Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
Browse
539 results
Search Results
Article Making Hierarchically Aware Decisions on Short Findings for Automatic Summarisation(Elsevier, 2025) Inan, EmrahAn impression in a typical radiology report emphasises critical information by providing a conclusion and reasoning based on the findings. However, the findings and impression sections of these reports generally contain brief texts, as they highlight crucial observations derived from the clinical radiograph. In this scenario, abstractive summarisation models often experience a degradation in performance when generating short impressions. To address this challenge in the summarisation task, our work proposes a method that combines well-known fine-tuned text classification and abstractive summarisation language models. Since fine-tuning a language model requires an extensive, well-defined training dataset and is a time-consuming task dependent on high GPU resources, we employ prompt engineering, which uses prompt templates to programme language models and improve their performance. Our method first predicts whether the given findings text is normal or abnormal by leveraging a fine-tuned language model. Then, we apply a radiology-specific BART model to generate the summary for abnormal findings. In the zero-shot setting, our method achieves remarkable results compared to existing approaches on a real-world dataset. In particular, our method achieves scores of 37.43 for ROUGE-1, 21.72 for ROUGE-2, and 35.52 for ROUGE-L.Article Citation - Scopus: 1Adulteration of Pomegranate Molasses With Sugar Syrups: Application of FTIR-ATR Spectroscopy and Chemometrics(Elsevier, 2025) Kilinc, Gizem Simge; Uncu, Oguz; Eren, Ismail; Bagdatlioglu, NerimanIn this study, it was aimed to determine the adulteration ratio of pomegranate molasses (PM) with sugar syrups by using FTIR spectroscopy based upon chemometrics. With this intention, 34 pure PM samples were supplied from local manufacturers and adulterated with high fructose corn syrup (HFCS), glucose-fructose syrup (GFS) and beet sugar syrup (BSS) in varying ratios (5-50 %, w/w). Authentic and adulterated PM samples were analyzed in the range of 4000 and 400 cm(-1) wavenumber by FTIR spectroscopy. PCA was applied as a pretreatment for classification and regression analysis to select the spectral region and data reduction. Whereby the DD-SIMCA models were created using this information. The adulterated and authentic samples were classified correctly by the developed DD-SIMCA models. In the calibration and prediction model of DD-SIMCA, authentic and adulterated PM samples were correctly classified with high sensitivity (>= 0.91) and specificity (>= 0.94), and a clear distinction was observed with high efficiency (>= 0.94). Adulteration rates in PM samples were determined by PLS-R analysis. The correlation coefficients (R-2 >= 0.98) of models were also found quite high. As a consequence, FTIR spectroscopy in conjunction with chemometric approaches could be applied as a quick, dependable, non-destructive, and environmentally friendly tool for categorizing, distinguishing, and quantifying adulteration rates in PM samples.Article Citation - WoS: 3Citation - Scopus: 3Design, Synthesis, Characterization and Biological Evaluation of Cobalt-Ferrite Nanoparticles for Biomedical Applications(Elsevier, 2025) Esmer, Ecem Fatma; Bilgi, Eyup; Dincay, Selin Cesmeli; Sakalli, Tugce; Karakus, Ceyda OkselCobalt-Ferrite nanoparticles (CF NPs) are increasingly used in biomedical applications due to their unique magnetic properties and biocompatibility. In this study, CF NPs were synthesized via co-precipitation, both in the presence and absence of oleic acid (OA) as a surfactant. Plackett-Burman Design was employed to study the influence of reaction conditions on the particle size distribution of bare and OA-coated CF NPs. Representative bare and OA-coated CF NP samples were characterized for morphology, composition, thermal stability, and optical and magnetic properties using TEM, XRD, FTIR, TGA, UV-Vis, and VSM. The highest saturation magnetization value (similar to 44 emu/g) was observed for bare CF NPs of smaller sizes. MTT assay results indicated that none of the tested samples showed significant cytotoxicity at the concentrations tested (1, 10, and 100 mu g/mL), except for the bare CF NPs, which reduced viability of A549 cells to approximately 50 % following 72-hour exposure at 100 mu g/mL. Following incubation in a cell culture medium for 48 h, proteins bound to the surface of CF NPs were analyzed using SDS-PAGE, revealing bovine serum albumin, apolipoprotein A-I and fibronectin as the most abundant proteins across samples. Overall, OA-coating slightly improved colloidal stability and reduced cytotoxicity, without significantly compromising the magnetic or protein-binding properties.Article Citation - WoS: 1Citation - Scopus: 1High-Performance Polyether Sulfone (PES) Membranes Modified With Sunflower Seed Shell-Derived Activated Carbon (SSAC)@zif-11 Nanoparticles for Enhanced Antibiotic Removal and Antifouling Properties(Elsevier, 2025) Alafi, Narges Mortazazad; Barzegar, Behrad; Habibi, Rezvan; Aghdasinia, Hassan; Altinkaya, Sacide Alsoy; Barzegar, B.This study investigates the impact of incorporating a novel composite filler on the antibiotic removal efficiency and protein fouling resistance of polyether sulfone (PES) membranes. The filler was synthesized from activated carbon derived from sunflower seed shells (SSAC) and modified with zeolitic imidazolate framework-11 (ZIF-11). The adsorption capacities of the composite for two model antibiotics, tetracycline (TC) and rifampicin (RP), were evaluated. Mixed matrix membranes were fabricated using the phase inversion method with varying SSAC@ZIF11 contents (0.2-1 wt%). The membrane containing 0.8 wt% SSAC@ZIF-11 exhibited improved structural and surface characteristics, including increased porosity, larger pore size, smoother morphology, and enhanced hydrophilicity, as reflected by a reduction in contact angle from 60.72 degrees to 46.45 degrees. At this optimal loading, the pure water flux increased significantly from 10.52 to 39.1 L/m2h. Moreover, the modified membrane demonstrated outstanding removal efficiencies for TC (99.12 %) and RP (89.9 %), alongside excellent antifouling performance, as indicated by a flux recovery ratio increase from 42.85 % to 99.74 %. These results confirm the potential of SSAC@ZIF-11 as an effective nanofiller for developing high-performance PES membranes in advanced water purification applications.Article Synthesis, Characterization, Crystal Structure, Electrochemical and Photoluminescence Properties, Dft and Molecular Docking Studies, and Antimicrobial Activities of Two Mononuclear Nickel (II) Complexes With Pyrazole-Derived Ligands(Elsevier, 2025) Amin, Mina A.; Diker, Halide; Sahin, Onur; Varlikli, Canan; Soliman, Ahmed A.Two octahedral nickel complexes; [Ni(fdtp)2(DMF)2] (1) and [Ni(dcdtp)2(DMF)2] (2), based on 4-((3-fluorophenyl)diazenyl)-3-(trifluoromethyl)-1H-pyrazol-5-ol (fdtp) and 4-((2,4-dichlorophenyl)diazenyl)-3-(trifluoromethyl)-1H-pyrazol-5-ol (dcdtp) were synthesized. The complexes were characterized spectroscopically (FTIR, UV-Vis, Photoluminescence), Mass spectrometry, elemental analyses, electrochemically, thermally, and through Single-crystal X-ray investigations. The formation of the complexes was confirmed by the existence of Ni-O and Ni-N vibrations at bonds were observed as weak bands at 526-497 and 470-438 cm-1. According to the thermogravimetric analyses, the complexes were thermally stable and had relatively high activation energies (585.81 and 730.07 kJ mol-1 for 1, and 2, respectively). Cyclic voltammograms showed that the anodic potential region of 1 and 2 exhibited two irreversible oxidation peaks at 1.34 V &1.55 V and 1.41 V & 1.63 V, respectively, attributed to metal-localized oxidation. The complexes showed enhanced antibacterial activities compared to free ligands and comparable to the standard. The inhibition zones exhibited via 1 were about 21.7, 19.3, and 26.7 mm versus Escherichia coli (E. coli), Staphylococcus aureus (S. Aureus), and Bacillus Subtits (B. Subtits), respectively. Docking studies supported the antibacterial investigations; the binding energies of the complexes were -8.81 and -9.69 kcal/mol for 1 and 2 respectively, against E. coli (PDB ID: 6F86).Article Citation - WoS: 2Citation - Scopus: 2Speciation of Inorganic and Organometallic Arsenic in Various Matrices With a Novel Spme Fiber Functionalized With Iron Nanoparticles Prior To Lc-Icp Determination(Elsevier, 2025) Boyaci, Ezel; Cagir, Ali; Shahwan, Talal; Eroglu, Ahmet E.A novel SPME-LC-ICP-MS methodology is described for the simultaneous microextraction/speciation/determination of the metabolically critical inorganic and organoarsenic species, namely, As(III), As(V), dimethylarsinic acid (DMA), and monomethylarsonic acid (MMA) in natural waters such as drinking and geothermal waters, and biological fluids such as urine. The novelty of the study stems also from the use of home-made SPME fibers for the extraction process, and from the proposed methodology needing no derivatization step. SPME fibers were prepared with in-tube capillary template approach through the immobilization of iron nanoparticles into agarose matrix. The fibers demonstrated reproducible extraction (<10 % RSD), good mechanical strength and good solvent resistivity. The separation of the analytes was realized by HPLC with a strong anion exchange column via gradient elution using different concentrations of (NH4)(2)CO3 (pH 8.50), and the on-line detection of eluted analytes was achieved by ICP-MS. The validity of the proposed methodology was verified via the analysis of certified reference materials (SRM 1643e, Natural Water-Trace Elements, and SRM 2669, Arsenic Species in Frozen Human Urine) and through spike recovery tests. The values of percentage recovery for SRM 2669 were 90.7 % for As(III), 99.8 % for As(V), 93.6 % for DMA, and 85.9 % for MMA. A good correlation was also found between the certified (60.45 mu gL(-1)) and determined (59.00 mu gL(-1)) values for SRM 1643e. Moreover, the speciation capability of the method was demonstrated on various natural waters and biological fluids.Article Plasma Proteomic Markers of Interleukin-1β Pathway Associated With Incident Age-Related Macular Degeneration in Persons With Aids(Elsevier, 2025) Hunt, Peter W.; Olshen, Adam B.; Murad, Natalia; Ambayec, Gabrielle C.; Sezgin, Efe; Schneider, Michael F.; Jabs, Douglas A.Objective To evaluate the associations of plasma inflammatory proteins with age-related macular degeneration (AMD) in persons with the AIDS, using a discovery-based proteomics approach. Design A nested case-control study (analysis 1) and nested cohort study (analysis 2). Participants Persons with AIDS enrolled in the Longitudinal Study of the Ocular Complications with AIDS (LSOCA). Methods Cryopreserved plasma specimens obtained at baseline were assayed for inflammatory proteins using the Olink Inflammation Explore Panel 1. In analysis 1, baseline proteomic profiles for 26 persons with AIDS and incident intermediate-stage AMD 5 to 10 years after baseline and 49 matched controls (matched for age, biologic sex, race/ethnicity, and follow-up) without AMD were compared. In analysis 2, 475 persons from LSOCA with baseline plasma inflammatory proteomic profile measurements were followed for incident cataract and mortality. Main Outcome Measures Incident intermediate-stage AMD; incident cataract; and mortality. Results Of 365 measurable plasma inflammatory proteins, 118 (32%) were associated with incident intermediate-stage AMD at the false discovery rate-adjusted Q < 0.05 level after adjustment for smoking, CD4+ T count, and plasma human immunodeficiency virus RNA level. Gene ontology pathway enrichment analysis identified the interleukin (IL)-1 beta pathway and wound healing pathways, including tissue inhibitor of metalloproteinase 3, as significantly associated with incident AMD. These associations were qualitatively different from those associated with incident cataracts, where elevated levels of inflammatory proteins were associated with a decreased risk of cataracts. A much broader number of inflammatory pathways, including those related to the adaptive immune system, were associated with mortality. Conclusions Upregulation of the IL-1 beta pathway appears to be associated with an increased risk of incident AMD in persons with AIDS. Given the availability of inhibitors of this pathway, inhibition of the IL-1 beta pathway may provide a therapeutic avenue for treatment of AMD. Financial Disclosure(s) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article. Ophthalmology Science 2025;5:100794 (c) 2025 by the American Academy of Ophthalmology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Article Ti-Cu Dry Electrodes for Biomedical Sensing: Tribocorrosion Performance Under Simulated Skin Conditions(Elsevier, 2025) Alves, A. C.; Lopes, C.; Camarinha, A.; Geraldo, D.; Toptan, F.; Ferreira, A.; Vaz, F.Monitoring electromyographic (EMG) activity is crucial for diagnosing musculoskeletal disorders and understanding neuromuscular systems. Dry electrodes represent a significant advancement over traditional wet electrodes by eliminating the need for gels, thereby extending lifespan, simplifying skin preparation, and facilitating prolonged remote monitoring. However, challenges such as higher impedance and susceptibility to motion artifacts, along with issues of user discomfort and signal distortion, persist with existing metal-coated or entirely metal dry electrodes. This study explores an alternative approach using Ti-Cu thin films deposited on polymeric substrates to enhance electrical, electrochemical, and tribo-electrochemical properties. The research specifically investigates the corrosion and tribocorrosion behaviour of these Ti-Cu thin films in an artificial sweat environment, comparing them to pure Ti and Cu films. Chemical, microstructural, topographical, and electrical characterizations were conducted, alongside evaluations of electrochemical and tribo-electrochemical behaviour. The results indicate that while all films showed rupture under sliding, TiCu0.34 thin films exhibited superior corrosion resistance due to their unique microstructure. This study suggests that TiCu0.34 electrodes may offer a promising balance between corrosion resistance and electrical performance for wearable applications, although improvements in adhesion are necessary to withstand mechanical loads.Article Citation - WoS: 3Citation - Scopus: 3An Ex Vivo Model for Evaluation of Prebiotic Activity of Xylan and Xylooligosaccharides(Elsevier, 2025) Sabanci, Kevser; Gulec, Sukru; Buyukkileci, Ali OguzEx vivo techniques can provide more physiologically significant insights into prebiotic activity and overcome some limitations of in vitro tests. In this study, an ex vivo model, formed of a large intestine of mice, was tested to assess the effects of the hydrocolloidal natural polymer, xylan (XY), and its hydrolysis product, xylooligosaccharides (XOS). XY and XOS were loaded separately into the cecum, proximal colon, and distal colon. Their utilization and short-chain fatty acid (SCFA) formation by the colonized microflora and levels of dominant phyla and key genera such as Bifidobacterium, Bacteroides, and Lactobacillus were followed. XY and XOS were metabolized in all sections, and SCFAs were released. The results suggest that the slower utilization of XY compared to XOS in the cecum can enable this polysaccharide to move towards distal parts of the large intestine and extend the sites of prebiotic activity. Unlike widely used in vitro models, the ex vivo model allowed testing the utilization pattern and effects of the prebiotics in the natural environment of the microflora and examining the intestinal sections separately.Article Citation - WoS: 1Citation - Scopus: 1Storage Tank Farming Planning Under Equipment and Port Operational Costs Through Mixed Integer Quadratically Constrained Programming(Elsevier, 2025) Yalcin, Damla; Deliismail, Ozgun; Tuncer, Basak; Sildir, HasanThe study contributes a new method for managing crude oil tank farms, focusing on scheduling and optimizing storage tanks using mathematical modeling. The short-term continuous-time scheduling model reduces tank requirements and performs selection with convenient capacities. The nonconvex mixed-integer quadratically constrained programming (MIQCP) model is used to account for tank farm scheduling dynamics. It focuses on the integration of ships, storage tanks, charging tanks, and crude oil distillation units. The study examines 8 cases focusing on oil supply, arrival times, prices, and maximum flow rate constraints to show the impact of real-world volatility. By incorporating process intensification principles, the mathematical model emphasizes the importance of optimizing storage tank usage to minimize port operational costs of crude oils.