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Publication Open Access Emergence of near-infrared photoluminescence via ZnS shell growth on the AgBiS2 nanocrystals(American Chemical Society, 2024) Department of Chemistry; Department of Electrical and Electronics Engineering; Önal, Asım; Kaya, Tarık Safa; Metin, Önder; Nizamoğlu, Sedat; Department of Chemistry; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of EngineeringAgBiS2 nanocrystals (NCs), composed of nontoxic, earth-abundant materials and exhibiting an exceptionally high absorption coefficient from visible to near-infrared (>105 cm(-1)), hold promise for photovoltaics but have lack of photoluminescence (PL) due to intrinsic nonradiative recombination and challenging shell growth. In this study, we reported a facile wet-chemical approach for the epitaxial growth of ZnS shell on AgBiS2 NCs, which triggered the observation of PL emission in the near-infrared (764 nm). Since high quality of the core is critical for epitaxial shell growth, we first obtained rock-salt structured AgBiS2 NCs with high crystallinity, nearly spherical shape and monodisperse size distribution (<6%) via a dual-ligand approach reacting Ag-Bi oleate with elemental sulfur in oleylamine. Next, a zincblende ZnS shell with a low-lattice mismatch of 4.9% was grown on as-prepared AgBiS2 NCs via a highly reactive zinc (Zn(acac)(2)) precursor that led to a higher photoluminescence quantum yield (PLQY) of 15.3%, in comparison with a relatively low reactivity precursor (Zn(ac)(2)) resulting in reduced PLQY. The emission from AgBiS2 NCs with ultrastrong absorption, facilitated by shell growth, can open up new possibilities in lighting, display, and bioimaging.Publication Open Access Multifunctional alginate-based hydrogel with reversible crosslinking for controlled therapeutics delivery(Elsevier, 2020) Ekinci, Duygu; N/A; Department of Chemical and Biological Engineering; Batool, Syeda Rubab; Nazeer, Muhammad Anwaar; Kızılel, Seda; Şahin, Afsun; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 28376; 171267Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barrier for clinical translation of these materials. Here, we report the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels leads to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two-fold with anthracene conjugation during photopolymerization and photodimerization. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision.Publication Open Access DNA methylation profiling identifies novel markers of progression in hepatitis B-related chronic liver disease(BioMed Central, 2016) Vatansever, Sezgin; Hardy, Timothy; Sarı, Aysegül Akder; Çakalağaoğlu, Fulya; Avcı, Arzu; Zeybel, Gemma Louise; Bashton, Matthew; Mathers, John C.; Ünsal, Belkis; Mann, Jelena; N/A; Department of Molecular Biology and Genetics; Zeybel, Müjdat; Karahüseyinoğlu, Serçin; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; School of Medicine; 214694; 110772Background: Chronic hepatitis B infection is characterized by hepatic immune and inflammatory response with considerable variation in the rates of progression to cirrhosis. Genetic variants and environmental cues influence predisposition to the development of chronic liver disease; however, it remains unknown if aberrant DNA methylation is associated with fibrosis progression in chronic hepatitis B. Results: To identify epigenetic marks associated with inflammatory and fibrotic processes of the hepatitis B-induced chronic liver disease, we carried out hepatic genome-wide methylation profiling using Illumina Infinium beadarrays comparing mild and severe fibrotic disease in a discovery cohort of 29 patients. We obtained 310 differentially methylated regions and selected four loci comprising three genes from the top differentially methylated regions: hypermethylation of HOXA2 and HDAC4 along with hypomethylation of PPP1R18 were significantly linked to severe fibrosis. We replicated the prominent methylation marks in an independent cohort of 102 patients by bisulfite modification and pyrosequencing. The timing and causal relationship of epigenetic modifications with disease severity was further investigated using a cohort of patients with serial biopsies. Conclusions: Our findings suggest a linkage of widespread epigenetic dysregulation with disease progression in chronic hepatitis B infection. Cpg methylation at novel genes sheds light on new molecular pathways, which can be potentially exploited as a biomarker or targeted to attenuate inflammation and fibrosis.Publication Open Access A stochastic representation for mean curvature type geometric flows(Institute of Mathematical Statistics (IMS), 2003) Touzi, N.; Department of Mathematics; Soner, Halil Mete; Faculty Member; Department of Mathematics; College of Administrative Sciences and EconomicsA smooth solution {Gamma(t)}(tis an element of[0,T]) subset of R-d of a parabolic geometric flow is characterized as the reachability set of a stochastic target problem. In this control problem the controller tries to steer the state process into a given deterministic set T with probability one. The reachability set, V(t), for the target problem is the set of all initial data x from which the state process X-X(v)(t) is an element of T for some control process v. This representation is proved by studying the squared distance function to Gamma(t). For the codimension k mean curvature flow, the state process is dX(t) = root2P dW(t), where W(t) is a d-dimensional Brownian motion, and the control P is any projection matrix onto a (d - k)-dimensional plane. Smooth solutions of the inverse mean curvature flow and a discussion of non smooth solutions are also given.Publication Open Access Compressed training based massive MIMO(Institute of Electrical and Electronics Engineers (IEEE), 2019) Yılmaz, Baki Berkay; Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 41624Massive multiple-input-multiple-output (MIMO) scheme promises high spectral efficiency through the employment of large scale antenna arrays in base stations. In time division duplexed implementations, co-channel mobile terminals transmit training information such that base stations can estimate and exploit channel state information to spatially multiplex these users. In the conventional approach, the optimal choice for training length was shown to be equal to the number of users, K. In this paper, we propose a new semiblind framework, named as "MIMO Compressed Training," which utilizes information symbols in addition to training symbols for adaptive spatial multiplexing. We show that this framework enables us to reduce (compress) the training length down to a value close to log(2) (K), i.e., the logarithm of the number of users, without any sparsity assumptions on the channel matrix. We also derive a prescription for the required packet length for proper training. The framework is built upon some convex optimization settings that enable efficient and reliable algorithm implementations. The numerical experiments demonstrate the strong potential of the proposed approach in terms of increasing the number of users per cell and improving the link quality.Publication Open Access TRMU-related transient liver failure of infancy presents with microcephaly and neurodevelopmental delay(Nature Publishing Group (NPG), 2019) N/A; N/A; Azaklı, Hülya; Börklü Yücel, Esra; Arıkan, Çiğdem; Armutlu, Ayşe; Eraslan, Serpil; Kayserili, Hülya; PhD Student; Faculty Member; Teaching Faculty; Researcher; Graduate School of Health Sciences; School of Medicine; N/A; N/A; N/A; N/A; N/A; 7945Publication Open Access Database for CO2 separation performances of MOFs based on computational materials screening(American Chemical Society (ACS), 2018) Eruçar, İlknur; Department of Chemical and Biological Engineering; Altıntaş, Çiğdem; Avcı, Gökay; Harman, Hilal Dağlar; Azar, Ayda Nemati Vesali; Velioğlu, Sadiye; Keskin, Seda; Researcher; Post Doctorate Student; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40548Metal-organic frameworks (MOFs) are potential adsorbents for CO2 capture. Because thousands of MOFs exist, computational studies become very useful in identifying the top performing materials for target applications in a time-effective manner. In this study, molecular simulations were performed to screen the MOF database to identify the best materials for CO2 separation from flue gas (CO2/N-2) and landfill gas (CO2/CH4) under realistic operating conditions. We validated the accuracy of our computational approach by comparing the simulation results for the CO2 uptakes, CO2/N-2 and CO2/CH4 selectivities of various types of MOFs with the available experimental data. Binary CO2/N-2 and CO2/CH4 mixture adsorption data were then calculated for the entire MOF database. These data were then used to predict selectivity, working capacity, regenerability, and separation potential of MOFs. The top performing MOF adsorbents that can separate CO2/N-2 and CO2/CH4 with high performance were identified. Molecular simulations for the adsorption of a ternary CO2/N-2/CH4 mixture were performed for these top materials to provide a more realistic performance assessment of MOF adsorbents. The structure-performance analysis showed that MOFs with Delta Q(st)(0) > 30 kJ/mol, 3.8 angstrom < pore-limiting diameter < 5 angstrom, 5 angstrom < largest cavity diameter < 7.5 angstrom, 0.5 < phi < 0.75, surface area < 1000 m(2)/g, and rho > 1 g/cm(3) are the best candidates for selective separation of CO2 from flue gas and landfill gas. This information will be very useful to design novel MOFs exhibiting high CO2 separation potentials. Finally, an online, freely accessible database https://cosmoserc.ku.edu.tr was established, for the first time in the literature, which reports all of the computed adsorbent metrics of 3816 MOFs for CO2/N-2, CO2/CH4, and CO2/N-2/CH4 separations in addition to various structural properties of MOFs.Publication Open Access The variable selection problem in the Three Worlds of Welfare literature(Springer, 2019) Öker, İbrahim; Yıldırım, Kerem; Yakut-Çakar, Burcu; Department of Sociology; Yörük, Erdem; Faculty Member; Department of Sociology; College of Social Sciences and Humanities; 28982Based on a quantitative meta-analysis of empirical studies, this article points out a significant flaw in the Three Worlds of Welfare literature, the variable selection problem. Compiling, classifying, and quantitatively analysing all variables that have been employed in this literature, the article shows first that variable selection has depended more on case selection than on theory. Scholars tend to employ variables based on data availability, rather than selecting variables according to theoretical frameworks. Second, the use of welfare policy variables is mostly limited to the analysis of Organization for Economic Co-operation and Development (OECD) countries, while studies analysing non-OECD countries, where data is limited, tend to use developmental outcome variables as a proxy. This tendency harms conceptualization and operationalization of welfare regimes, as well as blur the boundary between development and welfare regimes studies. Third, the use of original Esping-Andersen variables remains very limited, undermining continuity, comparability, and reliability within the literature.Publication Open Access Preparation of Pt/Al2O3 and PtPd/Al2O3 catalysts by supercritical deposition and their performance for oxidation of nitric oxide and propene(Elsevier, 2020) Şanlı Yıldız, D.; Özener, B.; Hisar, G.; Rommel, S.; Aindow, M.; Department of Chemical and Biological Engineering; Güneş, Hande; Bozbağ, Selmi Erim; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 29633Pt/Al2O3 and bimetallic PtPd/Al2O3 catalysts were prepared via supercritical deposition method using supercritical carbon dioxide. The effects of Pt loading of Pt/Al2O3 and Pd addition to Pt/Al2O3 on particle size, particle size distribution (PSD) and activity for NO and C3H6 oxidation and C3H6-selective catalytic reduction (C3H6-SCR) were investigated. Pt/Al2O3 catalysts were prepared with Pt loadings of 0.6, 1.2 and 2.1 wt% and a bimetallic PtPd/Al2O3 catalyst was prepared with total metal loading of 1.4 wt% and Pt:Pd molar ratio of 1.3:1. A small fraction of the particles agglomerated after calcination at 550 °C. Around 98 % of the particles had an average particle size of ?1 nm. The rest of the particles were larger and average size of these larger particles was ?10 nm for monometallic catalysts and ?6.5 nm for PtPd/Al2O3. All catalysts were found to be active for NO and C3H6 oxidation and C3H6-SCR reactions. NO oxidation performance of 1.2 wt% Pt/Al2O3 catalyst was the highest. C3H6 oxidation activity increased with increasing metal content. Light-off temperature for C3H6 oxidation shifted to higher temperature in the presence of NO, suggesting competitive oxidation of C3H6 and NO. Concentration profiles indicated that C3H6-SCR started when C3H6 conversion by oxidation reached 50 %; C3H6 was consumed both by oxidation and C3H6-SCR at higher conversions.Publication Open Access Outcome of extended right lobe liver transplants(Wiley, 2021) Lozanovski, Vladimir J.; Unterrainer, Christian; Dohler, Bernd; Mehrabi, Arianeb; Süsal, Caner; Other; School of Medicine; Koç University Hospital; 351800Split-liver transplantation offers a solution to the organ shortage problem. However, the outcomes of extended right lobe liver transplantation (ERLT) and whether it is a suitable alternative to full-size liver transplantation (FSLT) remain controversial. We compared the outcomes of ERLT and FSLT in adult recipients of 43,409 first deceased donor liver transplantations using Cox regression. We also analyzed 612 ERLT and 1224 FSLT 1:2 matched cases to identify factors that affect ERLT outcome. The risk of graft loss was significantly higher following ERLT than following FSLT during the first posttransplantation year in the matched and unmatched collective (hazard ratio [HR], 1.39 and 1.27 and P = 0.01 and 0.006, respectively). Every additional hour of cold ischemia time (CIT) increased the risk of 1-year graft loss by 10% in the ERLT group compared with only 3% in the FSLT group (P = 0.003 and <0.001, respectively). Importantly, the outcome of ERLT and FSLT did not differ significantly if the CIT was below 10 hours (HR, 0.71; P = 0.22). One-year graft and patient survival were lower in high-risk ERLT recipients with a Model for End-Stage Liver Disease (MELD) score of ?20 (HR, 1.88; P = 0.03 and HR, 2.03; P = 0.02). In the male recipient–male donor combination, ERLT recipients had a higher risk of 1-year graft loss than FSLT recipients (HR, 2.44; P = 0.006). This was probably because of the significantly higher MELD score in ERLT recipients (P = 0.004). ERLT in adults is an adequate alternative to FSLT and offers an elegant solution to the problem of organ shortage as long as the cold storage is less than 10 hours and the recipient’s MELD score is <20.