PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 12Citation - Scopus: 15The Role of Loco-Regional Treatment in Long-Term Quality of Life in De Novo Stage Iv Breast Cancer Patients: Protocol Mf07-01q(Springer Verlag, 2021) Soran, Atilla; Soyder, Aykut; Özbaş, Serdar; Özmen, Vahit; Karanlık, Hasan; İğci, Abdullah; Sezgin, EfeBackground/objective Since more solid evidence has emerged supporting the effectiveness of loco-regional treatment (LRT), clinicians consider LRT a treatment option for selected de novo stage IV breast cancer (BC) patients. This is the first report on long-term quality of life (QoL) in a cohort of patients who were randomized to receive either LRT and then systemic treatment (ST) or ST alone in the protocol MF07-01. We aimed to evaluate QoL in patients living at least 3 years since randomization using scores from the SF-12 health survey. Methods SF-12 (V2) forms were completed during visits of patients who were living 36 months after the randomization. We first calculated PCS-12 (Physical Health Composite Scale) and MCS-12 (Mental Health Composite Scale) scores from de novo stage IV BC patients and compared them with the scores of patients diagnosed with stage I-III BC who lived more than 3 years. Further, PCS-12 and MCS-12 scores were compared between the LRT and ST groups with de novo stage IV BC. Additionally, general health, physical functioning, role functioning, bodily pain, vitality, mental health, and social functioning were evaluated and compared between the groups. Considering age-related changes in QoL, we also compared PCS-12 and MCS-12 scores of patients below or above 55 and 65 years of age. Responses to four additional questions (compare your physical health, mental health, daily activities, and energy currently vs. at diagnosis of BC) were recorded, considering cultural differences. Results There were 81 patients in this analysis; 68% of patients (n = 55) had LRT, and 32% (n = 26) received ST. General health was good or very good in 62% (n = 34) in the LRT group and 66% (n = 17) in the ST-only group (p = 0.63). Mean PCS-12 score was 40.8 + 1.6, and mean MCS-12 score was 43.4 + 2.0 (p = 0.34 and p = 0.54, respectively). PCS-12 and MCS-12 score difference was lower than that of the general Turkish population (PCS-12 = 49.3 + 12.8 and MCS-12 = 46.8 + 13.0) and stage I-III BC patients (PCS-12 = 51.1 +/- 0.5, MCS-12 = 45.7 +/- 0.6). PCS-12 and MCS-12 scores were similar between the LRT and ST-only groups in patients younger and older than 55 and 65, but QoL scores were much better in stage I-III BC patients younger than 65 when compared to the scores of those with de novo stage IV BC. Although treatment with or without LRT did not affect physical health, mental health, daily activities, and energy at 3 years vs. at diagnosis of BC in de novo stage IV BC patients (p > 0.05), these variables were significantly better in stage I-III BC patients (p < 0.001). Conclusion The current MF07-01Q study demonstrates that patient who had LRT has similar physical and mental health outcomes compared to ST only in a cohort of patients who lived longer than 3 years. Trial registration This study is registered on clinicaltrials.gov with identifier number NCT00557986.Article Citation - WoS: 16Citation - Scopus: 20Groundwater Recharge Estimation Using Hydrus 1d Model in Alaşehir Sub-Basin of Gediz Basin in Turkey(Springer Verlag, 2019) Tonkul, Serhat; Baba, Alper; Şimşek, Celalettin; Durukan, Seda; Demirkesen, Ali Can; Tayfur, GökmenGediz Basin, located in the western part of Turkey constituting 2% land of the country, has an important groundwater potential in the area. Alasehir sub-basin, located in the southeast of the Gediz Basin and subject to the extensive withdrawal for the irrigation, constitutes the study area. Natural recharge to the sub-basin due to precipitation is numerically investigated in this study. For this purpose, 25 research wells, whose depths range from 20 to 50 m, were drilled to observe the recharge and collect the necessary field data for the numerical model. Meteorological data were collected from 3 weather stations installed in the study area. The numerical model HYDRUS was calibrated using the field water content data. Soil characterization was done on the core samples; the aquifer characterization was performed, and the alluvial aquifer recharge due to precipitation was calculated. As a result, the computed recharge value ranges from 21.78 to 68.52 mm, with an average value of 43.09 mm. According to the numerical model, this amount of recharge corresponds to 10% of the amount of annual rainfall.Article Citation - WoS: 19Citation - Scopus: 29Modeling of an Activated Sludge Process for Effluent Prediction—a Comparative Study Using Anfis and Glm Regression(Springer Verlag, 2018) Araromi, Dauda Olurotimi; Majekodunmi, Olukayode Titus; Adeniran, Jamiu Adetayo; Salawudeen, Taofeeq OlalekanIn this paper, nonlinear system identification of the activated sludge process in an industrial wastewater treatment plant was completed using adaptive neuro-fuzzy inference system (ANFIS) and generalized linear model (GLM) regression. Predictive models of the effluent chemical and 5-day biochemical oxygen demands were developed from measured past inputs and outputs. From a set of candidates, least absolute shrinkage and selection operator (LASSO), and a fuzzy brute-force search were utilized in selecting the best combination of regressors for the GLMs and ANFIS models respectively. Root mean square error (RMSE) and Pearson’s correlation coefficient (R-value) served as metrics in assessing the predicting performance of the models. Contrasted with the GLM predictions, the obtained modeling results show that the ANFIS models provide better predictions of the studied effluent variables. The results of the empirical search for the dominant regressors indicate the models have an enormous potential in the estimation of the time lag before a desired effluent quality can be realized, and preempting process disturbances. Hence, the models can be used in developing a software tool that will facilitate the effective management of the treatment operation.Article Citation - WoS: 23Citation - Scopus: 27Novel Poss Reinforced Chitosan Composite Membranes for Guided Bone Tissue Regeneration(Springer Verlag, 2018) Tamburacı, Sedef; Tıhmınlıoğlu, FundaIn this study, novel composites membranes composed of chitosan matrix and polyhedral oligomeric silsesquioxanes (POSS) were fabricated by solvent casting method. The effect of POSS loading on the mechanical, morphological, chemical, thermal and surface properties, and cytocompatibility of composite membranes were investigated and observed by tensile test, atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), protein adsorption assay, air/water contact angle analysis and WST-1 respectively. Swelling studies were also performed by water absorption capacity determination. Results showed that incorporation of Octa-TMA POSS® nanofiller to the chitosan matrix increased the surface roughness, protein adsorption and swelling capacity of membranes. The addition of POSS enhanced significantly the ultimate tensile strength and strain at break of the composite membranes up to 3 wt% POSS loaded samples. An increase of about 76% in tensile strength and of strain at break 1.28% was achieved for 3 wt% POSS loaded nanocomposite membranes compared with chitosan membranes. The presence of POSS filler into polymer matrix increased the plasma protein adsorption on the surface. Maximum protein capacity and swelling was obtained for 10 wt% loaded samples. High cell viability results were obtained with indirect extraction of chitosan/POSS composites. Besides, cell proliferation and ALP activity results showed that POSS incorporation significantly increased the ALP activity of Saos-2 cells cultured on chitosan membranes. This novel composite membranes with tunable properties could be considered as a potential candidate for guided bone regeneration applicationsArticle Citation - WoS: 18Citation - Scopus: 35Microparticle-Enhanced Polygalacturonase Production by Wild Type Aspergillus Sojae(Springer Verlag, 2017) Karahalil, Ercan; Demirel, Fadime; Evcan, Ezgi; Germeç, Mustafa; Tarı, Canan; Turhan, İrfanPolygalacturonases (PGs), an important industrial enzyme group classified under depolymerases, catalyze the hydrolytic cleavage of the polygalacturonic acid chain through the introduction of water across the oxygen bridge. In order to produce and increase the concentration of this enzyme group in fermentation processes, a new approach called microparticle cultivation, a promising and remarkable method, has been used. The aim of this study was to increase the PG activity of Aspergillus sojae using aluminum oxide (Al2O3) as microparticles in shake flask fermentation medium. Results indicated that the highest PG activity of 34.55 ± 0.5 U/ml was achieved with the addition of 20 g/L of Al2O3 while the lowest activity of 15.20 ± 0.2 U/mL was obtained in the presence of 0.1 g/L of Al2O3. In fermentation without microparticles as control, the activity was 15.64 ± 3.3 U/mL. Results showed that the maximum PG activity was 2.2-fold higher than control. Additionally, smaller pellets formed with the addition of Al2O3 where the lowest pellet diameter was 955.1 µm when 10 g/L of the microparticle was used. Also, it was noticed that biomass concentration gradually increased with increasing microparticle concentration in the fermentation media. Consequently, the PG activity was significantly increased in microparticle-enhanced shake flask fermentation. In fact, these promising preliminary data can be of significance to improve the enzyme activity in large-scale bioreactors.Article Citation - WoS: 39Citation - Scopus: 47Quality of Groundwater Resources in Afghanistan(Springer Verlag, 2017) Hayat, Ehsanullah; Baba, AlperWater is the main source of energy production and economy in Afghanistan where agriculture accounts for more than 50% of the country’s gross domestic product (GDP). Access to safe drinking water is still a problem in the country, which has caused different health issues and even child mortality especially in rural areas. Groundwater is the main source of drinking water in the country. However, little knowledge is available about the quality of groundwater throughout the entire country, and its quality has not been investigated extensively yet like in other countries in the world. While most people think that consuming groundwater is a reliable and safe source of drinking water for health, the United Nations (UN) agencies report various kinds of waterborne diseases and even child mortalities due to drinking water quality in the country. In this article, significant geogenic and anthropogenic factors that play a vital role in groundwater contamination of the country are identified and explained. Different geogenic contaminations such as arsenic, fluoride, sulfate, and boron occur in several areas of Afghanistan that have a direct effect on human health. The water quality mapping for Afghanistan is completed for half of the country, which shows that groundwater is plagued by high levels of fluoride and arsenic in some areas. The water quality mapping of the other half of the country cannot be completed due to security concerns currently. Also, there are different kinds of waterborne diseases such as diarrhea, cholera, and dysentery that can be seen in different parts of the country because of anthropogenic activities which continuously deteriorate groundwater.Article Citation - WoS: 9Citation - Scopus: 12Compositing Climate Change Vulnerability of a Mediterranean Region Using Spatiotemporally Dynamic Proxies for Ecological and Socioeconomic Impacts and Stabilities(Springer Verlag, 2017) Demirkesen, Ali Can; Evrendilek, FatihThe study presents a new methodology to quantify spatiotemporal dynamics of climate change vulnerability at a regional scale adopting a new conceptual model of vulnerability as a function of climate change impacts, ecological stability, and socioeconomic stability. Spatiotemporal trends of equally weighted proxy variables for the three vulnerability components were generated to develop a composite climate change vulnerability index (CCVI) for a Mediterranean region of Turkey combining Landsat time series data, digital elevation model (DEM)-derived data, ordinary kriging, and geographical information system. Climate change impact was based on spatiotemporal trends of August land surface temperature (LST) between 1987 and 2016. Ecological stability was based on DEM, slope, aspect, and spatiotemporal trends of normalized difference vegetation index (NDVI), while socioeconomic stability was quantified as a function of spatiotemporal trends of land cover, population density, per capita gross domestic product, and illiteracy. The zones ranked on the five classes of no-to-extreme vulnerability were identified where highly and moderately vulnerable lands covered 0.02% (12 km2) and 11.8% (6374 km2) of the study region, respectively, mostly occurring in the interior central part. The adoption of this composite CCVI approach is expected to lead to spatiotemporally dynamic policy recommendations towards sustainability and tailor preventive and mitigative measures to locally specific characteristics of coupled ecological–socioeconomic systems.Article Citation - WoS: 16Citation - Scopus: 16Therapeutic Effects of Aicar and Dox Conjugated Multifunctional Nanoparticles in Sensitization and Elimination of Cancer Cells Via Survivin Targeting(Springer Verlag, 2017) Dağlıoğlu, Cenk; Okutucu, BurcuPurpose: Resistance to chemotherapy is one of the major problems facing current cancer research. Enhancing tumor cell response to anticancer agents increases chemotherapeutic effectiveness. We have recently addressed this issue and reported on producing multifunctional nanoparticles (Fe3O4@SiO2(FITC)-FA/AICAR/DOX) aiming to overcome chemoresistance with synergetic effect of AICAR and DOX. In the present study, we demonstrated that these nanoparticles not only show enhanced cellular uptake and cytotoxic effect but can also show enhanced pro-apoptotic and anti-proliferative effects in five different tumor-derived cell lines (A549, HCT-116, HeLa, Jurkat and MIA PaCa-2). Methods: The nanoparticles were examined by using flow cytometric analyses of apoptosis and cell cycle. In addition, we performed caspase-3 activity assay, which supported our flow cytometric data. Furthermore, we demonstrated the applicability of this approach in a variety of cancer types confirming the potential widespread utility of this approach. Results: With the concept of co-delivery of AICAR and DOX in the nanoparticle formulation, the use of AICAR against survivin (BIRC5) sensitized cancer cells to DOX chemotherapy which resulted in effective cancer cell elimination. These result showed that combination therapy involving both a molecularly targeted therapy and chemotherapeutic agent has the ability to retain and enhance therapeutic efficacy. Conclusion: Fe3O4@SiO2(FITC)-FA/AICAR/DOX nanoparticles is superior to monotherapy via the synergetic effect of AICAR and DOX and also the nanoparticle formulation could overcome issues of toxicity with targeted therapy while maintaining the potent anticancer effects of AICAR and DOX.Article Citation - WoS: 24Citation - Scopus: 29Prediction of Acid Mine Drainage Generation Potential of Various Lithologies Using Static Tests: Etili Coal Mine (nw Turkey) as a Case Study(Springer Verlag, 2016) Şanlıyüksel Yücel, Deniz; Baba, AlperThe Etili neighborhood in Can County (northwestern Turkey) has large reserves of coal and has been the site of many small- to medium-scale mining operations since the 1980s. Some of these have ceased working while others continue to operate. Once activities cease, the mining facilities and fields are usually abandoned without rehabilitation. The most significant environmental problem is acid mine drainage (AMD). This study was carried out to determine the acid generation potential of various lithological units in the Etili coal mine using static test methods. Seventeen samples were selected from areas with high acidic water concentrations: from different alteration zones belonging to volcanic rocks, from sedimentary rocks, and from coals and mine wastes. Static tests (paste pH, standard acid–base accounting, and net acid generation tests) were performed on these samples. The consistency of the static test results showed that oxidation of sulfide minerals, especially pyrite—which is widely found not only in the alteration zones of volcanic rocks but also in the coals and mine wastes—is the main factor controlling the generation of AMD in this mine. Lack of carbonate minerals in the region also increases the occurrence of AMD.Article Citation - WoS: 21Citation - Scopus: 24Isolation and Identification of Arcobacter Species From Environmental and Drinking Water Samples(Springer Verlag, 2016) Talay, Funda; Molva, Çelenk; Atabay, Halil İbrahimWater plays an important role in the transmission of Arcobacter spp. to animals and humans. The aim of this study was to isolate and characterize Arcobacter spp. from 115 different water samples (66 sewage, 25 rivers, 16 spring water, and 8 drinking water) in Izmir, Turkey. In total, 41 samples (35.7 %) were found positive for Arcobacter spp. by the genus-specific PCR. Arcobacter butzleri was detected in 39 out of 115 samples (33.9 %) including 24 sewage, 13 rivers, and 2 spring water. The remaining Arcobacter spp. (n = 2) isolates could not be identified by m-PCR and 16S rRNA gene sequencing. Based on the phenotypic characterization, most of the Arcobacter species (87.8 %) indicated weak catalase activity. In addition, there were differences in phenotypic patterns among isolated species during growth at 37 °C under microaerobic and aerobic conditions, in the presence of 2 % (39/41) and 3.5 % (32/41) NaCl and 0.04 % TTC (39/41) and on MacConkey agar (38/41). The results of this study indicated that environmental water samples are common sources for Arcobacter spp. Therefore, effective control measures should be taken to protect human health.