PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Data Paper Citation - WoS: 3Citation - Scopus: 4Experimental data showing the thermal behavior of a flat roof with phase change material(Elsevier, 2015) Tokuç, Ayça; Başaran, Tahsin; Yesügey, Sadık CengizThe selection and configuration of building materials for optimal energy efficiency in a building require some assumptions and models for the thermal behavior of the utilized materials. Although the models for many materials can be considered acceptable for simulation and calculation purposes, the work for modeling the real time behavior of phase change materials is still under development. The data given in this article shows the thermal behavior of a flat roof element with a phase change material (PCM) layer. The temperature and energy given to and taken from the building element are reported. In addition the solid-liquid behavior of the PCM is tracked through images. The resulting thermal behavior of the phase change material is discussed and simulated in [1] A. Tokuç, T. Başaran, S.C. Yesügey, An experimental and numerical investigation on the use of phase change materials in building elements: the case of a flat roof in Istanbul, Build. Energy, vol. 102, 2015, pp. 91-104.Article Citation - WoS: 37Mechanisms of Cellular Resistance To Imatinib in Human Chronic Myeloid Leukemia Cells(Taylor and Francis Ltd., 2007) Baran, Yusuf; Ural, Ali Uğur; Gündüz, UfukA major advancement in the treatment of chronic myeloid leukemia (CML) has been the development of imatinib, which has shown striking activity in the chronic phase and the accelerated phase, but less so in the blast phase of the disease. Despite high rates of hematologic and cytogenetic responses to therapy, the emergence of resistance to imatinib has been recognized as a major problem in the treatment of patients with CML. Various cellular mechanisms may be involved in the nature of cellular resistance. Increased amount of target, alteration in structure of target proteins, decreased drug uptake and increased detoxification are well-known mechanisms of resistance. On the other hand, in some cases, even if anticancer drugs reach their sites of action, bypassing drug efflux system of the cells, some cells still may survive via the dysregulation of apoptotic signalling. In this study, mechanisms of resistance to imatinib-induced apoptosis in human Meg-01 CML cells were examined. Continuous exposure of cells to step-wise increasing concentrations of imatinib resulted in the selection of 200- and 1000 nM imatinib-resistant sub-lines referred to as Meg-01/IMA-0,2 and Meg-01/1MA-1, respectively. MTT cell proliferation, cell cycle analyses and trypan blue dye exclusion analyses showed that Meg-0l/IMA-1 cells were resistant to imatinib-induced apoptosis as compared to parental sensitive cells. There was an increased expression of BCR/ABL, Bcl-2 and an increase in mitochondrial membrane potential (MMP) detected in resistant cells comparing to parental sensitive cells. There was no mutation detected in imatinib binding site of ABL kinase region. Various diverse mechanisms have been reported for their involvement in the multidrug resistance. In this study, it has been shown that the degree of BCR/ABL expression appears to be directly proportional to the levels of imatinib resistance. In addition, there have been BCR/ABL-independent mechanisms reported for deriving resistance against imatinib. Our results revealed that besides BCR/ABL overexpression, imatinib resistance also depends on the inhibition of apoptosis as a result of up-regulation of anti-apoptotic stimuli and down-regulation of pro-apoptotic stimuli through MMP but does not depend on any mutation on imatinib binding site of ABL kinase.Article Citation - WoS: 3Citation - Scopus: 3Green Fabrication of Lanthanide-Doped Hydroxide-Based Phosphors: Y(oh)(3):eu3+ Nanoparticles for White Light Generation(Beilstein-Institut Zur Forderung der Chemischen Wissenschaften, 2019) Güner, Tuğrul; Kuş, Anılcan; Özcan, Mehmet; Genç, Aziz; Şahin, Hasan; Demir, Mustafa MuammerPhosphors can serve as color conversion layers to generate white light with varying optical features, including color rendering index (CRI), high correlated color temperature (CCT), and luminous efficacy. However, they are typically produced under harsh synthesis conditions such as high temperature, high pressure, and/or by employing a large amount of solvent. In this work, a facile, water-based, rapid method has been proposed to fabricate lanthanide-doped hydroxide-based phosphors. In this sense, sub-micrometer-sized Y(OH)(3):Eu3+ particles (as red phosphor) were synthesized in water at ambient conditions in <= 60 min reaction time. The doping ratio was controlled from 2.5-20 mol %. Additionally, first principle calculations were performed on Y(OH)(3):Eu3+ to understand the preferable doping scenario and its optoelectronic properties. As an application, these fabricated red phosphors were integrated into a PDMS/YAG:Ce3+ composite and used to generate white light. The resulting white light showed a remarkable improvement (approximate to 24%) in terms of luminous efficiency, a slight reduction of CCT (from 3900 to 3600 K), and an unchanged CRI (approximate to 60) as the amount of Y(OH)(3):Eu3+ was increased.Article Citation - WoS: 8Citation - Scopus: 10Auditory Event-Related Potentials Demonstrate Early Cognitive Impairment in Children With Subclinical Hypothyroidism(Walter de Gruyter GmbH, 2019) Çatlı, Gönül; Kocaaslan Atlı, Sibel; Olgaç Dündar, Nihal; Bayazıt, Onur; Evirgen Esin, Nur; Erdoğan, Uğraş; Dündar, Bumin NuriBackground: The aim of this study was to examine the cognitive functions of children with subclinical hypothyroidism (SH) and healthy children with the use of auditory event-related potentials (AERPs) and neuropsychological tests. Methods: Twenty children aged between 8 and 17 wars, diagnosed with SH, and 20 age-matched healthy controls were included in this study. A classical auditory oddball paradigm was applied during the electroencephalography (EEG) recordings, and event-related potentials (ERPs) were evaluated between the 0.5- and 20-Hz frequency intervals. P1, N1, P2, N2 and P3 amplitudes and latencies were measured in Fz, FCz, Cz, CPz, Pz and Oz electrodes. Additionally, a number of neuropsychological tests evaluating the reaction time and various cognitive functions were carried out. Results: In children with SH, P3 amplitudes in FCz, Cz and CPz electrodes were significantly lower than those in controls (p <0.05). In addition to this, the P1N1 and N1P2 peak-to-peak amplitude values were also found to be smaller for children with SH than controls (p <0.05). With regard to the neuropsychological tests, no significant difference was observed between the SH and control groups on any of the cognitive test parameters, reaction time or correct response rates. Conclusions: In the present study, while children with SI I did not differ from controls with respect to their cognitive functions evaluated via neuropsychological tests, cognitive differences were detected via electrophysiological investigations. This result implies that implicit changes in cognition which are not yet overtly reflected on neuropsychological tests may be detected at an early stage in children with SH.Article Citation - WoS: 25Citation - Scopus: 27Osteogenic Differentiation of Mesenchymal Stem Cells on Random and Aligned Pan/Ppy Nanofibrous Scaffolds(SAGE Publications, 2019) Selamet, Yusuf; İnce Yardımcı, Atike; Baskan, Öznur; Yılmaz, Selahattin; Meşe, Gülistan; Özçivici, EnginThe aim of this study was to develop random and aligned polyacrilonitrile (PAN)/polypyrrole (PPy) nanofibrous scaffolds by electrospinning technique for osteogenic differentiation of mesenchymal stem cells. Nanofibers were fabricated successfully as straight, smooth, and free from bead formation. The average diameter of random and aligned nanofibers was 268(+/- 49) nm and 225(+/- 72) nm, respectively. Alignment process increased the tensile strength of nanofibers 3.9-fold, while the tensile strain of nanofibers decreased by 78%. PAN/PPy nanofibers were hydrophilic with the contact angle value of about 32 degrees and alignment did not affect the contact angle value. Random and aligned PAN/PPy nanofibers were investigated as a scaffold material for osteogenic differentiation of D1 ORL UVA mouse bone marrow mesenchymal stem cells. Cells were able to attach and grow on nanofibers confirmed by cell viability results. Stem cells that were cultured with osteogenic induction were able to mineralize on electrospun nanofibers based on alizarin red and Von Kossa dye staining. For aligned PPy nanofibers, mineralization occurred in the fiber alignment direction. Consequently, PAN/PPy nanofibrous mats in both random and aligned forms would be potential candidates for bone tissue engineering.Article Citation - WoS: 9Citation - Scopus: 10Characterization of Long Living Yeast Deletion Mutants That Lack Mitochondrial Metabolism Genes Dss1, Ppa2 and Afg3(Elsevier, 2019) Muid, Khandaker Ashfaqul; Kimyon, Önder; Reza, Shahadat Hasan; Karakaya, Hüseyin Çağlar; Koç, AhmetMolecular mechanisms of aging and longevity are still mostly unknown. Mitochondria play central roles in cellular metabolism and aging. In this study, we identified three deletion mutants of mitochondrial metabolism genes (ppa2 Delta, dss1 Delta, and afg3 Delta) that live longer than wild-type cells. These long-lived cells harbored significantly decreased amount of mitochondria] DNA (mtDNA) and reactive oxygen species (ROS). Compared to the serpentine nature of wild-type mitochondria, a different dynamics and distribution pattern of mitochondria were observed in the mutants. Both young and old long-lived cells produced relatively low but adequate levels of ATP for cellular activities. The status of the retrograde signaling was checked by expression of CIT2 gene and found activated in long-lived mutants. The mutant cells were also profiled for their gene expression patterns, and genes that were differentially regulated were determined. All long-lived cells comprised similar pleiotropic phenotype regarding mitochondrial dynamics and functions. Thus, this study suggests that DSS1, PPA2, and AFG3 genes modulate the lifespan by altering the mitochondrial morphology and functions.Article Citation - WoS: 21Citation - Scopus: 22Green Function, Quasi-Classical Langevin and Kubo-Greenwood Methods in Quantum Thermal Transport(IOP Publishing, 2019) Sevinçli, Haldun; Roche, S.; Cuniberti, G.; Brandbyge, M.; Gutierrez, R.; Sandonas, L. MedranoWith the advances in fabrication of materials with feature sizes at the order of nanometers, it has been possible to alter their thermal transport properties dramatically. Miniaturization of device size increases the power density in general, hence faster electronics require better thermal transport, whereas better thermoelectric applications require the opposite. Such diverse needs bring new challenges for material design. Shrinkage of length scales has also changed the experimental and theoretical methods to study thermal transport. Unsurprisingly, novel approaches have emerged to control phonon flow. Besides, ever increasing computational power is another driving force for developing new computational methods. In this review, we discuss three methods developed for computing vibrational thermal transport properties of nano-structured systems, namely Green function, quasi-classical Langevin, and Kubo-Green methods. The Green function methods are explained using both nonequilibrium expressions and the Landauer-type formula. The partitioning scheme, decimation techniques and surface Green functions are reviewed, and a simple model for reservoir Green functions is shown. The expressions for the Kubo-Greenwood method are derived, and Lanczos tridiagonalization, continued fraction and Chebyshev polynomial expansion methods are discussed. Additionally, the quasi-classical Langevin approach, which is useful for incorporating phonon-phonon and other scatterings is summarized.Editorial Citation - WoS: 2Computational Mirnomics - Integrative Approaches(Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2017) Hofestaedt, Ralf; Schreiber, Falk; Sommer, Bjoern; Allmer, JensWith this special issue on Computational miRNomics, we would like to start a new generation of publications in the Journal of Integrative Bioinformatics (JIB). From 2017 onwards, JIB will be published by De Gruyter which is one of the largest Open Access publishers in Germany with a long history. Established in 1918 with roots reaching even further back, the JIB editorial board decided that De Gruyter is the perfect partner to increase the level of professionalism for our publication processing and journal development.Article Citation - WoS: 4Citation - Scopus: 9Pgminer Reloaded, Fully Automated Proteogenomic Annotation Tool Linking Genomes To Proteomes(Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2016) Has, Canan; Lashin, Sergey A.; Kochetov, Alexey; Allmer, JensImprovements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered. Mass spectrometry allows the identification and sequencing of proteins as major gene products; and it is only these proteins that conclusively show whether a part of a genome is a coding region or not to result in phenotypes. Therefore, in the field of proteogenomics, the validation of computational methods is done by exploiting mass spectrometric data. As a result, identification of novel protein coding regions, validation of current gene models, and determination of upstream and downstream regions of genes can be achieved. In this paper, we present new functionality for our proteogenomic tool, PGMiner which performs all proteogenomic steps like acquisition of mass spectrometric data, peptide identification against preprocessed sequence databases, assignment of statistical confidence to identified peptides, mapping confident peptides to gene models, and result visualization. The extensions cover determining proteotypic peptides and thus unambiguous protein identification. Furthermore, peptides conflicting with gene models can now automatically assessed within the context of predicted alternative open reading frames.Article Citation - WoS: 7Citation - Scopus: 5A Machine Learning Approach for Microrna Precursor Prediction in Retro-Transcribing Virus Genomes(Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2016) Saçar Demirci, Müşerref Duygu; Toprak, Mustafa; Allmer, JensIdentification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especially classification. In order to achieve successful classification, many parameters need to be considered such as data quality, choice of classifier settings, and feature selection. For the latter one, we developed a distributed genetic algorithm on HTCondor to perform feature selection. Moreover, we employed two widely used classification algorithms libSVM and random forest with different settings to analyze the influence on the overall classification performance. In this study we analyzed 5 human retro virus genomes; Human endogenous retrovirus K113, Hepatitis B virus (strain ayw), Human T lymphotropic virus 1, Human T lymphotropic virus 2, Human immunodeficiency virus 2, and Human immunodeficiency virus 1. We then predicted pre-miRNAs by using the information from known virus and human pre-miRNAs. Our results indicate that these viruses produce novel unknown miRNA precursors which warrant further experimental validation.