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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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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 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 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.Publication Open Access The MHC class I MICA gene is a histocompatibility antigen in kidney transplantation(Springer Nature, 2022) Carapito, Raphael; Aouadi, Ismail; Verniquet, Martin; Untrau, Meiggie; Pichot, Angelique; Beaudrey, Thomas; Bassand, Xavier; Meyer, Sebastien; Faucher, Loic; Posson, Juliane; Morlon, Aurore; Kotova, Irina; Delbos, Florent; Walencik, Alexandre; Aarnink, Alice; Kennel, Anne; Suberbielle, Caroline; Taupin, Jean-Luc; Matern, Benedict M.; Spierings, Eric; Congy-Jolivet, Nicolas; Essaydi, Arnaud; Perrin, Peggy; Blancher, Antoine; Charron, Dominique; Cereb, Nezih; Maumy-Bertrand, Myriam; Bertrand, Frederic; Garrigue, Valerie; Pernin, Vincent; Weekers, Laurent; Naesens, Maarten; Kamar, Nassim; Legendre, Christophe; Glotz, Denis; Caillard, Sophie; Ladriere, Marc; Giral, Magali; Anglicheau, Dany; Bahram, Seiamak; Süsal, Caner; Other; School of MedicineThe identity of histocompatibility loci, besides human leukocyte antigen (HLA), remains elusive. The major histocompatibility complex (MHC) class I MICA gene is a candidate histocompatibility locus. Here, we investigate its role in a French multicenter cohort of 1,356 kidney transplants. MICA mismatches were associated with decreased graft survival (hazard ratio (HR), 2.12; 95% confidence interval (CI): 1.45-3.11; P < 0.001). Both before and after transplantation anti-MICA donor-specific antibodies (DSA) were strongly associated with increased antibody-mediated rejection (ABMR) (HR, 3.79; 95% CI: 1.94-7.39; P < 0.001; HR, 9.92; 95% CI: 7.43-13.20; P < 0.001, respectively). This effect was synergetic with that of anti-HLA DSA before and after transplantation (HR, 25.68; 95% CI: 3.31-199.41; P = 0.002; HR, 82.67; 95% CI: 33.67-202.97; P < 0.001, respectively). De novo-developed anti-MICA DSA were the most harmful because they were also associated with reduced graft survival (HR, 1.29; 95% CI: 1.05-1.58; P = 0.014). Finally, the damaging effect of anti-MICA DSA on graft survival was confirmed in an independent cohort of 168 patients with ABMR (HR, 1.71; 95% CI: 1.02-2.86; P = 0.041). In conclusion, assessment of MICA matching and immunization for the identification of patients at high risk for transplant rejection and loss is warranted.Publication Open Access A proximity mapping journey into the biology of the mammalian centrosome/cilium complex(Multidisciplinary Digital Publishing Institute (MDPI), 2020) Department of Molecular Biology and Genetics; Arslanhan, Melis Dilara; Gülensoy, Dila; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 206349The mammalian centrosome/cilium complex is composed of the centrosome, the primary cilium and the centriolar satellites, which together regulate cell polarity, signaling, proliferation and motility in cells and thereby development and homeostasis in organisms. Accordingly, deregulation of its structure and functions is implicated in various human diseases including cancer, developmental disorders and neurodegenerative diseases. To better understand these disease connections, the molecular underpinnings of the assembly, maintenance and dynamic adaptations of the centrosome/cilium complex need to be uncovered with exquisite detail. Application of proximity-based labeling methods to the centrosome/cilium complex generated spatial and temporal interaction maps for its components and provided key insights into these questions. In this review, we first describe the structure and cell cycle-linked regulation of the centrosome/cilium complex. Next, we explain the inherent biochemical and temporal limitations in probing the structure and function of the centrosome/cilium complex and describe how proximity-based labeling approaches have addressed them. Finally, we explore current insights into the knowledge we gained from the proximity mapping studies as it pertains to centrosome and cilium biogenesis and systematic characterization of the centrosome, cilium and centriolar satellite interactomes.Publication Open Access Hypothetical yet effective: computational identification of high-performing MOFs for CO2 capture(Elsevier, 2022) Department of Chemical and Biological Engineering; Demir, Hakan; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; 40548With the advances in computational resources and algorithms, computer simulations are being increasingly used to tackle the most challenging problems of the world. Among them, CO2 capture is a topic that needs imminent attention as the presence of high levels of CO2 in the air can lead to drastic shifts in global climate. Here, a recently developed hypothetical metal-organic framework (MOF) database comprised of anion-pillared (AP) MOFs is computationally screened for the separation of CO2/CO, CO2/H-2, and CO2/N-2 gas mixtures at room temperature. The best performing MOFs are identified using three performance metrics, adsorption selectivity, working capacity, and regenerability, in conjunction. In these top materials, the preferential adsorption sites are illustrated, which will be useful in guiding the experimental design of new MOFs with extraordinarily high CO2 selectivities. The favorable separation performances of AP MOFs suggest that efficient gas separations can be conducted using MOFs without open metal sites.Publication Open Access A hybrid architecture for federated and centralized learning(Institute of Electrical and Electronics Engineers (IEEE), 2022) Elbir, Ahmet M.; Papazafeiropoulos, Anastasios K.; Kourtessis, Pandelis; Chatzinotas, Symeon; Department of Electrical and Electronics Engineering; Ergen, Sinem Çöleri; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 7211Many of the machine learning tasks rely on centralized learning (CL), which requires the transmission of local datasets from the clients to a parameter server (PS) entailing huge communication overhead. To overcome this, federated learning (FL) has been suggested as a promising tool, wherein the clients send only the model updates to the PS instead of the whole dataset. However, FL demands powerful computational resources from the clients. In practice, not all the clients have sufficient computational resources to participate in training. To address this common scenario, we propose a more efficient approach called hybrid federated and centralized learning (HFCL), wherein only the clients with sufficient resources employ FL, while the remaining ones send their datasets to the PS, which computes the model on behalf of them. Then, the model parameters are aggregated at the PS. To improve the efficiency of dataset transmission, we propose two different techniques: i) increased computation-per-client and ii) sequential data transmission. Notably, the HFCL frameworks outperform FL with up to 20% improvement in the learning accuracy when only half of the clients perform FL while having 50% less communication overhead than CL since all the clients collaborate on the learning process with their datasets.Publication Open Access Thiophene-based trimers for in vivo electronic functionalization of tissues(American Chemical Society (ACS), 2020) Mantione, Daniele; Dufil, Gwennael; Vallan, Lorenzo; Parker, Daniela; Brochon, Cyril; Cloutet, Eric; Hadziioannou, Georges; Berggren, Magnus; Stavrinidou, Eleni; Pavlopoulou, Eleni; Department of Mechanical Engineering; İstif, Emin; Faculty Member; Master Student; Department of Mechanical Engineering; College of EngineeringElectronic materials that can self-organize in vivo and form functional components along the tissue of interest can result in a seamless integration of the bioelectronic interface. Previously, we presented in vivo polymerization of the conjugated oligomer ETE-S in plants, forming conductors along the plant structure. The EDOT-thiophene-EDOT trimer with a sulfonate side group polymerized due to the native enzymatic activity of the plant and integrated within the plant cell wall. Here, we present the synthesis of three different conjugated trimers based on thiophene and EDOT or purely EDOT trimers that are able to polymerize enzymatically in physiological pH in vitro as well as in vivo along the roots of living plants. We show that by modulating the backbone and the side chain, we can tune the electronic properties of the resulting polymers as well as their localization and penetration within the root. Our work paves the way for the rational design of electronic materials that can self-organize in vivo for spatially controlled electronic functionalization of living tissue.Publication Open Access In situ formation of copper phosphate on hydroxyapatite for wastewater treatment(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Rahmani, Fatemeh; Ghadi, Arezoo; Khaksar, Samad; Doustkhah, Esmail; PhD Student; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM)Here, we control the surface activity of hydroxyapatite (HAp) in wastewater treatment which undergoes peroxodisulfate (PDS) activation. Loading the catalytically active Cu species on HAp forms a copper phosphate in the outer layer of HAp. This modification turns a low active HAp into a high catalytically active catalyst in the dye degradation process. The optimal operational conditions were established to be [Cu-THAp](0) = 1 g/L, [RhB](0) = 20 mg/L, [PDS](0) = 7.5 mmol/L, and pH = 3. The experiments indicate that the simultaneous presence of Cu-THAp and PDS synergistically affect the degradation process. Additionally, chemical and structural characterizations proved the stability and effectiveness of Cu-THAp. Therefore, this work introduces a simple approach to water purification through green and sustainable HAp-based materials.