PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

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Now showing 1 - 20 of 775

Citation - WoS: 6
Citation - Scopus: 7
1,2-Diborolanes With Strong Donor Substituents: Synthesis and High Antimicrobial Activity
(Academic Press, 2021) Şahin, Yüksel; Poyrazoğlu Çoban, Esin; Sevinçek, Resul; Bıyık, Halil H.; Özgener, Hüseyin; Aygün, Muhittin
1,2-diborolanes with strong and without strong donor substituents have been described, and are also referred to as 1,2-diboracyclopentane. The 1,2-diaryl/alkyl-amino-1,2-diboracyclopentanes 2, 3, and 4 were obtained in good yield after the reaction of 1,2-dichloro-1,2-diboracyclopentane 1 with ArNHLi and Me3Si-NR2. The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2b, 2c, 2e, 4, and 5f were also determined by single-crystal X-ray diffraction. The newly synthesized 1,2-borolanes are stable in air and showed particularly high activity against some Gram-positive bacteria. © 2020 Elsevier Inc.
Citation - WoS: 11
Citation - Scopus: 14
3D Bioprinting of mouse pre-osteoblasts and human MSCs using bioinks consisting of gelatin and decellularized bone particles
(Iop Publishing Ltd, 2024) Kara, Aylin; Distler, Thomas; Akkineni, Ashwini Rahul; Tihminlioglu, Funda; Gelinsky, Michael; Boccaccini, Aldo R.
One of the key challenges in biofabrication applications is to obtain bioinks that provide a balance between printability, shape fidelity, cell viability, and tissue maturation. Decellularization methods allow the extraction of natural extracellular matrix, preserving tissue-specific matrix proteins. However, the critical challenge in bone decellularization is to preserve both organic (collagen, proteoglycans) and inorganic components (hydroxyapatite) to maintain the natural composition and functionality of bone. Besides, there is a need to investigate the effects of decellularized bone (DB) particles as a tissue-based additive in bioink formulation to develop functional bioinks. Here we evaluated the effect of incorporating DB particles of different sizes (<= 45 and <= 100 mu m) and concentrations (1%, 5%, 10% (wt %)) into bioink formulations containing gelatin (GEL) and pre-osteoblasts (MC3T3-E1) or human mesenchymal stem cells (hTERT-MSCs). In addition, we propose a minimalistic bioink formulation using GEL, DB particles and cells with an easy preparation process resulting in a high cell viability. The printability properties of the inks were evaluated. Additionally, rheological properties were determined with shear thinning and thixotropy tests. The bioprinted constructs were cultured for 28 days. The viability, proliferation, and osteogenic differentiation capacity of cells were evaluated using biochemical assays and fluorescence microscopy. The incorporation of DB particles enhanced cell proliferation and osteogenic differentiation capacity which might be due to the natural collagen and hydroxyapatite content of DB particles. Alkaline phosphatase activity is increased significantly by using DB particles, notably, without an osteogenic induction of the cells. Moreover, fluorescence images display pronounced cell-material interaction and cell attachment inside the constructs. With these promising results, the present minimalistic bioink formulation is envisioned as a potential candidate for bone tissue engineering as a clinically translatable material with straightforward preparation and high cell activity.
Citation - WoS: 48
Citation - Scopus: 48
5-Fluorouracil Signaling Through a Calcium-Calmodulin Pathway Is Required for P53 Activation and Apoptosis in Colon Carcinoma Cells
(Nature Publishing Group, 2013-09) Can, G.; Akpınar, B.; Baran, Yusuf; Zhivotovsky, B.; Olsson, M.
5-Fluorouracil (5-FU) is an anti-metabolite that is in clinical use for treatment of several cancers. In cells, it is converted into three distinct fluoro-based nucleotide analogs, which interfere with DNA synthesis and repair, leading to genome impairment and, eventually, apoptotic cell death. Current knowledge states that in certain cell types, 5-FU-induced stress is signaling through a p53-dependent induction of tumor necrosis factor-receptor oligomerization required for death-inducing signaling complex formation and caspase-8 activation. Here we establish a role of calcium (Ca 2+) as a messenger for p53 activation in response to 5-FU. Using a combination of pharmacological and genetic approaches, we show that treatment of colon carcinoma cells stimulates entry of extracellular Ca 2+ through long lasting-type plasma membrane channels, which further directs posttranslational phosphorylation of at least three p53 serine residues (S15, S33 and S37) by means of calmodulin (CaM) activity. Obstructing this pathway by the Ca 2+ -chelator BAPTA (1,2-bis(o-aminophenoxy)ethane- N,N,N',N'-tetraacetic acid) or by inhibitors of CaM efficiently reduces 5-FU-induced caspase activities and subsequent cell death. Moreover, ectopic expression of p53 S15A in HCT116 p53 -/- cells confirmed the importance of a Ca 2+ -CaM-p53 axis in 5-FU-induced extrinsic apoptosis. The fact that a widely used therapeutic drug, such as 5-FU, is operating via this pathway could provide new therapeutic intervention points, or specify new combinatorial treatment regimes. © 2013 Macmillan Publishers Limited.
A Green Route to Albumin/Albumin Polyelectrolyte Complex Nanoparticles in Water With High Drug Loading for Drug Delivery
(Elsevier, 2025) Sozer-Demirdas, Sumeyra Cigdem; Erez, Ozlem; Cakan-Akdogan, Gulcin; Akdogan, Yasar
A polyelectrolyte complex (PEC) formation offers a simple and green approach to obtaining albumin nanoparticles (NPs) without the use of organic solvents, crosslinkers and specialized equipment. The prepared cationic albumin proteins interact with anionic albumin proteins to form albumin PEC NPs (110 nm) with +37 mV surface zeta potential. Furthermore, albumin PEC NPs preparation in water alone achieves chlorambucil (CHL) loading up to 17 times higher than the conventional desolvation method, largely due to the elimination of drug loss to organic solvents. CHL loaded albumin PEC NPs also decreased the cell viability (Huh-7) to 44 % within 24 h. This study demonstrates that high drug-loaded albumin NPs can be alternatively synthesized by using albumin polyelectrolyte properties, and applied in drug delivery applications.
Citation - WoS: 43
Citation - Scopus: 46
Aas, Xrpd, Sem/Eds, and Ftir Characterization of Zn2+ Retention by Calcite, Calcite–kaolinite, and Calcite–clinoptilolite Minerals
(Elsevier Ltd., 2005-04-08) Shahwan, Talal; Zünbül, Banu; Tunusoğlu, Özge; Eroğlu, Ahmet Emin
In this study, the sorption behavior of Zn2+ on calcite, kaolinite, and clinoptilolite, in addition to mixtures of calcite with kaolinite and clinoptilolite, was investigated at various loadings and mixture compositions using atomic absorption spectroscopy, scanning electron microscopy/energy dispersive X-ray spectroscopy, X-ray powder diffraction, and Fourier transform infrared techniques. According to the obtained results, within the experimental operating conditions, the sorption capacity was enhanced with increasing amount of calcite in both types of mixtures. Under neutral–alkaline pH conditions and high loadings, the order of Zn2+ retention was observed as calcite > clinoptilolite > kaolinite. The experiments on the retention of Zn2+ by pure calcite under conditions of oversaturation showed that the uptake process proceeds via an initial adsorption mechanism (possibly ion-exchange type) followed by a slower mechanism that leads to the overgrowth of the hydrozincite phase, Zn5(OH)6(CO3)2.
Citation - Scopus: 1
Abnormally Accumulated Gm2 Ganglioside Contributes To Skeletal Deformity in Tay-Sachs Mice
(Springer Heidelberg, 2024) Demir, Secil Akyildiz; Seyrantepe, Volkan
Tay-Sachs Disease is a rare lysosomal storage disorder caused by mutations in the HEXA gene, responsible for the degradation of ganglioside GM2. In addition to progressive neurodegeneration, Tay-Sachs patients display bone anomalies, including kyphosis. Tay-Sachs disease mouse model (Hexa-/-Neu3-/-) shows both neuropathological and clinical abnormalities of the infantile-onset disease phenotype. In this study, we investigated the effects of GM2 accumulation on bone remodeling activity. Here, we evaluated the bone phenotype of 5-month-old Hexa-/-Neu3-/- mice with age-matched control groups using gene expression analysis, bone plasma biomarker analysis, and micro-computed tomography. We demonstrated lower plasma alkaline phosphatase activity and calcium levels with increased tartrate-resistant acid phosphatase levels, indicating reduced bone remodeling activity in mice. Consistently, gene expression analysis confirmed osteoblast reduction and osteoclast induction in the femur of mice. Micro-computed tomography and analysis show reduced trabecular bone volume, mineral density, number, and thickness in Hexa-/-Neu3-/- mice. In conclusion, we demonstrated that abnormal GM2 ganglioside accumulation significantly triggers skeletal abnormality in Tay-Sachs mice. We suggest that further investigation of the molecular basis of bone structure anomalies is necessary to elucidate new therapeutic targets that prevent the progression of bone symptoms and improve the life standards of Tay-Sachs patients.
Citation - WoS: 93
Citation - Scopus: 111
The Accelerating Effects of the Microorganisms on Biodeterioration of Stone Monuments Under Air Pollution and Continental-Cold Climatic Conditions in Erzurum, Turkey
(Elsevier Ltd., 2006-07) Nuhoğlu, Yaşar; Ensar, Oğuz; Uslu, Hakan; Özbek, Ahmet; İpekoğlu, Başak; Ocak, İjlal; Hasenekoğlu, İsmet
The aim of this research was to determine the accelerating effects of microorganisms on the biodeterioration of stone under air pollution and continental-cold climatic region in Erzurum, Turkey. Studies have been carried out on specimens of the Rustempasa Bazaar, the Lalapasa Mosque, the Erzurum Castle Mosque, the Double Minarets-Madrasah, the Great Mosque and the Haji Mehmet Fountain aged from 441 to 823 years old. The results showed that vegetative and reproductive (generative) forms of the microorganisms could develop during the winter months when the night time average temperature was even - 25 °C. Also the reproductive forms had developed and the whole stone surface was covered with a biofilm caused by the microorganisms. Silicon, aluminum, calcium, potassium, titanium, magnesium, zinc, sulfur, iron, sodium, and niobium were found in the stones of the historical buildings with varying amounts through the SEM-EDS analysis. Some of these elements could be used as an energy resource for the microorganisms together with the air pollutants such as sulfur dioxide, nitrogen oxides and particles on the stone surfaces. Of 21 isolates, 15 species from 6 bacterium genera and 5 species from 5 fungi genera plus 1 fungi genera were identified on the deteriorated stone surfaces even during the coldest months by microbial identification system (MIS) and these findings were tested by SEM investigations.
Citation - WoS: 34
Citation - Scopus: 36
Acclimation To Heat During Incubation. 2. Embryo Composition and Residual Egg Yolk Sac Fatty Acid Profiles in Chicks
(Elsevier, 2008-06) Yalçın, S.; Bağdatlıoğlu, Neriman; Bruggeman, V.; Babacanoglu, E.; Uysal, İlke; Buyse, J.; Decuypere, E.; Siegel, P. B.
The aim of the research was to evaluate embryo composition and changes in egg yolk fatty acid composition during embryonic development as a function of incubation temperature and age of breeders. Eggs obtained from a common breeder stock at 3 ages: 32 (younger), 42 (mid age), and 65 (older) wk were divided into 2 groups and placed into 2 incubators: the control and the second where eggs were heat-acclimated (HA) at 38.5°C for 6 h daily from d 10 to 18 of incubation. Body composition of embryos and chicks were measured on d 14, 18, and at hatch, respectively. Fatty acid profiles of yolk and residual egg yolk sac of chicks were analyzed before incubation and at hatch, respectively. Moisture content of embryos was highest on d 14 and then decreased regardless of parental age and incubation temperature. Moisture content of chicks at hatch from 42- and 65-wk parents were lower than those of chicks from 32-wk parents, whereas the trend in chick fat content was opposite. Incubation temperature had no effect on composition of chicks. Consistently lower cis-4,7,10,13,16,19- eicosapentaenoic (docosahexaenoic acid, DHA; 22:6n-3) and cis-11,14,17- eicosatrienoic (20:3n-3) fatty acids in the residual yolk sac of chicks than in egg yolks before incubation may have resulted from preferential uptake from the yolk. The DHA content in the residual yolk sac was considerably higher in chicks from older parents incubated at HA, whereas, in contrast, levels of 18:3n-3 were lower. Also, chicks from younger parents in the HA treatment had lower transported 18:3n-3 and higher levels of transported DHA. It may be concluded that this process observed during the high incubation temperature may be related to a protective strategy and thus contributes to postnatal heat adaptation.
Citation - WoS: 70
Citation - Scopus: 87
Adsorption of Olive Leaf (olea Europaea L.) Antioxidants on Silk Fibroin
(American Chemical Society, 2007) Bayçın, Deniz; Altıok, Evren; Ülkü, Semra; Bayraktar, Oğuz
The adsorption isotherms of oleuropein and rutin were evaluated at different temperatures, pH values, and solid/liquid ratios. The experimental data of adsorption isotherms were well fitted to a Langmuir model. The maximum adsorption capacities were determined as 108 mg of oleuropein/g of silk fibroin and 21 mg of rutin/g of silk fibroin. After adsorption of oleuropein and rutin, the antioxidant capacity of silk fibroin increased from 1.93 to 3.61 mmol of TEAC/g. Silk fibroin also gained antimicrobial activity against Staphylococcus aureus and Klebsiella pneumoniae after adsorption of olive leaf antioxidants. In a desorption process, 81% of rutin and 85% of oleuropein were removed from the adsorbent surface in 70% aqueous ethanol solution. Consequently, silk fibroin was found to be a promising biomaterial for the production of functional food or dietary supplements and for the purification of oleuropein and rutin from olive leaf extracts.
Citation - WoS: 64
Citation - Scopus: 81
Advanced Backcross Qtl Analysis of a Lycopersicon Esculentum X L. Pennellii Cross and Identification of Possible Orthologs in the Solanaceae
(Springer Verlag, 2004-02) Frary, Anne; Fulton, Theresa M.; Zamir, Dani; Tanksley, Steven D.
In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC2 plants were genotyped with 150 molecular markers and BC2F1 plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs (fs2b.1, fw3.1/fsz3.1 andfs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.
Citation - WoS: 17
Citation - Scopus: 16
Aggregatibacter Actinomycetemcomitans Groel Protein Promotes Conversion of Human Cd4+ T Cells Into Ifn Gamma Il10 Producing Tbet+ Th1 Cells
(Public Library of Science, 2012-11) Saygılı, Tahsin; Akıncılar, Semih Can; Akgül, Bünyamin; Nalbant Aldanmaz, Ayten
One of the heat shock family protein (Hsp) expressing bacteria is the gram negative, periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa). A. actinomycetemcomitans' Hsp is a 64-kDa GroEL-protein, which has been shown to influence the host cells. In this study we used recombinant A. actinomycetemcomitans GroEL (rAaGroEL) protein as a model antigen to study GroEL-mediated T cell immune response. Human peripheral mononuclear cells (PBMCs), when stimulated with recombinant rAaGroEL, expressed early activation marker CD69 and IL-2R (CD25). CD25 and CD69 expressions were higher in CD4+ T cells compared to CD8+ T cells. rAaGroEL-responding CD4+ T cells expressed IL-10, IFNγ and TNFα cytokines. Interestingly, there were also IL-10 and IFNγ double cytokine producing CD4+ T cells. Additionally, IFNγ expressing CD4+ T cells were also T-bet positive. Altogether the results suggest that rAaGroEL protein affects CD4+ T cells to differentiate into IFNγ IL10-secreting T-bet+ Th1 cells.
Citation - WoS: 64
Citation - Scopus: 74
Air and Seawater Pollution and Air–sea Gas Exchange of Persistent Toxic Substances in the Aegean Sea: Spatial Trends of Pahs, Pcbs, Ocps and Pbdes
(Springer Verlag, 2015-08) Lammel, Gerhard; Audy, Ondrej; Besis, Athanasios; Efstathiou, Christos; Eleftheriadis, Kostas; Kohoutek, Jiri; Kukucka, Petr; Mulder, Marie D.; Pribylova, Petra; Prokes, Roman; Rusina, Tatsiana P.; Samara, Constantini; Sofuoğlu, Aysun; Sofuoğlu, Sait Cemil; Taşdemir, Yücel; Vassilatou, Vassiliki; Voutsa, Dimitra; Vrana, Branislav
Near-ground air (26 substances) and surface seawater (55 substances) concentrations of persistent toxic substances (PTS) were determined in July 2012 in a coordinated and coherent way around the Aegean Sea based on passive air (10 sites in 5 areas) and water (4 sites in 2 areas) sampling. The direction of air–sea exchange was determined for 18 PTS. Identical samplers were deployed at all sites and were analysed at one laboratory. hexachlorobenzene (HCB), hexachlorocyclohexanes (HCHs) as well as dichlorodiphenyltrichloroethane (DDT) and its degradation products are evenly distributed in the air of the whole region. Air concentrations of p,p′-dichlorodiphenyldichloroethylene (p,p′-DDE) and o,p′-DDT and seawater concentrations of p,p′-DDE and p,p′-DDD were elevated in Thermaikos Gulf, northwestern Aegean Sea. The polychlorinated biphenyl (PCB) congener pattern in air is identical throughout the region, while polybrominated diphenylether (PBDE)patterns are obviously dissimilar between Greece and Turkey. Various pollutants, polycyclic aromatic hydrocarbons (PAHs), PCBs, DDE, and penta- and hexachlorobenzene are found close to phase equilibrium or net-volatilisational (upward flux), similarly at a remote site (on Crete) and in the more polluted Thermaikos Gulf. The results suggest that effective passive air sampling volumes may not be representative across sites when PAHs significantly partitioning to the particulate phase are included.
Airborne and Dust-Bound PBDEs Indoors and Outdoors in Izmir, Türkiye: A Multi-Route Exposure - Risk Assessment
(Elsevier Sci Ltd, 2025) Genisoglu, Mesut; Edebali, Ozge; Sofuoglu, Aysun; Turgut, Cafer; Sofuoglu, Sait C.
Phased-out flame retardants, e.g., polybrominated diphenyl ethers (PBDEs), persist in environmental media due to their resistance to degradation and ongoing emissions from PBDE containing materials and industrial activities. This study addresses a notable data gap in a unique setting, i.e., & Idot;zmir, T & uuml;rkiye, by investigating PBDE levels at homes, schools, and caf & eacute;/bar/restaurants, and assessing exposure and associated health risks. Indoor and outdoor air and dust samples were collected from rural, suburban, and urban areas. Exposure through ingestion, dermal absorption, and inhalation routes, and associated chronic-toxic and carcinogenic risks were estimated with Monte Carlo Simulation. Despite having been phase-out, house-dust Sigma BDE concentrations remained prevalent with average levels of >2000 ng/g in schools and homes, while outdoors they were <500 ng/g. BDE-209 was the predominant congener with an indoor air concentration of 486 pg/m(3) in schools and 56.7 pg/m(3) in homes. BDE-209 contributed 83.5-90.4 % of the indoor air Sigma BDE concentration in schools, while in homes this contribution ranged from 70.8 to 75.8 %. Aggregate exposure estimates show the predominant PBDE congener, BDE-209, was primarily exposed by accidental ingestion (58.6 %) followed by dermal absorption (21.9 %) and inhalation (19.5 %). Chronic-toxic risk (CTR, for BDE-47, BDE-99, BDE-153, and BDE-209) and carcinogenic risk (CR, for BDE-209) for the ingestion and dermal absorption routes indicated that house-dust and indoor-air PBDE exposures are not found to be considerable for human health. However, the contribution of inhalation route to the aggregate exposure of BDE-28, BDE-47, BDE-100, BDE-99 (87.0 %, 60.5 %, 54.3 %, and 57.3 %, respectively) may indicate the evermore PBDE exposure by inhalation for lower brominated congeners as they become more significant through environmental debromination of the predominant BDE-209.
Citation - WoS: 7
Altorfev Facilitates the Prediction of Alternative Open Reading Frames in Eukaryotic Mrnas
(Oxford University Press, 2017) Kochetov, Alex V.; Allmer, Jens; Klimenko, Alexandra I.; Zuraev, Bulat S.; Matushkin, Yury G.; Lashin, Sergey A.
Motivation: Protein synthesis is not a straight forward process and one gene locus can produce many isoforms, for example, by starting mRNA translation from alternative start sites. altORF evaluator (altORFev) predicts alternative open reading frames within eukaryotic mRNA translated by a linear scanning mechanism and its modifications (leaky scanning and reinitiation). The program reveals the efficiently translated altORFs recognized by the majority of 40S ribosomal subunits landing on the 50-end of an mRNA. This information aids to reveal the functions of eukaryotic genes connected to synthesis of either unknown isoforms of annotated proteins or new unrelated polypeptides.
Citation - Scopus: 1
Analysis of Microplastic Flux From the Gediz River To the Aegean Sea: a Modeling Study for Environmental Management
(Academic Press Ltd- Elsevier Science Ltd, 2025) Kazanci, Yigithan; Alyuruk, Nefise; Alpergun, Cumana; Kara, Nursena; Baycan, Neval; Gunduz, Orhan
It is critical to determine the abundance of microplastics in terrestrial inland waters, understand their fate and transport mechanisms, and reveal their status in aquatic environments. This study aimed to develop and calibrate a mathematical model to simulate microplastic (MP) pollution in the Gediz River Basin, T & uuml;rkiye, which focused on MP fate and transport under existing conditions and various management scenarios. The baseline scenario revealed that, despite a ninefold difference in flow rates, the midstream and upstream parts of the basin also exhibited significant contamination, with an average concentration of 25 n/L compared to the downstream average of 29 n/L. The model was later simulated to test the effects of various mitigation scenarios including but not limited to reducing MP discharges from wastewater treatment plants (WWTPs) and implementing vegetative barriers in tributaries. Scenario 4, which involves reducing MP concentrations in upstream tributaries with vegetative barriers, achieved the highest average reduction across all segments (32 %) and specifically in the downstream area (47 %). In contrast, Scenario 1, aimed at reducing wastewater discharges from urban and industrial WWTPs through water reclamation, and Scenario 2, which focused on eliminating MP in Organized Industrial Zone (OIZ) discharges by changing industrial inputs, achieved the most effective MP reductions in the upper basin, with reductions of 20 % and 17 %, respectively. Scenario 3, targeting flow reduction and accumulation through constructed wetlands, had minimal impact, with reductions close to 0 % in most areas. These results highlight the need for comprehensive approaches to effectively reduce MP pollution, particularly in managing upstream and tributary sources.
An Analytical Methodology for the Determination of Cadmium Bound To Whey-Proteins by Laser-Induced Breakdown Spectroscopy at Low Pressures
(Elsevier, 2026) Erdogrul, Ilayda Yaman; Yalcin, Serife H.
In this study, a dried-droplet LIBS methodology for determining cadmium in cow milk has been developed. The performance of the methodology was shown by standard and real protein samples. A standard protein, bovine serum albumin (BSA), and whey protein extracted from skim cow milk were incubated in standard Cd solutions, and the complex solution was filtered through cut-off filters by centrifugation. The unreacted cadmium in the filtrate and Cd-bound protein in the filtered fraction were loaded separately onto a Si-wafer substrate and analyzed via dried-droplet LIBS methodology. Measurements were performed at reduced pressures by taking advantage of the signal enhancement effect. The optimum pressure for most Cd emission lines was found to be 100 mbar. It has been shown that the dried-droplet LIBS methodology at reduced pressures can be used for the identification and determination of free and protein-bound Cd in the whey matrix. The concentration-based detection limit of Cd bound to whey proteins was determined to be 20.2 ng mL- 1, which corresponds to as low as 10 pg in absolute amount with a sample volume of 500 nL. The LOQ value is estimated as 67.3 ng mL- 1 and 33.3 pg, in terms of concentration unit and absolute amount, respectively. The use of small sample volumes is important in the analysis of limited amounts of samples, such as body fluids. Preconcentration studies with multiple loadings of the sample on the same spot resulted in improvements in concentration-based detection. 8 ng mL- 1 Cd in the whey matrix that could not be determined by a single droplet loading due to being below the detection limit; could be determined after 10 consecutive loadings. The methodology may also be applied to the determination of other toxic metals bound to proteins for food quality control.
Citation - WoS: 23
Citation - Scopus: 24
Analytical Solution of Poisson-Boltzmann Equation for Interacting Plates of Arbitrary Potentials and Same Sign
(Elsevier Ltd., 2010-01) Polat, Mehmet; Polat, Hürriyet
Efficient calculation of electrostatic interactions in colloidal systems is becoming more important with the advent of such probing techniques as atomic force microscopy. Such practice requires solving the nonlinear Poisson-Boltzmann equation (PBE). Unfortunately, explicit analytical solutions are available only for the weakly charged surfaces. Analysis of arbitrarily charged surfaces is possible only through cumbersome numerical computations. A compact analytical solution of the one-dimensional PBE is presented for two plates interacting in symmetrical electrolytes. The plates can have arbitrary surface potentials at infinite separation as long they have the same sign. Such a condition covers a majority of the colloidal systems encountered. The solution leads to a simple relationship which permits determination of surface potentials, surface charge densities, and electrostatic pressures as a function of plate separation H for different charging scenarios. An analytical expression is also presented for the potential profile between the plates for a given separation. Comparison of these potential profiles with those obtained by numerical analysis shows the validity of the proposed solution. © 2009 Elsevier Inc. All rights reserved.
Citation - WoS: 64
Citation - Scopus: 67
Angle Resolved Vibrational Properties of Anisotropic Transition Metal Trichalcogenide Nanosheets
(Royal Society of Chemistry, 2017-03) Kong, Wilson; Bacaksız, Cihan; Chen, Bin; Wu, Kedi; Blei, Mark; Fan, Xi; Shen, Yuxia; Şahin, Hasan; Wright, David; Narang, Deepa S.; Tongay, Sefaattin
Layered transition metal trichalcogenides (TMTCs) are a new class of anisotropic two-dimensional materials that exhibit quasi-1D behavior. This property stems from their unique highly anisotropic crystal structure where vastly different material properties can be attained from different crystal directions. Here, we employ density functional theory predictions, atomic force microscopy, and angle-resolved Raman spectroscopy to investigate their fundamental vibrational properties which differ significantly from other 2D systems and to establish a method in identifying anisotropy direction of different types of TMTCs. We find that the intensity of certain Raman peaks of TiS3, ZrS3, and HfS3 have strong polarization dependence in such a way that intensity is at its maximum when the polarization direction is parallel to the anisotropic b-axis. This allows us to readily identify the Raman peaks that are representative of the vibrations along the b-axis direction. Interestingly, similar angle resolved studies on the novel TiNbS3 TMTC alloy reveal that determination of anisotropy/crystalline direction is rather difficult possibly due to loss of anisotropy by randomization distribution of quasi-1D MX6 chains by the presence of defects which are commonly found in 2D alloys and also due to the complex Raman tensor of TMTC alloys. Overall, the experimental and theoretical results establish non-destructive methods used to identify the direction of anisotropy in TMTCs and reveal their vibrational characteristics which are necessary to gain insight into potential applications that utilize direction dependent thermal response, optical polarization, and linear dichroism.
Anisotropic Structural, Vibrational, Electronic, Optical, and Elastic Properties of Single-Layer Hafnium Pentatelluride: an ab Initio Study
(Royal Soc Chemistry, 2024) Dogan, Kadir Can; Cetin, Zebih; Yagmurcukardes, Mehmet
Motivated by the highly anisotropic nature of bulk hafnium pentatelluride (HfTe5), the structural, vibrational, electronic, optical, and elastic properties of single-layer two-dimensional (2D) HfTe5 were investigated by performing density functional theory (DFT)-based first-principles calculations. Total energy and geometry optimizations reveal that the 2D single-layer form of HfTe5 exhibits in-plane anisotropy. The phonon band structure shows dynamic stability of the free-standing layer and the predicted Raman spectrum displays seven characteristic Raman-active phonon peaks. In addition to its dynamic stability, HfTe5 is shown to exhibit thermal stability at room temperature, as confirmed by quantum molecular dynamics simulations. Moreover, the obtained elastic stiffness tensor elements indicate the mechanical stability of HfTe5 with its orientation-dependent soft nature. The electronic band structure calculations show the indirect-gap semiconducting behavior of HfTe5 with a narrow electronic band gap energy. The optical properties of HfTe5, in terms of its imaginary dielectric function, absorption coefficient, reflectance, and transmittance, are shown to exhibit strong in-plane anisotropy. Furthermore, structural analysis of several point defects and their oxidized structures was performed by means of simulated STM images. Among the considered vacancy defects, namely , , VTeout, VTein, , and VHf, the formation of VTeout is revealed to be the most favorable defect. While and VHf defects lead to local magnetism, only the oxygen-substituted VHf structure possesses magnetism among the oxidized defects. Moreover, it is found that all the bare and oxidized vacant sites can be distinguished from each other through the STM images. Overall, our study indicates not only the fundamental anisotropic features of single-layer HfTe5, but also shows the signatures of feasible point defects and their oxidized structures, which may be useful for future experiments on 2D HfTe5.
Citation - WoS: 131
Citation - Scopus: 137
Antagonistic Roles of Notch and P63 in Controlling Mammary Epithelial Cell Fates
(Nature Publishing Group, 2010-10) Yalçın Özuysal, Özden; Fiche, M.; Guitierrez, M.; Wagner, K. U.; Raffoul, W.; Brisken, C.
The breast epithelium has two major compartments, luminal and basal cells, that are established and maintained by poorly understood mechanisms. The p53 homolog, p63, is required for the formation of mammary buds, but its function in the breast after birth is unknown. We show that in primary human breast epithelial cells, maintenance of basal cell characteristics depends on continued expression of the p63 isoform, ΔNp63, which is expressed in the basal compartment. Forced expression of ΔNp63 in purified luminal cells confers a basal phenotype. Notch signaling downmodulates ΔNp63 expression and mimics ΔNp63 depletion, whereas forced expression of ΔNp63 partially counteracts the effects of Notch. Consistent with Notch activation specifying luminal cell fate in the mammary gland, Notch signaling activity is specifically detected in mice at sites of pubertal ductal morphogenesis where luminal cell fate is determined. Basal cells in which Notch signaling is active show decreased p63 expression. Both constitutive expression of ΔNp63 and ablation of Notch signaling are incompatible with luminal cell fate. Thus, the balance between basal and luminal cell compartments of the breast is regulated by antagonistic functions of ΔNp63 and Notch. © 2010 Macmillan Publishers Limited All rights reserved.

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