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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 Ultraslow optical modes in Bose-Einstein condensates(Society of Photo-optical Instrumentation Engineers (SPIE), 2007) Tarhan, Devrim; Postacıoğlu, Nazmi; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674Light can be slowed down to ultraslow speeds via electromagnetically induced transparency in atomic Bose-Einstein condensates. This is thought to be useful for storage of quantum information for weak probe pulses. We investigate the effects of inhomogeneous density profile of-the condensate on propagation of such ultraslow pulses. We find that spatial density of an atomic condensate leads to a graded refractive index profile, for an off-resonant probe pulse when condensate parameters are suitably chosen. Within the window of negligible absorption, conditions for degenerate multiple waveguide modes are determined. Both analytical and numerical studies are presented to reveal the effects of experimentally controllable parameters, such as temperature and interatomic interaction strength on the number of modes. Group velocity dispersion and modal dispersion are discussed. The effect of waveguide dispersion, in addition to usual material dispersion, on ultraslow pulses is pointed out.Publication Open Access On the capacity of diffusion-based molecular communications with SiNW FET-based receiver(Institute of Electrical and Electronics Engineers (IEEE), 2016) Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; College of EngineeringMolecular communication (MC) is a bio-inspired communication method based on the exchange of molecules for information transfer among nanoscale devices. Although MC has been extensively studied from various aspects, limitations imposed by the physical design of transceiving units have been largely neglected in the literature. Recently, we have proposed a nanobioelectronic MC receiver architecture based on the nanoscale field effect transistor-based biosensor (bioFET) technology, providing noninvasive and sensitive molecular detection at nanoscale while producing electrical signals at the output. In this paper, we derive analytical closed-form expressions for the capacity and capacity-achieving input distribution for a memoryless MC channel with a silicon nanowire (SiNW) FET-based MC receiver. The resulting expressions could be used to optimize the information flow in MC systems equipped with nanobioelectronic receivers.Publication 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 3D printed personalized magnetic micromachines from patient blood-derived biomaterials(American Association for the Advancement of Science (AAAS), 2021) Ceylan, Hakan; Doğan, Nihal Olcay; Yaşa, İmmihan Ceren; Department of Mechanical Engineering; Sitti, Metin; Musaoğlu, Miraç Nur; Kulalı, Zeynep Umut; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104; N/A; N/AWhile recent wireless micromachines have shown increasing potential for medical use, their potential safety risks concerning biocompatibility need to be mitigated. They are typically constructed from materials that are not intrinsically compatible with physiological environments. Here, we propose a personalized approach by using patient blood-derivable biomaterials as the main construction fabric of wireless medical micromachines to alleviate safety risks from biocompatibility. We demonstrate 3D printed multiresponsive microswimmers and microrollers made from magnetic nanocomposites of blood plasma, serum albumin protein, and platelet lysate. These micro-machines respond to time-variant magnetic fields for torque-driven steerable motion and exhibit multiple cycles of pH-responsive two-way shape memory behavior for controlled cargo delivery and release applications. Their proteinaceous fabrics enable enzymatic degradability with proteinases, thereby lowering risks of long-term toxicity. The personalized micromachine fabrication strategy we conceptualize here can affect various future medical robots and devices made of autologous biomaterials to improve biocompatibility and smart functionality.Publication Open Access Improving CO2 separation performance of MIL-53(Al) by incorporating 1-N-Butyl-3-methylimidazolium methyl sulfate(Wiley, 2019) Department of Chemical and Biological Engineering; N/A; Kulak, Harun; Polat, Hüsamettin Mert; Kavak, Safiyye; Keskin, Seda; Uzun, Alper; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; N/A; N/A; N/A; 40548; 599171-n-Butyl-3-methylimidazolium methyl sulfate is incorporated into MIL-53(Al). Detailed characterization is done by X-ray fluorescence, Brunauer-Emmett-Teller surface area, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. Results show that ionic liquid (IL) interacts directly with the framework, significantly modifying the electronic environment of MIL-53(Al). Based on the volumetric gas adsorption measurements, CO2, CH4, and N-2 adsorption capacities decreased from 112.0, 46.4, and 19.6 cc (STP) g(MIL-53(Al))(-1) to 42.2, 13.0, and 4.3 cc (STP) g(MIL-53(Al))(-1) at 5 bar, respectively, upon IL incorporation. Data show that this postsynthesis modification leads to more than two and threefold increase in the ideal selectivity for CO2 over CH4 and N-2 separations, respectively, as compared with pristine MIL-53(Al). The isosteric heat of adsorption (Qst) values show that IL incorporation increases CO2 affinity and decreases CH4 and N-2 affinities. Cycling adsorption-desorption measurements show that the composite could be regenerated with almost no decrease in the CO2 adsorption capacity for six cycles and confirm the lack of any significant IL leaching. The results offer MIL-53(Al) as an excellent platform for the development of a new class of IL/MOF composites with exceptional performance for CO2 separation.Publication Open Access Self-Help Plus for refugees and asylum seekers; study protocol for a series of individual participant data meta-analyses(Taylor _ Francis, 2021) Karyotaki, Eirini; Sijbrandij, Marit; Purgato, Marianna; Lakin, Daniel; Bailey, Della; Peckham, Emily; Uygun, Ersin; Tedeschi, Federico; Wancata, Johannes; Augustinavicius, Jura; Carswell, Ken; Valimaki, Maritta; van Ommeren, Mark; Koesters, Markus; Popa, Mariana; Leku, Marx Ronald; Anttila, Minna; Churchill, Rachel; White, Ross; Al-Hashimi, Sarah; Lantta, Tella; Au, Teresa; Klein, Thomas; Tol, Wietse A.; Cuijpers, Pim; Barbui, Corrado; Department of Psychology; Acartürk, Ceren; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 39271Background: refugees and asylum seekers face various stressors due to displacement and are especially vulnerable to common mental disorders. To effectively manage psychological distress in this population, innovative interventions are required. The World Health Organization (WHO) Self-Help Plus (SH+) intervention has shown promising outcomes in reducing symptoms of common mental disorders among refugees and asylum seekers. However, individual participant differences in response to SH+ remain largely unknown. The Individual Participant Data (IPD) meta-analysis synthesizes raw datasets of trials to provide cutting-edge evidence of outcomes that cannot be examined by conventional meta-analytic approaches. Objectives: this protocol outlines the methods of a series of IPD meta-analyses aimed at examining the effects and potential moderators of SH+ in (a) reducing depressive symptoms at post-intervention and (b) preventing the six-month cumulative incidence of mental disorders in refugees and asylum seekers. Method: RCTs on SH+ have been identified through WHO and all authors have agreed to share the datasets of the trials. The primary outcomes of the IPD meta-analyses are (a) reduction in depressive symptoms at post-intervention, and (b) prevention of six-month cumulative incidence of mental disorders. Secondary outcomes include post-traumatic stress disorder symptoms, well-being, functioning, quality of life, and twelve-month cumulative incidence of mental disorders. One-stage IPD meta-analyses will be performed using mixed-effects linear/logistic regression. Missing data will be handled by multiple imputation. Conclusions: these results will enrich current knowledge about the response to SH+ and will facilitate its targeted dissemination. The results of these IPD meta-analyses will be published in peer-reviewed journals.