PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

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  • Article
    Alterations in Secondary Lipids Are Associated with Neuroinflammation in the Brain of Neu1-Deficient Mice
    (Springer, 2026) Ada, Ebru; Seyrantepe, Volkan
    Neu1 (lysosomal sialidase 1) is essential for removing sialic acid from oligosaccharides and glycoconjugates. Neu1 deficiency impairs lysosomal digestion, leading to sialidosis and sialoglycoprotein accumulation. It also increases lipids, including gangliosides GM3, GD3, GM4, and LM1, in the kidney, liver, and spleen. Neu1-/- mice display symptoms resembling Type II sialidosis, including enlarged spleen and liver, kidney issues, neurological problems, spinal defects, and oligosaccharide buildup. The study examined secondary lipid alterations and inflammation in the cortex and cerebellum of these mice. Lipidomic, molecular, and immunohistochemical analyses of tissues from 2 and 5 M Neu1-/- mice revealed reduced levels of lipids, including PC, PE, PS, and CL, along with increased pro-inflammatory cytokines and loss of oligodendrocytes and neurons. Signs of astrogliosis and microgliosis emerged in specific brain regions. These results indicate that reduced levels of glycerophospholipids could serve as an indicator of inflammation in sialidosis mice. Future research should investigate therapies targeting these lipid changes, as modulating glycerophospholipids might slow disease progression in sialidosis patients.
  • Article
    Liposomal Encapsulation of a Synthetic Bromophenol for Antitumor Efficacy and Apoptotic Activity in Cancer Cells
    (Springer, 2026) Oztanrikulu, Bercem Dilan; Ozdemir, Ekrem; Avci, Bahri; Goksu, Suleyman; Bayrakceken, Handan Uguz; Askin, Hakan
    A novel synthetic bromophenol (BP), inspired by marine-derived natural bromophenols, was evaluated for its antitumor activity and for the enhancement of its in vitro performance through liposomal encapsulation (LipoBP). Etoposide was used as a reference in characterization, release, and loading studies. PEGylated liposomes were employed to improve BP's solubility, bioavailability, and therapeutic potential. The cytotoxicity, apoptosis, and gene expression effects of free BP and LipoBP were assessed in A549 (lung) and MCF-7 (breast) cancer cell lines. WST-8 assays showed that encapsulation significantly increased BP's cytotoxic activity, particularly in A549 cells, while flow cytometry and Annexin V-FITC/PI analyses indicated more pronounced apoptotic induction by LipoBP compared with free BP. qRT-PCR analyses revealed upregulation of proapoptotic genes (BAX, CASP6, CASP3 and CASP9) and downregulation of antiapoptotic/survival genes (BCL-XL, IQSEC2) in both cell lines, indicating activation of intrinsic apoptotic pathways. Plain liposomes exhibited minimal cytotoxicity, confirming their biocompatibility. Liposomal bromophenol, which we have introduced to the literature for the first time, is expected to be a promising nanocarrier system that could be effective in cancer treatment by improving the therapeutic index of new drug candidates such as marine bromophenols.
  • Article
    Mass Spectrometric Profiling Reveals Alterations in N-Glycans and O-Glycans in Tay-Sachs Disease Under Autophagy-Induced Conditions
    (Springer, 2025) Can, Melike; Basirli, Hande; Jin, Chunsheng; Karlsson, Niclas G.; Bojar, Daniel; Seyrantepe, Volkan
    Tay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the alpha-subunit of the enzyme beta-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.
  • Article
    A Fiber-Driven Finite Element Model for Predicting Residual Limb Soft Tissue Deformation: Applications in Prosthetic Socket Design
    (Springer, 2025) Wang, Ling; Qiu, Ziyan; Tang, Lei; Huang, Fuhao; Wei, Pingping; Mihcin, Senay; Li, Dichen
    PurposeChanges in residual limb volume and shape pose significant challenges in achieving and maintaining an accurate and comfortable fit for prosthetic socket. While numerous techniques for measuring residual limb volume have been proposed, their clinical application remains limited by insufficient resolution and the inability to perform in-socket measurements. To address this issue, this study develops a novel method for predicting residual limb soft tissue deformation to guide prosthetic socket design.MethodsA three-dimensional (3D) finite element (FE) model of the human thigh was developed to simulate the soft tissue deformation during daily activities, driven by muscle contraction to replicate natural biomechanics. The model included hard tissue and muscle components, with the muscle modeled as a structure of evenly distributed, contractile fibers that generate movement. Parameters controlling fiber contraction were iteratively adjusted to best match the calculated tissue deformation and that observed in physical muscle models.ResultsThe optimized FE model significantly improved the accuracy of predicting dynamic soft tissue deformation, with average errors of 0.83% and 1.86% for tissue expansion and contraction regions, respectively. For various gait patterns, the average differences in equivalent volume and cross-sectional area changes were also less than 0.83% and 1.86%, respectively.ConclusionThe model demonstrated consistent prediction accuracy across different gait data. The fiber-driven soft tissue model developed offers a valuable tool for pre-design simulations of prosthetic sockets and orthoses. It is equally applicable to other wearable devices that interface with the skin, providing a robust framework for improving device design and functionality.
  • Article
    Citation - WoS: 7
    Citation - Scopus: 9
    A Holistic Overview of the Applications of Grace-Observed Terrestrial Water Storage in Hydrology and Climate Science
    (Springer, 2025) Khorrami, Behnam; Gunduz, Orhan
    Terrestrial 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
    Citation - WoS: 4
    Citation - Scopus: 4
    Estimation of Heat Production Rate Using Thermal Data During Exercise in Indoor Environments: a Study of Heat Storage Rate in Male Athletes
    (Springer, 2024) Balci, Gorkem Aybars; Avci, Ali Berkay; Colakoglu, Muzaffer; Basaran, Tahsin; Balcı, Görkem Aybars; Avcı, Ali Berkay; Çolakoğlu, Muzaffer; Başaran, Tahsin
    The increasing preference for indoor exercise spaces highlights the relationship between indoor thermal environments and physiological responses, particularly concerning thermal comfort during physical activity. Determining the metabolic heat production rate during exercise is essential for optimizing the thermal comfort, well-being, and performance of individuals engaged in physical activities. This value can be determined during the activity using several methods, including direct calorimetry measurement, indirect calorimetry that uses analysis of respiratory gases, or approximations using collected data such as speed, body mass, and heart rate. The study aimed to calculate the metabolic heat production rate by infrared thermal evaluation (ITE) based on the body's thermal balance approach and compare it with the values determined by indirect calorimetry (IC). Fourteen participants volunteered for the study, using a cycling ergometer in a controlled climatic chamber. After the familiarization sessions, maximal O-2 intake levels (VO2max) were determined through maximal graded exercise tests. Subsequently, constant work rate exercise tests were performed at 60% of VO2max for 20 min. The metabolic heat production rates were calculated by IC and ITE for each athlete individually. Respiratory gases were used to determine IC, while body skin and core temperatures, along with physical environmental data, were applied to calculate ITE using the human body thermal balance approximation of ASHRAE. According to the results, heat storage rates were misleading among the body's heat transfer modes, particularly during the first 8 min of the exercise. ITE showed a moderate level of correlation with IC (r: 0.03-0.86) with a higher level of dispersion relative to the mean (CV%: 12-84%). Therefore, a new equation (ITEnew) for the heat storage rates was proposed using the experimental data from this study. The results showed that ITEnew provided more precise estimations for the entire exercise period (p > 0.05). Correlations between ITEnew and IC values were consistently strong throughout the exercise period (r: 0.62-0.85). It can be suggested that ITEnew values can predict IC during the constant work rate steady-state exercise.
  • Article
    Estimation of Heat Production Rate Using Thermal Data During Exercise in Indoor Environments: a Study of Heat Storage Rate in Male Athletes
    (Springer, 2024) Balcı, Görkem Aybars; Avcı, Ali Berkay; Çolakoğlu, Muzaffer; Başaran, Tahsin
    The increasing preference for indoor exercise spaces highlights the relationship between indoor thermal environments and physiological responses, particularly concerning thermal comfort during physical activity. Determining the metabolic heat production rate during exercise is essential for optimizing the thermal comfort, well-being, and performance of individuals engaged in physical activities. This value can be determined during the activity using several methods, including direct calorimetry measurement, indirect calorimetry that uses analysis of respiratory gases, or approximations using collected data such as speed, body mass, and heart rate. The study aimed to calculate the metabolic heat production rate by infrared thermal evaluation (ITE) based on the body's thermal balance approach and compare it with the values determined by indirect calorimetry (IC). Fourteen participants volunteered for the study, using a cycling ergometer in a controlled climatic chamber. After the familiarization sessions, maximal O2 intake levels (VO2max) were determined through maximal graded exercise tests. Subsequently, constant work rate exercise tests were performed at 60% of VO2max for 20 min. The metabolic heat production rates were calculated by IC and ITE for each athlete individually. Respiratory gases were used to determine IC, while body skin and core temperatures, along with physical environmental data, were applied to calculate ITE using the human body thermal balance approximation of ASHRAE. According to the results, heat storage rates were misleading among the body's heat transfer modes, particularly during the first 8 min of the exercise. ITE showed a moderate level of correlation with IC (r: 0.03-0.86) with a higher level of dispersion relative to the mean (CV%: 12-84%). Therefore, a new equation (ITEnew) for the heat storage rates was proposed using the experimental data from this study. The results showed that ITEnew provided more precise estimations for the entire exercise period (p > 0.05). Correlations between ITEnew and IC values were consistently strong throughout the exercise period (r: 0.62-0.85). It can be suggested that ITEnew values can predict IC during the constant work rate steady-state exercise.
  • Correction
  • Article
    Citation - WoS: 21
    Citation - Scopus: 21
    Remote Sensing-Based Monitoring and Evaluation of the Basin-Wise Dynamics of Terrestrial Water and Groundwater Storage Fluctuations
    (Springer, 2023) Khorrami, Behnam; Gündüz, Orhan
    The recent dynamics of terrestrial water storage (TWS) and groundwater storage (GWS) fluctuations were investigated based on the Gravity Recovery And Climate Experiment (GRACE) observations over 25 basins of Türkiye. Coarse-resolution GRACE estimates were downscaled based on the Random Forest algorithm. The impacts of precipitation (P) and evapotranspiration (ET) on the variations of water storage were also assessed. The findings demonstrated good performance for the RF model in simulating finer resolution estimates of TWS. The results indicated a diminishing trend of TWS and its hydrologic components over all the basins from 2003 to 2020. The Doğu Akdeniz Basin with the annually decreasing TWS and GWS of 1.15cm/yr and 1.10cm/yr was the most critical basin of Türkiye. The least storage loss was observed in the Batı Karadeniz Basin with the annual TWS and GWS loss of 0.38cm/yr and 0.45cm/yr , respectively. Based on the results, Türkiye has lost, on average, an estimated 5.16km3/yr and 4.09km3/yr of its TWS and GWS, respectively, which are equivalent to the total storage loss of 92.88km3 and 73.62km3 of TWS and GWS during the last 18 years. The results also indicated that P and ET interact differently with the variations of TWS and GWS. The net water flux was revealed to be partially correlated with the total water storage fluctuations, suggesting the governing role of other deriving forces particularly the anthropogenic factors in the spatiotemporal variations of Türkiye’s water storage; therefore, a sector-specific analysis of the water storage variations is crucial for the country, particularly by concentrating more on the dynamics of GWS. Graphical Abstract: [Figure not available: see fulltext.]. © 2023, The Author(s), under exclusive licence to Springer Nature Switzerland AG.
  • Article
    Citation - WoS: 4
    Citation - Scopus: 5
    3d Modelling of Surface Spreading and Underground Dam Groundwater Recharge: Egri Creek Subbasin, Turkey
    (Springer, 2023) Şahin, Yavuz; Tayfur, Gökmen
    This study investigated surface spreading and underground dam recharge methods to replenish groundwater in Turkey's Egri Creek Sub-basin of the Kucuk Menderes River Basin. A three-dimensional numerical model was employed for this purpose. Field and lab data are provided to the model for realistic simulations. Pumping test results were used to determine the aquifer parameters. The laboratory works involved sieve analysis, permeability tests, and porosity and water content prediction. The numerical model's boundary conditions were determined from the geological and hydrogeological characteristics of the study area. Initial conditions were expressed regarding water content and pressure head in the vadose zone. The numerical model was satisfactorily validated by simulating water levels in three different pumping wells in the study area. Seven different scenarios, each having a different pool size, were investigated for the surface spreading recharge method. The results showed that a pool size of 30 x 30 m with a 6-m depth basin was the most optimal choice, raising the groundwater level to about 29.3 m. On the other hand, it was found that an underground dam could raise the levels by an average of 9.5 m, which might not be significant to warrant the construction.