PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
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Article Citation - WoS: 7Citation - Scopus: 9A Holistic Overview of the Applications of Grace-Observed Terrestrial Water Storage in Hydrology and Climate Science(Springer, 2025) Khorrami, Behnam; Gunduz, OrhanTerrestrial Water Storage (TWS) represents a vital element of the hydrological cycle, with its fluctuations significantly impacting the climate of the Earth and its ecological balance. Since its launch in 2002, the Gravity Recovery and Climate Experiment (GRACE) satellite mission has revolutionized the ability to observe and analyze large-scale mass changes within Earth's system components. This paper offers a comprehensive and current overview of GRACE satellite gravimetry, highlighting its relevance to hydrological and climate-related studies. It outlines the fundamental measurement principles of the GRACE mission, provides an in-depth explanation of GRACE data products (including spherical harmonic and mascon solutions), examines emerging trends in GRACE-based research, and reviews key applications in hydrology and climate science. Additionally, it addresses the major challenges in utilizing GRACE data and explores promising avenues for future research and applications.Article Biologically Informed Decision-Making for PMRT in PT3N0M0 Luminal Breast Cancers (Protocol MF22-02): International Multicenter Real-World Data(Cig Media Group, Lp, 2025) Soran, Atilla; Gultekin, Melis Bahadir; Venkatesulu, Bhanu Prasad; Barry, Parul Nafees; King, Caleb; Bhargava, Rohit; Vargo, John AustinTwo hundred and 2 women from 16 centers with pT3N0M0 hormone receptor (HR) positive, HER2 negative BC who underwent mastectomy were retrospectively analyzed. Patients were divided into 2 groups: PMRT (n = 130) and no PMRT (n = 69). Groups were compared in terms of overall survival (OS), loco-regional recurrence (LRR) rate, and distant metastases (DM) in light of Magee Equations Score (MS). At a median follow-up of 51.3 months for the no PMRT group and 65.9 months for the PMRT group (P =.041), 9% (n = 6) of patients from the no PMRT group and 2% (n = 3) from the PMRT group developed LRR (P = 0.047). There was no difference in local recurrence (1% in no PMRT group vs. 2% in PMRT group; P =.7) and distant recurrence (7% in no PMRT group vs. 3% in PMRT group; P =.16) in patients who received PMRT and no PMRT. Further comparison of the LRR in the no PMRT and PMRT groups in patients with an MS < 18 did not show a significant difference (3% vs. 4%; P =.64). However, among patients with an MS >= 18, no PMRT group had a higher LRR rate compared to the PMRT group (11% vs. 2%; P =.01). In patients with an MS >= 18, the administration of PMRT correlates with statistically significantly better LRR-free survival (HR 0.19; 95% CI 0.05-0.79; P =.02). Patients with MS <18 experience a comparable rate of recurrence irrespective of PMRT, while those with MS >= 18 have higher rates of LRR and thus should not omit PMRT. Background: Current guidelines do not list definitive recommendations for postmastectomy radiation therapy (PMRT) in patients with luminal pT3N0M0 breast cancer (BC). Increased data suggests de-escalation of radiation therapy (RT) in genomically defined biologically favorable luminal BCs. The goal of this study is to determine whether PMRT can be safely omitted for this specific subgroup of patients. Methods and materials: Two hundred and 2 women from 16 centers with pT3N0M0 hormone receptor (HR) positive, HER2 negative BC who underwent mastectomy were retrospectively analyzed. No patients received neoadjuvant chemotherapy. Three patients were excluded because of positive surgical margins. Patients were divided into 2 groups: PMRT (n = 130) and no PMRT (n = 69). Groups were compared in terms of overall survival (OS), loco-regional recurrence (LRR) rate, and distant metastases (DM) in light of the Magee Equations Score (MS), menopausal status/age, axillary surgery, pathology, lymphovascular invasion (LVI), adjuvant chemotherapy, and adjuvant endocrine therapy. Results: The majority of the patients had invasive ductal carcinoma (49%, n = 98). There was no significant difference regarding tumor size, axillary surgery, and adjuvant endocrine therapy between the 2 groups (P =.82, P =.28, P =.12, respectively). LVI was 19% (n = 39), and it was greater in the PMRT group (25% vs. 10%; P =.01). Patients in the PMRT group received more chemotherapy (66% vs. 30%; P <.001), had more grade 3 tumors (28% vs. 9%, P =.005), and were more premenopausal (49% vs. 22%; P =.0001). At a median follow-up of 51.3 months for the no PMRT group and 65.9 months for the PMRT group (P =.041), 9% (n = 6) of patients from the no PMRT group and 2% (n = 3) from the PMRT group developed LRR (P =.047). There was no difference in local recurrence (1% in no PMRT group vs. 2% in PMRT group; P =.7) and distant recurrence (7% in no PMRT group vs. 3% in PMRT group; P =.16) in patients who received PMRT and no PMRT. Further comparison of the LRR in the no PMRT and PMRT groups in patients with an MS < 18 did not show a significant difference (3% vs. 4%; P =.64). However, among patients with an MS >= 18, no PMRT group had a higher LRR rate compared to the PMRT group (11% vs. 2%; P =.01). In patients with an MS >= 18, the administration of PMRT correlates with statistically significantly better LRR-free survival (HR 0.19; 95% CI 0.05-0.79; P =.02). Conclusions: Our findings imply that when considering PMRT for patients with pT3N0M0, HR-positive, and HER2-negative BC, clinicians can benefit from a combination of pathological risk factors and recurrence prediction models. Patients with MS < 18 experience a comparable rate of recurrence irrespective of PMRT, while those with MS >= 18 have higher rates of LRR and thus should not omit PMRT. (c) 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.Article Influence of Soil Characteristics on the Phytochemistry of Evergreen Ivy (Hedera Helix L.) Leaves in Deciduous Forests(Wiley-v C H verlag Gmbh, 2025) Yildirim, Elif Begum; Ozer, Gulcin; Sen, Nisa Beril; Ozdemir, Emrah; Makineci, Ender; Ozdemir, Durmus; Guzelmeric, EtilThe evergreen ivy (Hedera helix L.), traditionally used to treat respiratory conditions, contains triterpene saponins, primarily hederacoside C, and various phenolic compounds. This study investigated the relationships between the chemical composition of ivy leaves and their natural growing conditions (moisture, temperature, pH, and electrical conductivity of soil). Ivy leaves were collected monthly over 1 year from oak and beech forests. Hederacoside C, rutin, chlorogenic acid (ChA), neoChA, 4,5-dicaffeoylquinic acid (DCQA), and 3,5-DCQA were analyzed by high-performance thin-layer chromatography (HPTLC) and high-performance liquid chromatography (HPLC). Soil parameter data, along with the quantitative HPLC results of ivy leaves, were first subjected to bivariate analysis, which revealed significant correlations, particularly between soil moisture, soil temperature, and the chemical composition of ivy leaves. In addition, ivy samples were classified and clustered based on seasons by principal component analysis (PCA) and hierarchical cluster analysis (HCA), regardless of their collection sites. Digitized HPTLC chromatograms were evaluated by PCA and partial least squares discriminant analysis (PLS-DA) analyses; PCA enabled the grouping of ivy leaves based on their collection sites, and PLS-DA categorized the samples by seasons. The evaluation of the relationships between the phytochemistry of ivy leaves and their natural growing conditions has been reported for the first time.Article Citation - WoS: 1Citation - Scopus: 1Imbalance in Redox Homeostasis Is Associated With Neurodegeneration in the Murine Model of Tay-Sachs Disease(Springer, 2025) Basirli, Hande; Ates, Nurselin; Seyrantepe, VolkanBackgroundTay-Sachs disease is a neurodegenerative disorder characterized by a build-up of GM2 ganglioside in the brain, which results in progressive central nervous system dysfunction. Our group recently generated Hexa-/-Neu3-/- mice, a murine model with neuropathological abnormalities similar to the infantile form of Tay-Sachs disease. Previously, we reported progressive neurodegeneration with neuronal loss in the brain sections of Hexa-/-Neu3-/- mice. However, the relationship between the severity of neurodegeneration and the imbalance in redox homeostasis was not yet clarified in Hexa-/-Neu3-/- mice. Here, we evaluated whether neurodegeneration is associated with oxidative stress in the tissues and cells of Hexa-/-Neu3-/- mice and neuroglia cells from Tay-Sachs patients.Methods and resultsCell death and oxidative stress-related markers were evaluated in four brain regions and fibroblasts of 5-month-old WT, Hexa-/-, Neu3-/-, and Hexa-/-Neu3-/- mice and human neuroglia cells using Western blot, RT-PCR, and immunohistochemistry analyses. We further analyzed oxidative stress levels in the samples using flow cytometry analyses. We discovered neuronal death, alterations in intracellular ROS levels, and damaging effects of oxidative stress, especially in the cerebellum and fibroblasts of Hexa-/-Neu3-/- mice.ConclusionsOur results showed that alteration in redox homeostasis might be related to neurodegeneration in the murine model of Tay-Sachs Disease. These findings suggest that targeting the altered redox balance and increased oxidative stress might be a rational therapeutic approach for alleviating neurodegeneration and treating Tay-Sachs disease.Review Citation - WoS: 1Citation - Scopus: 2Organ-On Platforms for Drug Development, Cellular Toxicity Assessment, and Disease Modeling(Tubitak Scientific & Technological Research Council Turkey, 2024) Khurram, Muhammad Maaz; Cinel, Gokturk; Yesil Celiktas, Ozlem; Bedir, ErdalOrgans-on-chips (OoCs) or microphysiological platforms are biomimetic systems engineered to emulate organ structures on microfluidic devices for biomedical research. These microdevices can mimic biological environments that enable cell-cell interactions on a small scale by mimicking 3D in vivo microenvironments outside the body. Thus far, numerous single and multiple OoCs that mimic organs have been developed, and they have emerged as forerunners for drug efficacy and cytotoxicity testing. This review explores OoC platforms to highlight their versatility in studies of drug safety, efficacy, and toxicity. We also reflect on the potential of OoCs to effectively portray disease models for possible novel therapeutics, which is difficult to achieve with traditional 2D in vitro models, providing an essential basis for biologically relevant research.Article Citation - WoS: 3Citation - Scopus: 3Β-Ketoenamine-linked covalent organic framework for efficient iodine capture(Tubitak Scientific & Technological Research Council Turkey, 2024) Büyükçakır, OnurExploring the materials that effectively capture radioactive iodine is crucial in managing nuclear waste produced from nuclear power plants. In this study, a β-ketoenamine-linked covalent organic framework (bCOF) is reported as an effective adsorbent to capture iodine from both vapor and solution. The bCOF’s high porosity and heteroatom-rich skeleton offer notable iodine vapor uptake capacity of up to 2.51g $g^{–1}$ at 75 °C under ambient pressure. Furthermore, after five consecutive adsorption-desorption cycles, the bCOF demonstrates high reusability performance with significant iodine vapor capacity retention. The adsorption mechanism was also investigated using various ex situ structural characterization techniques, and these mechanistic studies revealed the existence of a strong chemical interaction between the bCOF and iodine. The bCOF also showed good iodine uptake performance of up to 512 mg $g^{–1}$ in cyclohexane with high removal efficiencies. The bCOF’s performance in adsorbing iodine from both vapor and solution makes it a promising material to be used as an effective adsorbent in capturing radioactive iodine emissions from nuclear power plants.Article Citation - WoS: 1Citation - Scopus: 1Canine Oocyte Nuclear Maturation With Nano-Ozone (nzs) Supplementation: the Alterations of Antioxidant, and Oxidant Status and Cdk1, Cyclin B1 Expressions(Elsevier, 2024) Bari, O.; Sabanci, A. U.; Avci, G.; Bozkurt, B.; Ustuner, B.; Denk, B.; Ozalp, G. R.This study aims to evaluate the effects of nano-ozone solution (NZS) on canine oocyte nuclear maturation, associated with the alterations of antioxidant and oxidant status and cyclin-dependent kinase 1 (CDK1), cyclin B1 gene expressions. Oocytes were cultured in four distinct concentrations of NZS (0.5, 1, 2, and 5 mu g/mL) and parthenogenetically activated. The rates of oocytes arrested at the Germinal Vesicle (GV), Germinal Vesicle Breakdown (GVBD), Metaphase I (MI), and Metaphase II (MII) stages were statistically different among groups (P < 0.05). The oocytes cultured in 1 <mu>g/mL NZS yielded the best oocyte maturation rate at the MI and MII stages; however, the lowest maturation and high degeneration rates were observed in Group E. The measurements of Malondialdehyde (MDA), reduced Glutathione (GSH), Superoxide Dismutase (SOD), and Ferric Reducing/Antioxidant Power assay (FRAP) were performed from IVM culture media. No statistical difference was observed in SOD and MDA results (P > 0.05). GSH levels were statistically significant between Group AGroup E (p = 0.003), Group B-Group E (p = 0.045), and Group E-Group D (p = 0.021). The culture media in Group D and Group E had high FRAP concentrations and significantly differed between groups (P < 0.05). CDK1, and cyclin B1 genes, which are subunits of maturation-promoting factor (MPF), are upregulated in Group B and Group C, while are downregulated in oocytes of Group E. This study showed that low, controlled doses of NZS (1 <mu>g/mL) supplementation could improve the meiotic competence of canine oocytes and lead to positive response in expressions of CDK1 and cyclin B1 on the gene level.Article Citation - WoS: 2Citation - Scopus: 2Prediction of Single-Layer Antimony Oxyselenide (sb2o2se2): Metal-To Transition Via Hydrogenation(2024) Bozkurt,Y.; Cetin,Z.; Yagmurcukardes,M.In this study, the structural, electronic, vibrational, and mechanical properties of single-layer Antimony Oxyselenide (Sb2O2Se2) and its hydrogenated structure (Sb2O2Se2H2) are investigated by performing density functional theory-based first principles calculations. Geometry optimizations reveal that single-layer Sb2O2Se2crystallizes in tetragonal structure which is shown to possess dynamical stability by means of phonon band dispersions. In addition, the mechanical stability of the predicted single layer is satisfied via the linear-elastic parameters. Electronically, it is revealed that single-layer Sb2O2Se2exhibits metallic behavior whose highest occupied states are found to arise from the surface Se atoms, may be an indication for tuning the electronic features via surface functionalization. For the surface modification of Sb2O2Se2, top of each Se atom is saturated with a H atom and fully hydrogenated single-layer Sb2O2Se2H2is shown to be an in-plane anisotropic structure. Phonon band dispersion calculations indicate the dynamical stability of Sb2O2Se2H2. Mechanically stable Sb2O2Se2H2is found to possess anisotropic linear-elastic behavior, which is much softer than its pristine structure. Moreover, electronically a metallic-to-semiconducting transition is shown to occur as the unoccupied Se-orbitals are saturated via H atoms. Our work offers insights into prediction of a novel single-layer material, namely Sb2O2Se2, and reports the chemically-driven semiconducting behavior via hydrogenation, which may lead to the use of hydrogenated structure in solar cell, photoelectrode, or photocatalyst applications owing to its suitable band gap. © 2024 IOP Publishing Ltd.Article Citation - WoS: 5Citation - Scopus: 8Textural, Rheological, Melting Properties, Particle Size Distribution, and Nmr Relaxometry of Cocoa Hazelnut Spread With Inulin-Stevia Addition as Sugar Replacer(John Wiley and Sons Inc, 2024) Berk,B.; Cosar,S.; Mazı,B.G.; Oztop,M.H.This study investigated the influence of substituting 60, 80, and 100% of the sugar in traditional cocoa hazelnut paste (control) formulation with inulin-stevia (90:10, w/w) mixture on textural and rheological characteristics, melting behavior, water activity (aw), particle size distribution (PSD), and color. Textural, rheological, melting properties, and color of samples were analyzed after 1, 2, and 3 months of storage at 11°C. Nuclear magnetic resonance (NMR) relaxometry experiments were also performed to understand the interaction of new ingredients with oil. Replacement of sugar with inulin-stevia gave darker color, reduced Casson yield stress, and changed the textural parameters and melting profile of the samples depending on the level but did not create a remarkable effect on PSD and Casson plastic viscosity. Increasing inulin-stevia content yielded lower aw and higher T2a values indicating decreased mobility of water. Complete removal of sugar caused low spreadability. The results showed that an 80% replacement level yielded a product with similar textural parameters and fat-melting mouth feeling compared to control sample. Cocoa hazelnut spreads prepared with inulin and stevia showed good textural stability during storage. © 2024 The Authors. Journal of Texture Studies published by Wiley Periodicals LLC.Article Citation - WoS: 3Citation - Scopus: 4Patient-Specific Finite Element Analysis for Assessing Hip Fracture Risk in Aging Populations(Iop Publishing Ltd, 2024) Chethan, K. N.; Waldschmidt, Nadine Schmidt Genannt; Corda, John Valerian; Shenoy, Satish B.; Shetty, Sawan; Keni, Laxmikant G.; Mihcin, SenayThe femur is one of the most important bone in the human body, as it supports the body's weight and helps with movement. The aging global population presents a significant challenge, leading to an increasing demand for artificial joints, particularly in knee and hip replacements, which are among the most prevalent surgical procedures worldwide. This study focuses on hip fractures, a common consequence of osteoporotic fractures in the elderly population. To accurately predict individual bone properties and assess fracture risk, patient-specific finite element models (FEM) were developed using CT data from healthy male individuals. The study employed ANSYS 2023 R2 software to estimate fracture loads under simulated single stance loading conditions, considering strain-based failure criteria. The FEM bone models underwent meticulous reconstruction, incorporating geometrical and mechanical properties crucial for fracture risk assessment. Results revealed an underestimation of the ultimate bearing capacity of bones, indicating potential fractures even during routine activities. The study explored variations in bone density, failure loads, and density/load ratios among different specimens, emphasizing the complexity of bone strength determination. Discussion of findings highlighted discrepancies between simulation results and previous studies, suggesting the need for optimization in modelling approaches. The strain-based yield criterion proved accurate in predicting fracture initiation but required adjustments for better load predictions. The study underscores the importance of refining density-elasticity relationships, investigating boundary conditions, and optimizing models through in vitro testing for enhanced clinical applicability in assessing hip fracture risk. In conclusion, this research contributes valuable insights into developing patient-specific FEM bone models for clinical hip fracture risk assessment, emphasizing the need for further refinement and optimization for accurate predictions and enhanced clinical utility.