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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only The balance between memory and regulatory cell populations in kidney transplant recipients with operational tolerance(Oxford Univ Press, 2024) Alvarez, Cristiam M.; Benning, Louise; Daniel, Volker; Zeier, Martin; Schaier, Matthias; Morath, Christian; Speer, Claudius; Süsal, Caner; Koç University Transplant Immunology Research Centre of Excellence (TIREX); School of Medicine; Koç University HospitalDonor-reactive memory cells represent a barrier to long-term kidney graft survival. A better understanding of regulatory mechanisms that counterbalance alloreactive memory responses may help to identify patients with operational tolerance. This prospective study investigated the equilibrium between memory T cell subsets and regulatory T or B cells (Tregs, Bregs) in peripheral blood of kidney transplant recipients with operational tolerance (N=8), chronic rejection (N=8), and different immunosuppressive treatment regimens (N=81). Patients on hemodialysis and healthy individuals served as controls (N=50). In addition, the expression of Treg- and Breg-associated molecule genes was analyzed. Patients with chronic rejection showed a disrupted memory T cell composition with a significantly higher frequency of circulating CD8(+) terminally differentiated effector memory (TEMRA) T cells than patients with operational tolerance, patients on hemodialysis, or healthy controls (P<0.001). Low frequency of CD8(+) TEMRA and high frequency of Tregs and transitional Bregs were found in operationally tolerant patients. Consequently, operationally tolerant patients showed, as compared to all other transplant recipients with different immunosuppressive regiments, the lowest ratios between CD8(+) TEMRA T cells and Tregs or Bregs (for both P<0.001). Moreover, a specific peripheral blood transcription pattern was found in operationally tolerant patients with an increased expression of Breg- and Treg-associated genes CD22 and FoxP3 and a decreased Fc gamma RIIA/Fc gamma RIIB transcript ratio (for all P<0.001). In conclusion, monitoring the balance between circulating CD8(+) TEMRA T cells and regulatory cell subsets and their transcripts may help to distinguish transplant recipients with operational tolerance from recipients at risk of graft loss.Publication Metadata only FlexDPDP: flexlist-based optimized dynamic provable data possession(assoc Computing Machinery, 2016) N/A; N/A; N/A; Department of Computer Engineering; Department of Computer Engineering; Department of Computer Engineering; Esiner, Ertem; Kachkeev, Adilet; Küpçü, Alptekin; Özkasap, Öznur; Master Student; Master Student; N/A; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 168060; 113507With increasing popularity of cloud storage, efficiently proving the integrity of data stored on an untrusted server has become significant. authenticated skip lists and rank-based authenticated skip lists (RBaSL) have been used to provide support for provable data update operations in cloud storage. However, in a dynamic file scenario, An RBaSL based on block indices falls short when updates are not proportional to a fixed block size; such an update to the file, even if small, may result in O(n) updates on the data structure for a file with n blocks. To overcome this problem, we introduce FlexList, A flexible length-based authenticated skip list. FlexList translates variable-size updates to O(inverted right perpendicularu/Binverted left perpendicular) insertions, removals, or modifications, where u is the size of the update and B is the (average) block size. We further present various optimizations on the four types of skip lists (regular, Authenticated, rank-based authenticated, and FlexList). We build such a structure in O(n) time and parallelize this operation for the first time. We compute one single proof to answer multiple (non) membership queries and obtain efficiency gains of 35%, 35%, and 40% in terms of proof time, energy, and size, respectively. We propose a method of handling multiple updates at once, Achieving efficiency gains of up to 60% at the server side and 90% at the client side. We also deployed our implementation of FlexDPDP (dynamic provable data possession (DPDP) with FlexList instead of RBaSL) on PlanetLab, demonstrating that FlexDPDP performs comparable to the most efficient static storage scheme (provable data possession (PDP)) while providing dynamic data support.Publication Metadata only Discretionary bonuses and turnover(Elsevier, 2019) Department of Economics; Ekinci, Emre; Faculty Member; Department of Economics; College of Administrative Sciences and Economics; 309364This paper develops a signaling model to investigate the effects of discretionary bonuses and wage increases on turnover. When the worker's output is not contractible and the firm privately learns about the match quality between the firm and the worker, bonus payments and wage increases can convey the firm's private information to the worker. If the firm credibly communicates favorable information about the match quality to a worker, the worker develops higher expectations concerning her career outcomes at the firm (such as future wage increases and promotions) and, consequently, becomes less likely to separate. The analysis demonstrates that although a wage increase and a bonus reflect the same information regarding the match quality, each serves a distinctly different role in terms of the worker's turnover decision. Specifically, the firm pays bonuses to signal a good match while using wages to respond to competing offers the worker receives. The model yields testable predictions that concern how bonuses are related to wage increases and promotions and how bonuses and wage increases are related to turnover. The empirical analysis based on the data constructed from the personnel records of a large firm in the financial services industry provides support for the model's implications.Publication Metadata only Official arbitration with secure cloud storage application(Oxford University Press (OUP), 2015) Department of Computer Engineering; Küpçü, Alptekin; Faculty Member; Department of Computer Engineering; College of Engineering; 168060In a secure cloud storage setting, a client outsources storage of her data to a server, who may, willingly or not, corrupt the data, or delete infrequently accessed parts to save space. Existing proof of storage schemes only solve part of this problem: The client may obtain a cryptographic proof of integrity. But what happens if this proof fails to verify? We argue that in such a case, both the client and the server should be able to contact an official court, providing cryptographic proofs, to resolve this dispute. We show that, this property is stronger than what is known as public verifiability since we must handle a malicious client as well. We present multiple schemes that work for various static and dynamic storage solutions. We showimplementation results where the overhead for adding the ability to resolve such disputes at a court is only 2 ms and 80 bytes for each update on the stored data, using standard desktop hardware. Finally, we note that disputes may arise in many other situations, such as when two parties exchange items (e.g. e-commerce) or agree on something (e.g. contract-signing). We extend our official arbitration protocols for a general case, including dynamic authenticated data structures.Publication Metadata only Edge density of new graph types based on a random digraph family(Elsevier Science Bv, 2016) Department of Mathematics; Ceyhan, Elvan; Undergraduate Student; Department of Mathematics; College of Sciences; N/AWe consider two types of graphs based on a family of proximity catch digraphs (PCDs) and study their edge density. in particular, the PCDs we use are a parameterized digraph family called proportional-edge (PE) PCDs and the two associated graph types are the "underlying graphs" and the newly introduced "reflexivity graphs" based on the PE-PCDs. these graphs are extensions of random geometric graphs where distance is replaced with a dissimilarity measure and the threshold is not fixed but depends on the location of the points. PCDs and the associated graphs are constructed based on data points from two classes, say X and y, where one class (say class X) forms the vertices of the PCD and the Delaunay tessellation of the other class (i.e., class y) yields the (Delaunay) cells which serve as the support of class X points. We demonstrate that edge density of these graphs is a U-statistic, hence obtain the asymptotic normality of it for data from any distribution that satisfies mild regulatory conditions. the rate of convergence to asymptotic normality is sharper for the edge density of the reflexivity and underlying graphs compared to the arc density of the PE-PCDs. for uniform data in Euclidean plane where Delaunay cells are triangles, we demonstrate that the distribution of the edge density is geometry invariant (i.e., independent of the shape of the triangular support). We compute the explicit forms of the asymptotic normal distribution for uniform data in one Delaunay triangle in the Euclidean plane utilizing this geometry invariance property. We also provide various versions of edge density in the multiple triangle case. the approach presented here can also be extended for application to data in higher dimensions.Publication Metadata only Adsorption, folding, and packing of an amphiphilic peptide at the air/water interface(amer Chemical Soc, 2012) N/A; Department of Mechanical Engineering; Engin, Özge; Sayar, Mehmet; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering, College of Engineering; N/A; 109820Peptide oligomers play an essential role as model compounds for identifying key motifs in protein structure formation and protein aggregation. Here, we present our results, based on extensive molecular dynamics simulations, on adsorption, folding, and packing within a surface monolayer of an amphiphilic peptide at the air/water interface. Experimental results suggest that these molecules spontaneously form ordered monolayers at the interface, Adopting a beta-hairpin-like structure within the surface layer. Our results reveal that the beta-hairpin structure can be observed both in bulk and at the air/water interface. However, the presence of an interface leads to ideal partitioning of the hydrophobic and hydrophilic residues, and therefore reduces the conformational space for the molecule and increases the stability of the hairpin structure. We obtained the adsorption free energy of a single beta-hairpin at the air/water interface, and analyzed the enthalpic and entropic contributions. the adsorption process is favored by two main factors: (1) Free-energy reduction due to desolvation of the hydrophobic side chains of the peptide and release of the water molecules which form a cage around these hydrophobic groups in bulk water. (2) Reduction of the total air/water contact area at the interface upon adsorption of the peptide amphiphile. By performing mutations on the original molecule, we demonstrated the relative role of key design features of the peptide. Finally, by analyzing the potential of mean force among two peptides at the interface, we investigated possible packing mechanisms for these molecules within the surface monolayer.Publication Metadata only Making the indebted citizen: an inquiry into state benevolence in Turkey(Wiley Periodicals, inc, 2020) N/A; Yoltar, Çağrı; Researcher; N/A; N/AThis article concerns the making of the indebted citizen in Turkey through state benevolence. It focuses on the materialization of a debt relationship between state and citizen in everyday workings of state-sponsored welfare programs in the Kurdish region, in the shadow of a protracted armed conflict between the Turkish military forces and the Partiya Karkeren Kurdistan (Kurdistan Workers' Party). in Turkey, As in many other places, welfare benefits are promoted as a state benevolence rather than a citizenship right, and many officials seek to ensure that beneficiaries are credible enough to honor their debts to the state in the form of loyalty and obedience. Examining bureaucratic processes of beneficiary selection, I demonstrate how a dialectic of generous giving and forceful taking congeals in welfare distribution, compelling compliant behavior among the beneficiaries through the power of debt. I argue that what seems to be a free provision by the Turkish state-social assistance-often operates as a mechanism of debt production in practice-another form of political and economic dispossession for the Kurds in Turkey.