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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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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; Department of Molecular Biology and Genetics; Zeybel, Müjdat; Karahüseyinoğlu, Serçin; Faculty Member; Faculty Member; 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; Department of Mathematics; Soner, Halil Mete; Faculty Member; 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 Multidimensional wave packet dynamics within the fluid dynamical formulation of the Schrodinger equation(American Institute of Physics (AIP) Publishing, 1998) Rabitz, H.; Department of Mathematics; Department of Mathematics; Aşkar, Attila; Dey, Bijoy K.; Faculty Member; Faculty Member; College of Sciences; 178822; N/AThis paper explores the quantum fluid dynamical (QFD) representation of the time-dependent Schrodinger equation for the motion of a wave packet in a high dimensional space. A novel alternating direction technique is utilized to single our each of the many dimensions in the QFD equations. This technique is used to solve the continuity equation for the density and the equation for the convection of the flux for the quantum particle. The ability of the present scheme to efficiently and accurately describe the dynamics of a quantum particle is demonstrated in four dimensions where analytical results are known. We also apply the technique to the photodissociation of NOCl and NO2 where the systems are reduced to two coordinates by freezing the angular variable at its equilibrium value.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; Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; 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; 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; 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; Department of Sociology; Yörük, Erdem; Faculty Member; 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 Turkey's two elections: the AKP comes back(Johns Hopkins University (JHU) Press, 2016) Öniş, Ziya; Department of International Relations; Department of International Relations; Faculty Member; College of Administrative Sciences and EconomicsIn power since 2002, the Justice and Development Party (AKP) of Recep Tayyip Erdoğan seemed as if it might be losing its hold when Turkish voters went to the polls in June 2015. Yet that “hung election” gave way to another contest in November, and the AKP came roaring back.Publication Open Access The noisy channel mode for unsupervised word sense disambiguation(Massachusetts Institute of Technology (MIT) Press, 2010) Department of Computer Engineering; Department of Computer Engineering; Yüret, Deniz; Yatbaz, Mehmet Ali; Faculty Member; PhD Student; College of Engineering; 179996; 192506We introduce a generative probabilistic model, the noisy channel model, for unsupervised word sense disambiguation. In our model, each context C is modeled as a distinct channel through which the speaker intends to transmit a particular meaning S using a possibly ambiguous word W. To reconstruct the intended meaning the hearer uses the distribution of possible meanings in the given context P(S|C) and possible words that can express each meaning P(W|S). We assume P(W|S) is independent of the context and estimate it using WordNet sense frequencies. The main problem of unsupervised WSD is estimating context-dependent P(S|C) without access to any sense-tagged text. We show one way to solve this problem using a statistical language model based on large amounts of untagged text. Our model uses coarse-grained semantic classes for S internally and we explore the effect of using different levels of granularity on WSD performance. The system outputs fine-grained senses for evaluation, and its performance on noun disambiguation is better than most previously reported unsupervised systems and close to the best supervised systems.Publication Open Access BCS theory of time-reversal-symmetric Hofstadter-Hubbard model(American Physical Society (APS), 2017) Umucalılar, Rıfat Onur; Department of Physics; Department of Physics; Işkın, Menderes; Faculty Member; College of Sciences; 29659The competition between the length scales associated with the periodicity of a lattice potential and the cyclotron radius of a uniform magnetic field is known to have dramatic effects on the single-particle properties of a quantum particle, e.g., the fractal spectrum is known as the Hofstadter butterfly. Having this intricate competition in mind, we consider a two-component Fermi gas on a square optical lattice with opposite synthetic magnetic fields for the components, and study its effects on the many-body BCS-pairing phenomenon. By a careful addressing of the distinct superfluid transitions from the semimetal, quantum spin-Hall insulator, or normal phases, we explore the low-temperature phase diagrams of the model, displaying lobe structures that are reminiscent of the well-known Mott-insulator transitions of the Bose-Hubbard model.