TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article Symmetric Orthogonalization and Probabilistic Weights in Resource Quantification(Tubitak Scientific & Technological Research Council Turkey, 2026-02-18) Torun, GokhanTransforming nonorthogonal bases into orthogonal ones often compromises essential properties or physical meaning in quantum systems. Here, we demonstrate that Löwdin symmetric orthogonalization (LSO) outperforms the widely used Gram-Schmidt orthogonalization (GSO) in characterizing and quantifying quantum resources, with particular emphasis on coherence and superposition. We employ LSO both to construct an orthogonal basis from a nonorthogonal one and to obtain a nonorthogonal basis from an orthogonal set, thereby mitigating ambiguity related to the basis choice in defining quantum coherence. Unlike GSO, which depends on the ordering of input states, LSO applies a symmetric transformation that treats all vectors equally and minimizes deviation from the original basis. This procedure yields basis sets with enhanced stability, preserving the closest possible correspondence to the original physical states while satisfying orthogonality. Building on LSO, we also introduce Löwdin weights - probabilistic weights for nonorthogonal representations that provide a consistent measure of resource content. We explicitly contrast these with Chirgwin-Coulson weights, demonstrating that Löwdin weights ensure nonnegativity, a prerequisite for information-theoretic measures. These weights further enable the quantification of coherence and the characterization of superposition, providing a degree of superposition as a distinct measure, as well as facilitating the assessment of state delocalization through entropy and participation ratios. Our theoretical and numerical analyses confirm LSO's superior preservation of quantum state symmetry and resource characteristics, underscoring the critical role of orthogonalization methods and Löwdin weights in resource theory frameworks involving nonorthogonal bases.Article Expressions of the Satellite Repeat Hsat5 and Transposable Elements Are Implicated in Disease Progression and Survival in Glioma(Tubitak Scientific & Technological Research Council Turkey, 2024-08-23) Köse, Sıla Naz; Yaraş, Tutku; Bursalı, Ahmet; Oktay, Yavuz; Yandım, Cihangir; Karakulah, GökhanThe glioma genome encompasses a complex array of dysregulatory events, presenting a formidable challenge in managing this devastating disease. Despite the widespread distribution of repeat and transposable elements across the human genome, their involvement in glioma's molecular pathology and patient survival remains largely unexplored. In this study, we aimed to characterize the links between the expressions of repeat/transposable elements with disease progression and survival in glioma patients. Hence, we analyzed the expression levels of satellite repeats and transposons along with genes in low-grade glioma (LGG) and high-grade glioma (HGG). Endogenous transposable elements LTR5 and HERV_a-int exhibited higher expression in HGG patients, along with immune response-related genes. Altogether, 16 transposable elements were associated with slower progression of disease in LGG patients. Conversely, 22 transposons and the HSAT5 satellite repeat were linked to a shorter event-free survival in HGG patients. Intriguingly, our weighted gene coexpression network analysis (WGCNA) disclosed that the HSAT5 satellite repeat resided in the same module network with genes implicated in chromosome segregation and nuclear division; potentially hinting at its contribution to disease pathogenesis. Collectively, we report for the first time that repeat and/or transposon expression could be related to disease progression and survival in glioma. The expressions of these elements seem to exert a protective effect during LGG-to-HGG progression, whereas they could have a detrimental impact once HGG is established. The results presented herein could serve as a foundation for further experimental work aimed at elucidating the molecular regulation of glioma genome.