of the measurement tool to be used on the results
Köprü derzlerinin sismik performansı: Boşluk mesafesinin yapısal darbelere etkisi
No full textProviding a uniform gap between adjacent spans of a bridge can lead to pounding between structural components during earthquakes, and pounding is considered one of the primary causes of damage observed after seismic events. The gap distance between structures has a direct influence on the likelihood of pounding. Following the recent major earthquakes in Türkiye, which affected 11 provinces, investigations revealed that although no bridge collapses occurred, significant damage was observed due to insufficiently designed gap distances for non-uniform seismic movements. This study investigates the effect of gap distance on seismic-induced pounding to minimize the resulting structural damage to bridge components. Nonlinear time history analyses were conducted using the SAP2000 analysis program, based on earthquake records from the earthquakes that occurred in Türkiye in February 2023, for four different gap distances: 3 cm, 6 cm, 9 cm, and 12 cm. The primary objective of this study is to observe how pounding forces vary with different gap distances and to reveal the relationship between these parameters. As a result of analyses conducted using 20 different ground motion records, the threshold PGA values corresponding to the onset of pounding were identified as 0.22 g, 0.24 g, 0.35 g, and 0.42 g for 3 cm, 6 cm, 9 cm, and 12 cm gap distances, respectively. In addition, the threshold PGV values, pounding probabilities, and axial force, shear force, and moment values in columns located at the gaps were also evaluated for each gap configuration.Komşu açıklıklar arasında düzgün bir derz boşluğu sağlanması, depremler sırasında yapısal bileşenler arasında çarpmaya yol açabilir ve çarpma, sismik olaylar sonrasında gözlemlenen hasarların başlıca nedenlerinden biri olarak kabul edilmektedir. Yapılar arasındaki boşluk mesafesi, çarpma olasılığı üzerinde doğrudan etkiye sahiptir. Türkiye’de yakın zamanda meydana gelen ve 11 ili etkileyen büyük depremler sonrasında yapılan incelemelerde, her ne kadar köprü yıkılmaları yaşanmasa da, yapısal olmayan sismik hareketler için yetersiz tasarlanmış boşluk mesafeleri nedeniyle önemli hasarların meydana geldiği gözlemlenmiştir. Bu çalışma, köprü bileşenlerinde meydana gelen yapısal hasarları en aza indirmek amacıyla, deprem kaynaklı çarpmanın üzerindeki etkisini derz boşluğu mesafesine bağlı olarak incelemektedir. Çalışmada, Şubat 2023’te Türkiye’de meydana gelen depremlere ait yer hareketi kayıtları esas alınarak, SAP2000 analiz programında doğrusal olmayan zaman tanım alanında analizler gerçekleştirilmiştir. Analizler, 3 cm, 6 cm, 9 cm ve 12 cm olmak üzere dört farklı boşluk mesafesi için yapılmıştır. Bu çalışmanın temel amacı, farklı boşluk mesafelerinde çarpma kuvvetlerinin nasıl değiştiğini gözlemlemek ve bu parametreler arasındaki ilişkiyi ortaya koymaktır. Yapılan analizler sonucunda, 20 farklı yer hareketi kaydı kullanılarak çarpmanın başladığı eşik PGA değerleri sırasıyla 3 cm, 6 cm, 9 cm ve 12 cm boşluk mesafeleri için 0.22 g, 0.24 g, 0.35 g ve 0.42 g olarak belirlenmiştir. Ayrıca, eşik PGV değerleri, çarpma olasılıkları ve boşlukta yer alan kolonlarda oluşan eksenel kuvvet, kesme kuvveti ve moment değerleri de her bir boşluk konfigürasyonu için değerlendirilmiştir.M.S. - Master of Scienc
The Role of Intergroup Contact and Ethnic Identification in Predicting Acceptance of Primary and Secondary Outgroups Among Majority and Minority Groups
No full textRecent studies have highlighted the importance of intergroup contact and ethnic identification in shaping attitudes toward outgroups. However, not enough consideration has been given to the influence of group status across different settings, as well as how positive attitudes toward one outgroup may translate into other groups (i.e., secondary transfer effect), who are geographically far away from one's own country. This set of studies aims to investigate the roles of both the quality and quantity of contact and ethnic identification in outgroup acceptance. We focus on the same ethnic group in three different contexts: Turks in Turkey (Study 1), Turks in Germany (Study 2a), and Turks in Bulgaria (Study 2b). For majority and minority group members, lower ethnic identification and higher quality of contact with the primary outgroup predicted more acceptance of the secondary outgroups through more acceptance of the primary outgroup. These investigations could facilitate the development of favourable intergroup relationships among minority and majority populations across various settings