Özyeğin University

Topological domains(TADs) are consecutive genomic locations with denser local interactions to a certain extent, and they are important for cellular gene expression control and modulation. TADs were first identified when studying three-dimensional genomic structures over Hi-C interaction datasets. Many studies have focused on developing approaches in inferring TADs, which led to multiple TAD-caller approaches development. On the other hand, the number of RNA interactome datasets, such as RNA-RNA and RNA-DNA interactions, has recently been increasing. Even though TADs have been extensively studied in Hi-C datasets, they have not been studied across these RNA interactomes. We conducted a systematized comparison of 28 TAD-callers across mammalians over RNA-associated interactomes(RAIs), especially RNA-RNA and RNA-DNA interaction datasets at a high resolution. Our findings highlighted the significant enrichment of Cohesin/CTCF proteins at RNA-TAD boundaries for both RNA-RNA and RNA-DNA interactomes, especially those with corner dots, which are similar to the results for original TADs. The sizes and numbers of RNA-TADs vary significantly between different TAD caller approaches and RNA interactome resolution, suggesting the importance of considering RNA-TADs as hierarchical domains rather than distinct intervals. We examined the core principles and assumptions behind TAD-callers over RNA interactomes. To our best knowledge, this is the first time that many TAD inference methods are adapted to infer TAD-like domains on RNAs. Our results provide valuable guidance in selecting the most suitable methods for TAD inference over RNA interactomes.

ABSTRACT Reliability assessment of complex engineering systems is crucial for ensuring safety, performance, and cost‐effectiveness. Traditional reliability models frequently treat failure rates as static and analyze component failure rates in isolation. When dependencies are acknowledged, they are typically considered in a linear manner. This approach, however, fails to adequately capture the dynamic and nonlinear interactions that characterize real‐world systems. This paper proposes a novel reliability modeling framework that integrates dynamic failure rates and nonlinear dependencies to enhance predictive accuracy in reliability analysis. The model considers time‐varying operational and environmental factors that influence failure behavior, along with nonlinear interdependencies among system components, which can amplify risks in unpredictable ways. The proposed framework improves reliability estimation under evolving conditions. To illustrate the implications of the proposed model assumptions, the model is applied on two numerical examples and to demonstrate the impact of the model assumptions, the reliability is compared with the case where these assumptions are not considered. The findings of this research contribute to the advancement of reliability engineering by providing a more comprehensive approach to modeling failures in dynamic, interconnected systems.

The study aims to explore the barriers to accessibility encountered by persons with reduced mobility and persons with disabilities during air travel, and the solutions they propose based on their lived experience. In-depth interviews were conducted with twenty-four participants to examine the ongoing challenges regarding the accessibility of air travel from the perspective of those affected, as well as to gather suggestions for solutions. The findings reveal that numerous barriers persist at various stages of the journey for individuals with diverse needs, while also demonstrating that improvements can be standardized for all locations but tailored to meet the specific needs of each individual. Based on the data, this study introduces two concepts to the literature. One is the cumulative effect of barriers, and the other is standardized flexibility. Thus, this study broadens the perspective on accessibility and advances the current debate.

In this paper, we present new results regarding the orbital stability of solitary standing waves for the general fourth-order Schrödinger equation with mixed dispersion. The existence of solitary waves can be determined both explicitly and by using a numerical approach. These explicit solutions cannot be seen as a smooth curve of solitary waves, and this fact prevents their determination of stability using classical approaches in the current literature. To overcome this difficulty, we employ a numerical approach to construct a smooth curve of solitary waves. The existence of a smooth curve is useful for showing the existence of a threshold power α0 ≈ α4.8 of the nonlinear term such that if α ∈ (0, α0), the explicit solitary wave is stable, and if α > α0, the wave is unstable. An important feature of our work, caused by the presence of the mixed dispersion term, concerns the fact that the threshold value α0 ≈ 4.8 is not the same as that established for proving the existence of global solutions in the energy space, as is well known for the classical nonlinear Schrödinger equation. © (2026), Society for Industrial and Applied Mathematics.

The paper investigates the optimal purchasing and production control policy within a circular production system that processes two returned material types through a shared manufacturing center. Materials are purchased or rejected upon arrival, with differences in procurement cost. At each decision epoch, the system must decide whether to purchase incoming materials and which type to prioritize for production. The problem is formulated as a Markov decision process, and a linear programming approach is developed to compute the optimal purchasing and production policy for the system under both non-preemption and preemption rules. Theoretically, the structure of the optimal policy is analytically characterized under the preemption rule in the case of equal production rates. Numerical experiments reveal that this policy remains optimal or near-optimal for the system under non-preemption and preemption rules with varying production rates. Additionally, comparisons of the optimal policies between non-preemption and preemption rules demonstrate that the system under the preemption rule yields higher average reward than that under the non-preemption rule, to varying degrees depending on system parameters, such as production rate, holding cost, and arrival rate.