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Mahmutyazicioglu N.,Bogazici University | Albayrak O.,Mersin University | Ipekoglu M.,German-Turkish University | Altintas S.,Bogazici University
Journal of Materials Research | Year: 2013

In this study, a powder blend representing 6061 Al-alloy was first mixed with Al2O3 ceramic particles and then foamed by using the powder compact melting method. 6061-Al2O3 foams and control specimens 6061 foams (without ceramic reinforcement) were produced. The effects of both different ratios of Al2O3 particle addition and different kinds of heat treatment on hardenability, structure and mechanical behavior of the final foams were investigated. Foams that were fully heat treated had the highest hardness values, and they performed best with an increase in collapse strength up to 100% over the untreated samples. Improved cell structure and decreased drainage were obtained when the Al 2O3 addition was not more than 5 vol%. The compression test results were interpreted in terms of the foam's microstructure, and correlations were made relating to the unloading modulus and compression strength of the foams to the relative density. © Materials Research Society 2013.


Ozben Onhon N.,German-Turkish University | Cetin M.,Sabanci University
European Signal Processing Conference | Year: 2013

SAR imaging of scenes containing moving targets results in defocusing in the reconstructed images if the SAR observation model used in imaging does not take the motion into account. SAR data from a scene with motion can be viewed as data from a stationary scene, but with phase errors due to motion. Based on this perspective, we formulate the moving target SAR imaging problem as one of joint imaging and phase error compensation. Based on the assumption that only a small percentage of the entire scene contains moving targets, phase errors exhibit a group sparse nature, when the entire data for all the points in the scene are handled together. Considering this structure of motion-related phase errors and that many scenes of interest admit sparse representation in SAR imaging, we solve this joint problem by minimizing a cost function which involves two nonquadratic regularization terms one of which is used to enforce the sparsity of the reflectivity field to be imaged and the other is used to exploit the group sparse nature of the phase errors. © 2013 EURASIP.


Cetin M.,Sabanci University | Stojanovic I.,Nokia Inc. | Onhon O.,German-Turkish University | Varshney K.,IBM | And 3 more authors.
IEEE Signal Processing Magazine | Year: 2014

This article presents a survey of recent research on sparsity-driven synthetic aperture radar (SAR) imaging. In particular, it reviews 1) the analysis and synthesis-based sparse signal representation formulations for SAR image formation together with the associated imaging results, 2) sparsity-based methods for wide-angle SAR imaging and anisotropy characterization, 3) sparsity-based methods for joint imaging and autofocusing from data with phase errors, 4) techniques for exploiting sparsity for SAR imaging of scenes containing moving objects, and 5) recent work on compressed sensing (CS)-based analysis and design of SAR sensing missions. © 2014 IEEE.


Gok M.,Yalova University | Herand D.,German-Turkish University
MATEC Web of Conferences | Year: 2016

Prediction of bacterial virulent proteins is critical for vaccine development and understanding of virulence mechanisms in pathogens. For this purpose, a number of feature encoding methods based on sequences and evolutionary information of a given protein have been proposed and applied with some classifier algorithms so far. In this paper, we performed composition moment vector (CMV), which includes information about both composition and position of amino acid in the protein sequence to predict bacterial virulent proteins. The tests were validated in three different independent datasets. Experimental results show that CMV feature encoding method leads to better classification performance in terms of accuracy, sensitivity, f-measure and the Matthews correlation coefficient (MCC) scores on diverse classifiers. © Owned by the authors, published by EDP Sciences 2016.


Unal C.M.,German-Turkish University | Unal C.M.,TU Braunschweig | Steinert M.,TU Braunschweig | Steinert M.,Helmholtz Center for Infection Research
Biochimica et Biophysica Acta - General Subjects | Year: 2015

Background FK506-binding proteins (FKBPs) contain a domain with peptidyl-prolyl-cis/trans-isomerase (PPIase) activity and bind the immunosuppressive drugs FK506 and rapamycin. FKBPs belong to the immunophilin family and are found in eukaryotes and bacteria. Scope of review In this review we describe two major groups of bacterial virulence-associated FKBPs, the trigger factor and Mip-like PPIases. Moreover, we discuss the contribution of host FKBPs in bacterial infection processes. Major conclusions Since PPIases are regarded as alternative antiinfective drug targets we highlight current research strategies utilizing pipecolinic acid and cycloheximide derivatives as well as substrate based inhibitors. General significance The current research strategies suggest a beneficial synergism of drug development and basic research. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets. © 2014 Elsevier B.V. All rights reserved.


Unal C.M.,TU Braunschweig | Unal C.M.,German-Turkish University | Steinert M.,TU Braunschweig | Steinert M.,Helmholtz Center for Infection Research
Expert Opinion on Therapeutic Targets | Year: 2016

Introduction: In recent years, Clostridium difficile has become the primary cause of antibiotic-associated diarrhea and pseudomembranous colitis, resulting in long and complicated hospital stays that represent a serious burden for patients as well as health care systems. Currently, conservative treatment of C. difficile infection (CDI) relies on the antibiotics vancomycin, metronidazole or fidaxomicin, or in case of multiple recurrences, fecal microbiota transplantation (FMT).Areas covered: The fast-spreading, epidemic nature of this pathogen urgently necessitates the search for alternative treatment strategies as well as antibiotic targets. Accordingly, in this review, we highlight the recent findings regarding virulence associated traits of C. difficile, evaluate their potential as alternative drug targets, and present current efforts in designing inhibitory compounds, with the aim of pointing out possibilities for future treatment strategies.Expert opinion: Increased attention on systematic analysis of the virulence mechanisms of C. difficile has already led to the identification of several alternative drug targets. In the future, applying state of the art omics and the development of novel infection models that mimic the human gut, a highly complex ecological niche, will unveil the genomic and metabolic plasticity of this pathogen and will certainly help dealing with future challenges. © 2016 Taylor & Francis.


Xiong Q.,University of Cologne | Unal C.,TU Braunschweig | Unal C.,German-Turkish University | Matthias J.,University of Cologne | And 3 more authors.
Open Biology | Year: 2015

Macroautophagy is a highly conserved intracellular bulk degradation system of all eukaryotic cells. It is governed by a large number of autophagy proteins (ATGs) and is crucial for many cellular processes. Here, we describe the phenotypes of Dictyostelium discoideum ATG16- and ATG9-/16- cells and compare them to the previously reported ATG9- mutant. ATG16 deficiency caused an increase in the expression of several core autophagy genes, among thematg9 and the two atg8 paralogues. The single and double ATG9 and ATG16 knock-out mutants had complex phenotypes and displayed severe and comparable defects in pinocytosis and phagocytosis. Uptake of Legionella pneumophila was reduced. In addition, ATG9- and ATG16- cells had dramatic defects in autophagy, development and proteasomal activity which were much more severe in the ATG9-/16- double mutant. Mutant cells showed an increase in poly-ubiquitinated proteins and contained large ubiquitinpositive protein aggregates which partially co-localized with ATG16-GFP in ATG9-/16- cells. The more severe autophagic, developmental and proteasomal phenotypes of ATG9-/16- cells imply that ATG9 and ATG16 probably function in parallel in autophagy and have in addition autophagy-independent functions in further cellular processes. © 2015 The Authors.


Biberoglu M.,Yalova University | Ince K.,German-Turkish University | Karaosmanoglu F.,Technical University of Istanbul
2015 International Conference on Renewable Energy Research and Applications, ICRERA 2015 | Year: 2015

Globally increasing energy demand, running short of fossil fuels and researches for finding environment friendly choices strengthen a solution of local electricity production, especially from renewable energy sources. In this type of systems, inverters play a key role by providing power transforms. Multilevel inverters can achieve very low total harmonic distortion (THD) values at low switching frequencies without using any filtering units when compared with classic two-level inverters. However, multilevel inverters use high number of semiconductor elements, which increases the probability of any fault in the circuit, which may cause the whole system stopping for a long time. This is very critical issue for the buildings that have vital importance like hospitals or the industries where faults cost large amounts of money. In this work, a Fault-tolerant cascaded H-Bridge quasi-eight-level multilevel inverter with a single DC source and with output-side transformers was designed and application of reconfiguration technique was shown. The proposed inverter system can continue working if a fault occurs in one of H-Bridges with a one-level decrement in the output voltage in quarter period. © 2015 IEEE.


Rasch U.,TU Braunschweig | Unal C.M.,TU Braunschweig | Unal C.M.,German-Turkish University | Steinert M.,Helmholtz Center for Infection Research
Biochemical Society Transactions | Year: 2014

Legionella pneumophila, typically a parasite of free-living protozoa, can also replicate in human alveolar macrophages and lung epithelial cells causing Legionnaires' disease in humans, a severe atypical pneumonia. The pathogen encodes six peptidylprolyl cis-trans isomerases (PPIases), which generally accelerate folding of prolyl peptide bonds, and influence protein folding. PPIases can be divided into three classes, cyclophilins, parvulins and FK506-binding proteins (FKBPs). They contribute to a multitude of cellular functions including bacterial virulence. In the present review, we provide an overview of L. pneumophila PPIases, discussing their known and anticipated functions as well as moonlighting phenomena. By taking the example of the macrophage infectivity potentiator (Mip) of L. pneumophila, we highlight the potential of PPIases as promising drug targets. compilation © 2014 Biochemical Society.


Unal C.M.,German-Turkish University | Unal C.M.,TU Braunschweig | Steinert M.,TU Braunschweig | Steinert M.,Helmholtz Center for Infection Research
Microbiology and Molecular Biology Reviews | Year: 2014

Initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (PPIases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. Intense searches revealed that PPIases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. Despite the clear-cut enzymatic activity and ubiquitous distribution of PPIases, reports on solely PPIase-dependent biological roles remain scarce. Nevertheless, they have been found to be involved in a plethora of biological processes, such as gene expression, signal transduction, protein secretion, development, and tissue regeneration, underscoring their general importance. Hence, it is not surprising that PPIases have also been identified as virulence-associated proteins. The extent of contribution to virulence is highly variable and dependent on the pleiotropic roles of a single PPIase in the respective pathogen. The main objective of this review is to discuss this variety in virulence-related bacterial and protozoan PPIases as well as the involvement of host PPIases in infectious processes. Moreover, a special focus is given to Legionella pneumophila macrophage infectivity potentiator (Mip) and Mip-like PPIases of other pathogens, as the best-characterized virulence-related representatives of this family. Finally, the potential of PPIases as alternative drug targets and first tangible results are highlighted. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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