PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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Citation - WoS: 3
Citation - Scopus: 3
Alantolactone Ameliorates Graft Versus Host Disease in Mice
(Elsevier, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Serife; Cakir, Mustafa; Unal, Ekrem
The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naive (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2-18 (n = 4) and non-GVHD patients between ages 2-50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naive phenotype (CD62L+ CD44-). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.
Citation - WoS: 34
Citation - Scopus: 40
Big Data Acquired by Internet of Things-Enabled Industrial Multichannel Wireless Sensors Networks for Active Monitoring and Control in the Smart Grid Industry 4.0
(Elsevier, 2021) Faheem, Muhammad; Fizza, Ghulam; Ashraf, Muhammad Waqar; Butt, Rizwan Aslam; Ngadi, Md. Asri; Gungor, Vehbi Cagri
Smart Grid Industry 4.0 (SGI4.0) defines a new paradigm to provide high-quality electricity at a low cost by reacting quickly and effectively to changing energy demands in the highly volatile global markets. However, in SGI4.0, the reliable and efficient gathering and transmission of the observed information from the Internet of Things (IoT)-enabled Cyberphysical systems, such as sensors located in remote places to the control center is the biggest challenge for the Industrial Multichannel Wireless Sensors Networks (IMWSNs). This is due to the harsh nature of the smart grid environment that causes high noise, signal fading, multipath effects, heat, and electromagnetic interference, which reduces the transmission quality and trigger errors in the IMWSNs. Thus, an efficient monitoring and real-time control of unexpected changes in the power generation and distribution processes is essential to guarantee the quality of service (QoS) re-quirements in the smart grid. In this context, this paper de-scribes the dataset contains measurements acquired by the IMWSNs during events monitoring and control in the smart grid. This work provides an updated detail comparison of our proposed work, including channel detection, channel assign-ment, and packets forwarding algorithms, collectively called CARP [1] with existing G-RPL [2] and EQSHC [3] schemes in the smart grid. The experimental outcomes show that the dataset and is useful for the design, development, testing, and validation of algorithms for real-time events monitoring and control applications in the smart grid. (C) 2021 The Authors. Published by Elsevier Inc.
Citation - WoS: 26
Citation - Scopus: 33
Big Datasets of Optical-Wireless Cyber-Physical Systems for Optimizing Manufacturing Services in the Internet of Things-Enabled Industry 4.0
(Elsevier, 2022) Faheem, Muhammad; Butt, Rizwan Aslam
The Industry 4.0 revolution is aimed to optimize the product design according to the customers' demand, quality requirements and economic feasibility. Industry 4.0 employs advanced two-way communication technologies for optimizing the manufacturing process to increase the sales of the products and revenues to cope the existing global economy issues. In Industry 4.0, big data obtained from the Internet of Things (IoT)-enabled industrial Cyber-Physical Systems (CPS) plays an important role in enhancing the system service performance to boost the productivity with enhanced quality of customer experience. This paper presents the big datasets obtained from the Internet of things (IoT)-enabled Optical Wireless Sensor Networks (OWSNs) for optimizing service systems' performance in the electronics manufacturing Industry 4.0. The updated raw and analyzed big datasets of our published work [3] contain five values namely, data delivery, latency, congestion, throughput, and packet error rate in OWSNs. The obtained dataset are useful for optimizing the service system performance in the electronics manufacturing Industry 4.0. (c) 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)
Citation - WoS: 1
Citation - Scopus: 1
Cinnamomum Zeylanicum Extract Incorporated Electrospun Poly(Lactic Acid)/ Gelatin Membrane as a New Wound Dressing
(Elsevier, 2025) Tarhan, Seray Zora; Pepe, Nihan Aktas; Sen, Alaattin; Isoglu, Ismail Alper
In this study, we fabricated poly(lactic acid)/gelatin electrospun membranes containing various concentrations of Cinnamomum zeylanicum extract and evaluated them as a novel wound dressing. The electrospun membranes were chemically, morphologically, and mechanically characterized, and the results were discussed in comparison with the literature. Electrospun membranes' biodegradability, swelling, and release properties were evaluated, with the CE7.5 membrane having values of 29.60 f 7.20 and 542.1 f 48.3 % and 66.9 %, respectively. Antibacterial activity was observed in CE7.5 and CE10 membranes against E. coli and S. aureus strains. At the highest concentration (CE10), 111.7 f 5.6 % and 96 f 12.375 % cell viability were detected in fibroblasts and differentiated LPS-induced THP-1 cells. Cell viability was further evaluated by Annexin-V/PI staining, revealing that 97.95 f 1.63 % of the cells remained viable in the CE7.5-treated membranes, while only 1.85 f 1.49 % of necrotic cells were detected in the treated cell population. Fibroblasts treated with the CE7.5 membrane showed a 42 % improvement in wound closure compared to non-treated cells. The anti-inflammatory properties of the electrospun membranes were also investigated. Treatment with the conditioned CE7.5 membrane downregulated Tba1 and tau proteins by 45.1 and 51.055 %, respectively. This study concluded that the newly developed Cinnamomum zeylanicum extract incorporated poly(lactic acid)/gelatin electrospun membranes could be a promising wound dressing material.
Citation - WoS: 7
Citation - Scopus: 6
Comparative Genomics of Loigolactobacillus Coryniformis With an Emphasis on L. Coryniformis Strain FOL-19 Isolated From Cheese
(Elsevier, 2023) Gumustop, Ismail; Ortakci, Fatih
Loigolactobacillus coryniformis is a member of lactic acid bacteria isolated from various ecological niches. We isolated a novel L. coryniformis strain FOL-19 from artisanal Tulum cheese and performed the whole-genome sequencing for FOL-19. Then, genomic characterization of FOL-19 against ten available whole genome sequences of the same species isolated from kimchi, silage, fermented meat, air of cowshed, dairy, and pheasant chyme was performed to uncover the genetic diversity and biotechnological potential of overall species. The average genome size of 2.93 +/- 0.1 Mb, GC content of 42.96% +/- 0.002, number of CDS of 2905 +/- 165, number of tRNA of 56 +/- 10, and number of CRISPR elements of 6.55 +/- 1.83 was found. Both Type I and II Cas clusters were observed in L. coryniformis. No bacteriocin biosynthesis gene clusters were found. All strains harbored at least one plasmid except KCTC 3167. All strains were predicted to carry multiple IS elements. The most common origin of the IS elements was belong to Lactiplantibacillus plantarum. Comparative genomic analysis of L. coryniformis revealed hypervariability at the strain level and the presence of CRISPR/Cas suggests that L. coryniformis holds a promising potential for being a reservoir for new CRISPR-based tools. All L. coryniformis strains except PH-1 were predicted to harbor pdu and cbi-cob-hem gene clusters encoding industrially relevant traits of reuterin and cobalamin biosynthesis, respectively. These findings put a step forward for the genomic characterization of L. coryniformis strains for biotechnological applications via genome-guided strain selection to identify industrially relevant traits.
Development and Characterization of Starch-Fatty Acid Complexes Produced with Buckwheat Starch and Capric/Stearic Acid Using Different Reaction Conditions
(Elsevier, 2025) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, Kevser
The aim of present study was to investigate the impact of reaction parameters on the complex formation between buckwheat starch and capric acid (B-Capric) or stearic acid (B-Stearic). The most effective parameters on complex formation indicator (Complex index (CI) value) were found as reaction temperature (60-90 degrees C) and pH (5-8). Additionally, the effect of these parameters on physicochemical, pasting, and in-vitro digestibility properties of complex samples were evaluated. XRD and FTIR was also used in characterize the complex samples. In general, increasing pH increased the CI values of B-Stearic samples while decreasing those of B-Capric samples. Syneresis of buckwheat starch increased after complexation while paste clarity and swelling power diminished. The pasting properties of native starch significantly changed after complex formation. The FTIR results showed that starch structure changed with complex formation. XRD revealed that buckwheat starch, having an A-type pattern, converted to V-type pattern after complexation. Complex formation of buckwheat starch with capric and stearic acid significantly increased the RS content of buckwheat starch (19.01 %) by up to 36.25 % and 30.60 %, respectively. These results highlight the possibility of using buckwheat starch-capric acid/stearic acid complexes in food formulation to enhance the RS content.
Citation - WoS: 8
Citation - Scopus: 13
A Fractional-Order Mathematical Model Based on Vaccinated and Infected Compartments of Sars-Cov With a Real Case Study During the Last Stages of the Epidemiological Event
(Elsevier, 2023) Bilgil, Halis; Yousef, Ali; Erciyes, Ayhan; Erdinc, Ummugulsum; Ozturk, Zafer
In 2020 the world faced with a pandemic spread that affected almost everything of humans' social and health life. Regulations to decrease the epidemiological spread and studies to produce the vaccine of SARS-CoV-2 were on one side a hope to return back to the regular life, but on the other side there were also notable criticism about the vaccines itself. In this study, we established a fractional order differential equations system incorporating the vaccinated and re-infected compartments to a SIR frame to consider the expanded and detailed form as an SVIIvR model. We considered in the model some essential parameters, such as the protection rate of the vaccines, the vaccination rate, and the vaccine's lost efficacy after a certain period. We obtained the local stability of the disease-free and co-existing equilibrium points under specific conditions using the Routh-Hurwitz Criterion and the global stability in using a suitable Lyapunov function. For the numerical solutions we applied the Euler's method. The data for the simulations were taken from the World Health Organization (WHO) to illustrate numerically some scenarios that happened.(c) 2022 Elsevier B.V. All rights reserved.
Citation - WoS: 1
Citation - Scopus: 1
The Impact of COVID-19 on Healthcare Utilization in Turkey
(Elsevier, 2024) Ugur, Zeynep B.; Durak, Aysenur
Objectives: This study investigates the impact of the COVID-19 pandemic on healthcare utilization in Turkey. Methods: We utilized individual-level data derived from Turkish Statistical Institute 's annual surveys between 2014 and 2022 and estimated probit regression models. Results: We find that COVID-19 pandemic reduced healthcare utilization by 11.8% after taking into account a large set of background variables. Although our study finds that the elderly and those with health problems are more likely to use healthcare services under normal circumstances, the COVID-19 pandemic has caused notable drops in the healthcare utilization among the elderly (-6.5%) and those with health problems (-3.8%). Although those without health insurance had lower utilization of healthcare services before the pandemic, during the pandemic they were not particularly hit. Conclusion: We conclude that the pandemic did not lower the healthcare utilization in Turkey because of the supply constraints. Also, the evidence points to the reduced demand due to the fear of contagion rather than financial concerns.
Citation - WoS: 135
Citation - Scopus: 137
The Impacts of Different Proxies for Financialization on Carbon Emissions in Top-Ten Emitter Countries
(Elsevier, 2020) Amin, Azka; Dogan, Eyup; Khan, Zeeshan
The nexus of financialization and carbon emissions has been widely discussed in the literature. A vast body of literature that estimates the impact of financialization on carbon emissions proxies financialization with either domestic credit or market capitalization. However, these representatives do not fully respond to the complicated nature of financial development. To till the gaps in the existing literature, nine different proxies for financial development are used in the links with carbon emissions in the framework of EKC theory for the years 1980-2014. This study exposes reliable and robust empirical results due to the use of a number of proxies for financialization and second-generation econometric approaches in the empirical analysis. The quantile regression approach deals with unobserved heterogeneity for each cross-section and estimates different slope parameters at varying quantiles. Because non-normality and heterogeneity are detected in datasek quantile regression provides more robust and reliable estimates than conventional econometric techniques. Results from quantile regression estimator support mixed effects of financial development on carbon emissions over quantiles: in addition, the impact of financial development on carbon emissions is varying not only for each quantile but also for different proxies of financial development. The EKC hypothesis is validated for the top-ten emitter economies. Interpretations and policy suggestions are further discussed in the present study. (C) 2020 Elsevier B.V. All rights reserved.
Citation - WoS: 17
Citation - Scopus: 26
Leisure Mobility Changes During the COVID-19 Pandemic- An Analysis of Survey and Mobile Phone Data in Sweden
(Elsevier, 2023) Osth, John; Toger, Marina; Turk, Umut; Kourtit, Karima; Nijkamp, Peter
The COVID-19 pandemic affected travelling in general, and the leisure mobility and the spatial distribution of travellers in particular. In most parts of the world, both domestic and international travel has been replaced by restrictive policies and recommendations on mobility. A modal shift from public transport towards private cars and micro-mobility was also observed. This study seeks to trace the implications of the COVID-19 pandemic for leisure mobility. We use a unique Swedish database containing daily mobility patterns of pseudonymised mobile phone users, combined with a survey on vacation transport behaviour. By contrasting mobility patterns for selected holiday days during the unaffected summer of 2019 with corresponding dates in 2020 and 2021, we are able to model and detect the pandemic effects on tourism and recreational mobility. Moreover, by identifying the general mobility patterns, we analyse whether and how the transport mode has changed. Using data on the spatial distribution of recreational amenities, we identify locations that were favoured during the pandemic. In Sweden, even though the pandemic decreased in spread and severity during the summers, most travel restrictions were still enforced, international vacations uncommon, and larger vacation spots, such as amusement parks and cultural institutions, were closed down. Swedish vacation homes in remote or rural areas were quickly booked. This change in recreational behaviour, where less populated areas, open air and nature recreation were favoured over indoor or crowded urban cultural activities, was more substantial in 2021 than in 2020. This result shows how policies can effectively be developed, so that Swedes respond properly to recommendations and adjust their vacation plans.
Citation - WoS: 2
Citation - Scopus: 2
Membrane Binding and Lipid-Protein Interaction of the C2 Domain From Coagulation Factor V
(Elsevier, 2024) Ohkubo, Y. Zenmei; Radulovic, Peter W.; Kahira, Albert N.; Madsen, Jesper J.
Anchoring of coagulation factors to anionic regions of the membrane involves the C2 domain as a key player. The rate of enzymatic reactions of the coagulation factors is increased by several orders of magnitude upon membrane binding. However, the precise mechanisms behind the rate acceleration remain unclear, primarily because of a lack of understanding of the conformational dynamics of the C2-containing factors and corresponding complexes. We elucidate the membrane-bound form of the C2 domain from human coagulation factor V (FV-C2) by characterizing its membrane binding the specific lipid -protein interactions. Employing all-atom molecular dynamics simulations and leveraging the highly mobile membrane-mimetic (HMMM) model, we observed spontaneous binding of FV-C2 to a phosphatidylserine (PS)-containing membrane within 2-25 ns across twelve independent simulations. FV-C2 interacted with the membrane through three loops (spikes 1-3), achieving a converged, stable orientation. Multiple HMMM trajectories of the spontaneous membrane binding provided extensive sampling and ample data to examine the membrane-induced effects on the conformational dynamics of C2 as well as specific lipid -protein interactions. Despite existing crystal structures representing presumed "open" and "closed" states of FV-C2, our results revealed a continuous distribution of structures between these states, with the most populated structures differing from both "open" and "closed" states observed in crystal environments. Lastly, we characterized a putative PS-specific binding site formed by K23, Q48, and S78 located in the groove enclosed by spikes 1-3 (PS-specificity pocket), suggesting a different orientation of a bound headgroup moiety compared to previous proposals based upon analysis of static crystal structures.
Citation - WoS: 2
Citation - Scopus: 3
Multi Fragment Melting Analysis System (MFMAS) for One-Step Identification of Lactobacilli
(Elsevier, 2020) Kesmen, Zulal; Kilic, Ozge; Gormez, Yasin; Celik, Mete; Bakir-Gungor, Burcu
The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.
A Novel Germline Pregnane X Receptor (PXR) Variant Predisposing to Hodgkin Lymphoma in Two Siblings
(Elsevier, 2024) Khodzhaev, Khusan; Sudutan, Tugce; Erbilgin, Yucel; Saritas, Merve; Yegen, Gulcin; Bozkurt, Ceyhun; Kebudi, Rejin
Hodgkin's lymphoma (HL) is the most common cancer in adolescents and young adults. A family history of HL increases the risk of developing HL in other family members. Identification of genetic predisposition variants in HL is important for understanding disease aetiology, prognosis, and response to treatment. Aberrant activation of the NF-kappa B pathway is a hallmark feature of HL, contributing to the survival and proliferation of the malignant cells' characteristic of HL. The family with multiple consanguineous marriages with siblings of diagnosed HL was examined by whole-exome sequencing. We found a germline homozygous variation in the PXR ligand binding domain (NM_003889.3:c.811G>A, p.(Asp271Asn)), which was classified as pathogenic by prediction tools and segregated in HL cases. Increased PXR expression was found in homozygous variant carriers compared to heterozygous carriers by quantitative real time PCR (qRT-PCR) and immunofluorescence staining of patients' formalin-fixed paraffin-embedded tissues showed upregulation of PXR, particularly in Hodgkin Reed/Sternberg (HRS) cells. Patients with homozygous PXR variant showed significantly high expression compared to PXR wild-type HL, heterozygous and controls (p = 0.0001, p = 0.0004 and p = 0.0001, respectively). PXR homozygous HRS cells had significantly higher PXR expression compared to PXR wild-type HRS cells (p < 0.0001, 3.27-fold change). Albeit PXR's prominent expression in cytoplasm of HRS cells, homozygous PXR HRS cells showed increased PXR expression in nucleus (p < 0.001). PXR is a member of the nuclear receptor superfamily and previous studies have demonstrated a pleiotropic effect of PXR on malignant transformation. Expression analysis showed that cell proliferation, apoptosis and inflammation related genes were deregulated, in homozygous PXR HL cases. This study provided clinical evidence to previously reported Sxr(-/-) mice model that develop multifocal lymphomas, had an aberrantly increased NF-kappa B expression and consistent inflammation. Further functional studies are needed to elucidate the exact mechanisms of action of PXR in HL pathogenesis.
Citation - WoS: 4
Citation - Scopus: 5
Novel Insights Into Bacillus Thuringiensis: Beyond Its Role as a Bioinsecticide
(Elsevier, 2025) Jouzani, Gholamreza Salehi; Sharafi, Reza; Argentel-Martinez, Leandris; Penuelas-Rubio, Ofelda; Ozkan, Ceyda; Incegul, Bengisu; Azizoglu, Ugur; Salehi Jouzani, Gholamreza
This review explores the diverse applications of Bacillus thuringiensis (Bt) beyond its traditional role as a bioinsecticide. Bt produces a variety of compounds with distinct chemical structures and biological activities. These include antimicrobial agents effective against plant pathogens and bioactive compounds that promote plant growth through the production of siderophores, hormones, and enzymes. Additionally, Bt's industrial potential is highlighted, encompassing biofuel production, bioplastics, nanoparticle synthesis, food preservation, anticancer therapies, and heavy metal bioremediation. This critical analysis emphasizes recent advancements and applications, providing insights into Bt's role in sustainable agriculture, biotechnology, and environmental management.
Citation - WoS: 40
Citation - Scopus: 63
Optimization of Resistant Starch Formation From High Amylose Corn Starch by Microwave Irradiation Treatments and Characterization of Starch Preparations
(Elsevier, 2017) Mutlu, Selime; Kahraman, Keyser; Ozturk, Serpil
The effects of microwave irradiation on resistant starch (RS) formation and functional properties in high-amylose corn starch, Hylon VII, by applying microwave-storing cycles and drying processes were investigated. The Response Surface Methodology (RSM) was used to optimize the reaction conditions, microwave time (2-4min) and power (20-400%), for RS formation. The starch:water (1:10) mixtures were cooked and autoclaved and then different microwave-storing cycles and drying (oven or freeze drying) processes were applied. The RS contents of the samples increased with increasing microwave storing cycle. The highest RS (43.4%) was obtained by oven drying after 3 cycles of microwave treatment at 20% power for 2 min. The F, p (<0.05) and R-2 values indicated that the selected models were consistent. Linear equations were obtained for oven-dried samples applied by 1 and 3 cycles of microwave with regression coefficients of 0.65 and 0.62, respectively. Quadratic equation was obtained for freeze-dried samples applied by 3 cycles of microwave with a regression coefficient of 0.83. The solubility, water binding capacity (WBC) and RVA viscosity values of the microwave applied samples were higher than those of native Hylon VII. The WBC and viscosity values of the freeze-dried samples were higher than those of the oven-dried ones. (C) 2016 Elsevier B.V. All rights reserved.
Citation - WoS: 2
Citation - Scopus: 3
Prediction of Biomechanical Properties of Ex Vivo Human Femoral Cortical Bone Using Raman Spectroscopy and Machine Learning Algorithms
(Elsevier, 2025) Unal, Mustafa; Unlu, Ramazan; Uppuganti, Sasidhar; Nyman, Jeffry S.
This study applied Raman spectroscopy (RS) to ex vivo human cadaveric femoral mid-diaphysis cortical bone specimens (n = 118 donors; age range 21-101 years) to predict fracture toughness properties via machine learning (ML) models. Spectral features, together with demographic variables (age, sex) and structural parameters (cortical porosity, volumetric bone mineral density), were fed into support vector regression (SVR), extreme tree regression (ETR), extreme gradient boosting (XGB), and ensemble models to predict fracture-toughness metrics such as crack-initiation toughness (Kinit) and energy-to-fracture (J-integral). Feature selection was based on Raman-derived mineral and organic matrix parameters, such as nu 1Phosphate (PO4)/CH2-wag, nu 1PO4/ Amide I, and others, to capture the complex composition of bone. Our results indicate that ensemble models consistently outperformed individual models, with the best performance for crack initiation toughness (Kinit) prediction being achieved using the ensemble approach. This yielded a coefficient of determination (R2) of 0.623, root-mean squared error (RMSE) of 1.320, mean absolute error (MAE) of 1.015, and mean percentage absolute error (MAPE) of 0.134. For prediction of the overall energy to propagate a crack (J-integral), the XGB model achieved an R2 of 0.737, RMSE of 2.634, MAE of 2.283, and MAPE of 0.240. This study highlights the importance of incorporating mineral quality properties (MP) and organic matrix properties (OMP) for enhanced prediction accuracy. This work represents the first-ever study combining Raman spectroscopy with other clinical and structural features to predict fracture toughness of human cortical bone, demonstrating the potential of artificial intelligence (AI) and ML in advancing bone research. Future studies could focus on larger datasets and more advanced modeling techniques to further improve predictive capabilities.
Citation - WoS: 12
Citation - Scopus: 14
Prevention of Cisplatin-Induced Nephrotoxicity by Kidney-Targeted siRNA Delivery
(Elsevier, 2022) Aydin, Erkin; Cebeci, Aysun; Lekesizcan, Ayca
Cisplatin is a potent and widely used chemotherapy agent, however, nephrotoxicity limits its use. Many patients need to pause or withdraw from chemotherapy to prevent acute kidney injury. To prevent cisplatin damage, we designed chitosan/siRNA nanoparticleswhich are nontoxic and are readily taken up by HEK293 cells. The nanoparticles contained siRNA against cationic membrane transport (OCT1&2) and apoptosis related proteins (p53, PKC8, and gamma GT). In mice treated with cisplatin, serum creatinine levels increased from 15 to 88 mg/dL and blood urea nitrogen levels increased from 0.25 to 1.7 mg/dL, however, siRNA nanoparticles significantly limited these levels to 30 mg/dL and 0.55 mg/dL, respectively. Western and IHC analyses showed lower p53, PKC8, and gamma GT expressions in siRNA treated mice. Histomorphological evaluation revealed high-level protection of kidney proximal tubules from cisplatin damage. Protein expressions and extent of kidney protection were directly correlated with number of siRNA applications. Our results suggest that this novel approach for kidney -targeted delivery of select siRNAs may represent a promising therapy for preventing cisplatin-induced nephro-toxicity. Furthermore, this or other similarly sized nanocarriers could potentially be utilized to passively target kidneys for diagnostic, protective, or treatment purposes.
Citation - WoS: 22
Citation - Scopus: 30
Production of Buckwheat Starch-Myristic Acid Complexes and Effect of Reaction Conditions on the Physicochemical Properties, X-Ray Pattern and FT-IR Spectra
(Elsevier, 2022) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, Kevser
In this study, the effect of reaction parameters on complex index (CI%) value of complexes formed between buckwheat starch (BS) and myristic acid (MA) was investigated. The temperature (60-90 ?C) and MA to BS ratio (0.1-0.8 mmoL/g) were determined as the most effective parameters and their effect on CI% was evaluated using response surface methodology. The MA to BS ratio, temperature, and interaction between them had an influence on CI%. The CI% of BS-MA complexes increased with increasing MA ratio until a certain level of MA. Principal component analysis (PCA) was used for correlation analysis between parameters. Swelling power and paste clarity of BS decreased with complex formation while syneresis increased. Peak and final viscosity values of the BS-MA complexes were significantly lower than those of BS. FT-IR revealed the complex formation led to change in starch structure. The XRD confirmed the BS-MA complex formation but the BS-MA produced using 0.1 mmoL/ g at 60 ?C was not detected by XRD due to having low crystallinity, and expectedly, the lowest relative crystallinity value was achieved with this sample among complex samples. All results showed that the buckwheat be an alternative starch source for starch formation.
Citation - WoS: 26
Citation - Scopus: 30
Proteomic Fertility Markers in Ram Sperm
(Elsevier, 2021) Hitit, Mustafa; Ozbek, Mehmet; Ayaz-Guner, Serife; Guner, Huseyin; Oztug, Merve; Bodu, Mustafa; Kaya, Abdullah
Precise estimation of ram fertility is important for sheep farming to sustain reproduction efficiency and profitability of production. There, however, is no conventional method to accurately predict ram fertility. The objective of this study, therefore, was to ascertain proteomic profiles of ram sperm having contrasting fertility phenotypes. Mature rams (n = 66) having greater pregnancy rates than average (89.4 +/- 7.2%) were assigned into relatively-greater fertility (GF; n = 31; 94.5 +/- 2.8%) whereas those with less-than-average pregnancy rates were assigned into a lesserfertility (LF; n = 25; 83.1 +/- 5.73%; P = 0.028) group. Sperm samples from the outlier greatestand least-fertility rams (n = 6, pregnancy rate; 98.4 +/- 1.8% and 76.1 +/- 3.9%) were used for proteomics assessments utilizing Label-free LC-MS/MS. A total of 997 proteins were identified, and among these, 840 were shared by both groups, and 57 and 93 were unique to GF and LF, respectively. Furthermore, 190 differentially abundant proteins were identified; the abundance of 124 was larger in GF while 66 was larger in LF rams. The GF ram sperm had 79 GO/pathway terms in ten major biological networks while there were 47 GO/pathway terms in six biological networks in sperm of LF rams. Accordingly, differential abundances of sperm proteins between sperm of GF and LF rams were indicative of functional implications of sperm proteome on male fertility. The results of this study emphasize there are potential protein markers for evaluation of semen quality and estimation of ram sperm fertilizing capacity.
Citation - WoS: 4
Citation - Scopus: 4
Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells
(Elsevier, 2022) Ayaz-Guner, Serife; Acar, Mustafa Burak; Boyvat, Dudu; Guner, Huseyin; Bozalan, Habibe; Guzel, Melis; Ozcan, Servet
Analysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnet-ically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, fol-lowed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.

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