Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 5Citation - Scopus: 5A Microrna-Regulated Transcriptional State Defines Intratumoral Cd8+t Cells That Respond To Immunotherapy(Cell Press, 2025) Tang, William W.; Battistone, Ben; Bauer, Kaylyn M.; Weis, Allison M.; Barba, Cindy; Fadlullah, Muhammad Zaki Hidayatullah; O'Connell, Ryan M.The rising incidence of advanced-stage colorectal cancer (CRC) and poor survival outcomes necessitate new and effective therapies. Immune checkpoint inhibitors (ICIs), specifically anti-PD-1 therapy, show promise, yet clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8+ T cell-infiltrated tumors through an unbiased in vivo CRISPR-Cas9 screen identifying functional tumor antigen-specific CD8+ T cell-expressed microRNAs. T cell miR-155 is required for anti-PD-1 responses and for a vital intratumor CD8+ T cell differentiation cascade by repressing Ship-1, inhibiting Tcf-1 and stemness, and subsequently enhancing Cxcr6 expression, anti-tumor immunity, and effector functions. Based on an underlying miR-155-dependent CD8+ T cell transcriptional profile, we identify a gene signature that predicts ICI responses across 12 diverse cancers. Together, our findings support a model whereby miR155 serves as a central regulator of CD8+ T cell-dependent cancer immunity and ICI responses that may be leveraged for future therapeutics.Article Citation - WoS: 2Citation - Scopus: 2The Markers of the Predictive Dna Test for Canine Hip Dysplasia May Have a Stronger Relationship With Elbow Dysplasia(Cell Press, 2024) Ardicli, Sena; Yigitgor, Pelin; Babayev, Huseyn; Ozen, Dogukan; Bozkurt, Berkay; Senturk, Nursen; Intas, Deniz SeyrekCanine hip and elbow dysplasias, which are prevalent orthopedic conditions rooted in developmental and hereditary factors are yet to be comprehensively assessed. This study aimed to address this gap by exploring the prognostic significance of five markers linked to canine hip dysplasia using available genome-wide association studies (GWAS) data. The influence of these markers on both hip and elbow dysplasia was examined in dogs exposed to standardized environmental conditions. We made a groundbreaking discovery using custom primers, qPCR assays, and evaluation of fluorescent resonance energy transfer (FRET) probes. Three specific SNPs previously associated with the risk of canine hip dysplasia demonstrated a potentially stronger correlation with elbow dysplasia. Notably, the SNP at nucleotide position 22691322, located near the canine CHST3 gene, displayed significance as a marker in multivariable logistic regression analysis. Surprisingly, none of the initially targeted SNPs showed a direct association with hip dysplasia. The genomic positions of these SNPs reside within a region conserved across mammals. In silico analyses suggested that the relevant variant might be positioned in a region linked to bone and muscle structures. Our findings revealed a remarkable relationship between SNP2 genotypes and methylation patterns, shedding light on the underlying mechanism that partially explains the genotype-phenotype correlation in canine CHST3. These groundbreaking findings offer essential insights for future, more extensive investigations into canine orthopedic health. This research significantly contributes to our understanding of the molecular foundations of hip and elbow dysplasia in dogs by charting a course for advancements in veterinary medicine and the overall well-being of canine companions.Article Citation - WoS: 2Citation - Scopus: 2Further Developments of the Extended Quadrature Method of Moments To Solve Population Balance Equations(Cell Press, 2023) Turan, Meltem; Dutta, AbhishekDeveloping numerical methods to solve polydispersed flows using a Population Balance Equation (PBE) is an active research topic with wide engineering applications. The Extended Quadrature Method of Moments (EQMOM) approximates the number density as a positive mixture of Kernel Density Functions (KDFs) that allows physical source terms in the PBEs to compute continuous or point-wise form according to the moments. The moment-inversion procedure used in EQMOM has limitations such as the inability to calculate certain roots even if it is defined, absence of consistent result when multiple roots exist or when the roots are nearly equal. To address these limitations, the study proposes a modification of the moment-inversion procedure to solve the PBE based on the proposed Halley-Ridder (H-R) method. Although there is no significant improvement in the extent of variability relative to the mean of the tested shape parameter cr values, an increase in the number of floating point operations (FLOPS) is observed which the proposed algorithm responds in limitations mentioned above. The total number of FLOPS for all the kernels used for the approximation increased by around 30%. This is an improvement towards the development of a more reliable and robust moment-inversion procedure.Article Citation - WoS: 35Citation - Scopus: 36Understanding Radiative Transitions and Relaxation Pathways in Plexcitons(Cell Press, 2021) Finkelstein-Shapiro, Daniel; Mante, Pierre-Adrien; Sarısözen, Sema; Wittenbecher, Lukas; Minda, Iulia; Balcı, Sinan; Pullerits, TonuMolecular aggregates on plasmonic nanoparticles have emerged as attractive systems for the studies of polaritonic light-matter states, called plexcitons. Such systems are tunable, scalable, easy to synthesize, and offer sub-wavelength confinement, all while giving access to the ultrastrong light-matter coupling regime, promising a plethora of applications. However, the complexity of these materials prevented the understanding of their excitation and relaxation phenomena. Here, we follow the relaxation pathways in plexcitons and conclude that while the metal destroys the optical coherence, the molecular aggregate coupled to surface processes significantly contributes to the energy dissipation. We use two-dimensional electronic spectroscopy with theoretical modeling to assign the different relaxation processes to either molecules or metal nanoparticle. We show that the dynamics beyond a few femtoseconds has to be considered in the language of hot electron distributions instead of the accepted lower and upper polariton branches and establish the framework for further understanding.