PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
Browse
38 results
Filters
Settings
Search Results
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: 1The Role of Trna Fragments on Neurogenesis Alteration by H2o2-Induced Oxidative Stress(Springernature, 2025) Karacicek, Bilge; Katkat, Esra; Binokay, Leman; Ozhan, Gunes; Karakulah, Goekhan; Genc, SerminTransfer RNAs (tRNAs) are small non-coding RNA molecules transcribed from tRNA genes. tRNAs cleaved into a diverse population tRNA fragments (tRFs) ranging in length from 18 to 40 nucleotides, they interact with RNA binding proteins and influence the stability and translation. Stress is one of the reasons for tRFs cleavage. In our study, we modeled oxidative stress conditions with hydrogen peroxide (H2O2) exposure and dealt with one of the frequently expressed tRF in the hippocampus region of the brain, which is tRF-Glu-CTC. For this purpose, neural stem cells (NSCs) were exposed to H2O2, and tRF-Glu-CTC levels were increased in various H(2)O(2 )concentrations. A decrease was seen in microtubule-associated protein 2 (MAP2) marker expression. To understand the H(2)O(2)oxidative stress condition on the expression of tRNA fragments, 72 hpf zebrafish embryos exposed to different H(2)O(2 )concentrations, an increase in the level of tRF-Glu-CTC was observed in all concentrations of H(2)O(2 )compared to control. Subsequently, neurogenesis markers were figured out via Calb2a (calbindin 2a) in situ hybridization (ISH) and HuC/D immunofluorescence staining (IF) staining experiments. Under H(2)O(2 )exposure, a decline was observed in Calb2a and HuC/D markers. To understand the inhibitory role of tRF-Glu-CTC on neurogenesis, NSCs were transfected via tRF-Glu-CTC inhibitor, and neurogenesis markers (ss III-tubulin, MAP2, and GFAP) were determined with qRT-PCR and IF staining. tRF-Glu-CTC inhibitor reversed the diminished neuronal markers expression under the exposure of H2O2. Gene Ontology (GO) enrichment analysis showed us that targets of tRF-Glu-CTC are generally related to neuronal function and synaptic processes.Article Citation - WoS: 2Citation - Scopus: 2Exploring the Use of Water-Extracted Flaxseed Hydrocolloids in Three-Dimensional Cell Culture(Mary Ann Liebert, inc, 2024) Yildirim-Semerci, Ozum; Bilginer-Kartal, Rumeysa; Arslan-Yildiz, AhuPlant-derived hydrocolloids offer promising prospects in biomedical applications. Among these, Flaxseed hydrocolloid (FSH) can form a soft, elastic, and biocompatible hydrocolloid with tunable viscosity and superior swelling capacity, making it an attractive scaffold. This study introduces a green extraction method for FSH, employing a single-step aqueous extraction process and fabrication of FSH scaffold. Despite growing interest, the pristine form of FSH has not been investigated for sustainable long-term three-dimensional (3D) cell culture. Here, FSH scaffolds were thoroughly characterized for their morphological, chemical, mechanical, and biological properties. 3D cell culture experiments were conducted using NIH-3T3 mouse fibroblast cells, and cell viability was assessed using live/dead and Alamar Blue assays. High cell viability was sustained for long term compared with 2D cell culture. Cell adhesion and 3D cellular morphology on FSH scaffold for 30 days were monitored by scanning electron microscopy analysis. Also, collagen type-I and F-actin expressions were analyzed by immunostaining after 30 days of culture, resulting in 5- and 4-fold increments of fluorescence intensity, respectively. Results indicate sustained cell viability in the long term and favorable cell-material interaction, demonstrating the potential of FSH as a scaffold. This study emphasizes the importance of the green extraction approach, improving the biocompatibility and functionality of FSH tissue engineering applications. Impact Statement Flaxseed hydrocolloid (FSH) is a promising scaffold for biomedical applications due to its biocompatibility and tunable properties. This study introduces a green extraction method for FSH and evaluates its use in 3D cell culture with NIH-3T3 mouse fibroblast cells. The findings indicate high cell viability and enhanced cell-material interactions over 30 days, highlighting the potential of FSH for tissue engineering.Article Citation - WoS: 1Citation - Scopus: 1Assessment of the Validity and Reliability of Edinburgh Postpartum Depression Scale in Turkish Men(Walter de Gruyter GmbH, 2024) Alkan, C.; Didikoǧlu, A.; Çöme, O.; Yllmaz, B.; Mevsim, V.Objectives: Perinatal depression (PD) affects individuals during pregnancy and early parenthood, resembling major depression. Recent research highlights paternal perinatal depression (PPD) in fathers. PPD has adverse effects on fathers and their children. This study assesses the Turkish version of the Edinburgh Postnatal Depression Scale (EPDS) for Turkish fathers, aiming to provide a tool for PPD identification. Methods: This methodological study validates the EPDS for Turkish fathers and explores associations with demographic and psychosocial factors. The study involved 295 fathers with infants aged 2 weeks to 12 months. The EPDS, originally designed for perinatal depression and validated in Turkish women, was used. Fathers completed a participant information questionnaire, the EPDS, and the Beck Depression Inventory (BDI) during clinic visits. Data on sociodemographic factors, paternal roles, and pregnancy and postpartum support were collected. Mothers also completed the EPDS. Descriptive statistics, exploratory factor analysis, confirmatory factor analysis, and correlation tests were used. Results: The study included fathers with an average age of 30.5 years, mostly with a high school education or higher. The EPDS had a mean total score of 3.1. Factor analysis suggested a three-factor structure for the EPDS in Turkish fathers, including anhedonia, anxiety, and depression. Confirmatory factor analysis validated the three-factor structure, with acceptable model fit indices. Positive correlations were found between fathers' EPDS scores, maternal EPDS scores, and paternal BDI scores. The EPDS effectively discriminated between different levels of depression severity. Various factors, such as education level and lack of support during pregnancy and after childbirth, were associated with higher EPDS scores. Conclusions: These findings emphasize the significance of assessing and addressing PPD in fathers, supporting the use of the EPDS as a valid tool in the Turkish context. The three-factor structure aligns with international research, highlighting the importance of a multi-dimensional approach to PPD assessment. Early intervention can mitigate PPD's impact on fathers, mothers, and children, benefiting mental health and well-being. © 2024 Walter de Gruyter GmbH, Berlin/Boston.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: 4Citation - Scopus: 4Ultra-Thin Double-Layered Hexagonal Cui: Strain Tunable Properties and Robust Semiconducting Behavior(Iop Publishing Ltd, 2024) Demirok, A. C.; Sahin, H.; Yagmurcukardes, M.In this study, the freestanding form of ultra-thin CuI crystals, which have recently been synthesized experimentally, and their strain-dependent properties are investigated by means of density functional theory calculations. Structural optimizations show that CuI crystallizes in a double-layered hexagonal crystal (DLHC) structure. While phonon calculations predict that DLHC CuI crystals are dynamically stable, subsequent vibrational spectrum analyzes reveal that this structure has four unique Raman-active modes, allowing it to be easily distinguished from similar ultra-thin two-dimensional materials. Electronically, DLHC CuI is found to be a semiconductor with a direct band gap of 3.24 eV which is larger than that of its wurtzite and zincblende phases. Furthermore, it is found that in both armchair (AC) and zigzag (ZZ) orientations the elastic instabilities occur over the high strain strengths indicating the soft nature of CuI layer. In addition, the stress-strain curve along the AC direction reveal that DLHC CuI undergoes a structural phase transition between the 4% and 5% tensile uniaxial strains as indicated by a sudden drop of the stress in the lattice. Moreover, the phonon band dispersions show that the phononic instability occurs at much smaller strain along the ZZ direction than that of along the AC direction. Furthermore, the external strain direction can be deduced from the predicted Raman spectra through the splitting rates of the doubly degenerate in-plane vibrations. The mobility of the hole carriers display highly anisotropic characteristic as the applied strain reaches 5% along the AC direction. Due to its anomalous strain-dependent electronic features and elastically soft nature, DLHC of CuI is a potential candidate for future electro-mechanical applications.Article Citation - WoS: 7Citation - Scopus: 8Investigation of Stair Ascending and Descending Activities on the Lifespan of Hip Implants(Elsevier Sci Ltd, 2024) Alpkaya, Alican Tuncay; Yilmaz, Mehmet; Sahin, Ahmet Mert; Mihcin, SenayTotal hip arthroplasty (THA) surgeries among young patients are on the increase, so it is crucial to predict the lifespan of hip implants correctly and produce solutions to improve longevity. Current implants are designed and tested against walking conditions to predict the wear rates. However, it would be reasonable to include the additional effects of other daily life activities on wear rates to predict convergent results to clinical outputs. In this study, 14 participants are recruited to perform stair ascending (AS), descending (DS), and walking activities to obtain kinematic and kinetic data for each cycle using marker based Qualisys motion capture (MOCAP) system. AnyBody Modeling System using the Calibrated Anatomical System Technique (CAST) full body marker set are performed Multibody simulations. The 3D generic musculoskeletal model used in this study is a markerbased full-body motion capture model (AMMR,2.3.1 MoCapModel) consisting of the upper extremity and the Twente Lower Extremity Model (TLEM2). The dynamic wear prediction model detailing the intermittent and overall wear rates for CoCr-on-XLPE bearing couple is developed to investigate the wear mechanism under 3D loading for AS, DS, and walking activities over 5 million cycles (Mc) by using finite element modelling technique. The volumetric wear rates of XLPE liner under AS, DS, and walking activities over 5-Mc are predicted as 27.43, 23.22, and 18.84 mm3/Mc respectively. Additionally, the wear rate was predicted by combining stair activities and gait cycles based on the walk-to-stair ratio. By adding the effect of stair activities, the volumetric wear rate of XLPE is predicted as 22.02 mm3/Mc which is equivalent to 19.41% of walking. In conclusion, in this study, the effect of including other daily life activities is demonstrated and evidence is provided by matching them to the clinical data as opposed to simulator test results of implants under ISO 14242 boundary conditions.