WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 1Pupillometric and Perceptual Approaches Provide Independent Estimates of Melanopsin Activity in Humans(Oxford University Press, 2025) Woelders, T.; Didikoglu, A.; Bickerstaff, L.; Brown, T.M.; Lucas, R.J.Study Objectives: Melanopsin-expressing retinal ganglion cells, which provide light information to time sleep and entrain circadian clocks, also influence perceived brightness raising the possibility that psychophysical paradigms could be used to explore the origins and implications of variability in melanopic sensitivity. We aimed to develop accessible psychophysical tests of melanopic vision and relate outcomes with a pupillometric measure of melanopsin function (post-illumination pupil response) and prior light exposure. Methods: Individually calibrated pairs of isoluminant stimuli differing in melanopic radiance from a four primary source were presented sequentially with superimposed random color offsets in a two alternative forced choice brightness preference paradigm to 41 naïve adult participants with personal light exposure data for the prior 7 days and post-illumination pupil response measures defined by comparing maintained pupil constriction for luminance matched “red” vs “blue” pulses. Results: Across participants we observed the expected tendency to report positive melanopsin contrast stimuli as “brighter” (one-tailed t-test p < 0.001), but with substantial inter-individual variability in both sensitivity (melanopsin contrast at criterion preference p = 0.75) and amplitude (preference at maximum melanopic contrast). There was little correlation between these psychophysical outcomes and post-illumination pupil response magnitude, or between either psychophysical or post-illumination pupil response measures and light history metrics (pairwise Pearson correlation coefficients -0.5> < 0.5). Random forest machine learning failed to satisfactorily predict outcome for either psychophysical or post-illumination pupil response measures based upon these inputs. Conclusions: Our findings reveal that estimates of melanopic function provided by perceptual and pupillometric paradigms can be largely independent of one another and of recent history of light exposure. © The Author(s) 2024. Published by Oxford University Press on behalf of Sleep Research Society.Article Citation - WoS: 3Citation - Scopus: 4Measuring the Performance of an Artificial Intelligence-Based Robot That Classifies Blood Tubes and Performs Quality Control in Terms of Preanalytical Errors: a Preliminary Study(Oxford University Press, 2024) Şişman,A.R.; Başok,B.I.; Karakoyun,I.; Çolak,A.; Bilge,U.; Demirci,F.; Başoglu,N.Objectives: Artificial intelligence-based robotic systems are increasingly used in medical laboratories. This study aimed to test the performance of KANKA (Labenko), a stand-alone, artificial intelligence-based robot that performs sorting and preanalytical quality control of blood tubes. Methods: KANKA is designed to perform preanalytical quality control with respect to error control and preanalytical sorting of blood tubes. To detect sorting errors and preanalytical inappropriateness within the routine work of the laboratory, a total of 1000 blood tubes were presented to the KANKA robot in 7 scenarios. These scenarios encompassed various days and runs, with 5 repetitions each, resulting in a total of 5000 instances of sorting and detection of preanalytical errors. As the gold standard, 2 experts working in the same laboratory identified and recorded the correct sorting and preanalytical errors. The success rate of KANKA was calculated for both the accurate tubes and those tubes with inappropriate identification. Results: KANKA achieved an overall accuracy rate of 99.98% and 100% in detecting tubes with preanalytical errors. It was found that KANKA can perform the control and sorting of 311 blood tubes per hour in terms of preanalytical errors. Conclusions: KANKA categorizes and records problem-free tubes according to laboratory subunits while identifying and classifying tubes with preanalytical inappropriateness into the correct error sections. As a blood acceptance and tube sorting system, KANKA has the potential to save labor and enhance the quality of the preanalytical process. © 2024 The Author(s).Article Citation - WoS: 6Citation - Scopus: 10Efficient Privacy-Preserving Whole-Genome Variant Queries(Oxford University Press, 2022) Akgün, Mete; Pfeifer, Nico; Kohlbacher, OliverMotivation: Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease-gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data. Results: We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3 000 000 variants with five genomic query predicates under 400 ms. Querying 1 048 576 genomes, each containing 1 000 000 variants, for the presence of five different query variants can be achieved approximately in 6 min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.Article Artisans Meet Design: the Reception of the Turkish Handicraft Development Office in Turkey(Oxford University Press, 2020) Emgin, BaharPeter Muller-Munk Associates, an American industrial design firm, established the Turkish Handicraft Development Office in 1957 in Ankara as part of the US technical assistance program to developing nations. The aim of the program was to improve selected local crafts products in order to make them appealing for the American market. To this end, American designers and local craftspeople produced about 150 prototypes formed by creative combinations of meerschaum, copperware, ceramics, woodwork and basket weaving. When the office was closed in the early 1960s because of its failure to mass-produce the samples, it left behind a lively debate regarding the improvement of craft production and its relation to industrialization and economic growth. This article focuses on these debates to determine the place allocated to design within the discussions of crafts as a socio-economic activity. The article will focus on the reception of the design assistance program among the local actors to answer how Turkish crafts practitioners and officials perceived design, how the emergent concept of design was linked with handicraft and artisanal production, and how it took place as part of the agenda of economic and industrial development.Article Citation - WoS: 13Multisite Photometric Campaign on the High-Amplitude Delta Scuti Star Kic 6382916(Oxford University Press, 2013) Ulusoy, Ceren; Ulas, B.; Guelmez, T.; Balona, L. A.; Stateva, I.; Iliev, I. Kh.; Carbognani, A.We present results of a multisite photometric campaign on the high-amplitude delta Scuti star KIC 6382916 in the Kepler field. The star was observed over a 85-d interval at five different sites in North America and Europe during 2011. Kepler photometry and ground-based multicolour light curves of KIC 6382916 are used to investigate the pulsational content and to identify the principal modes. High-dispersion spectroscopy was also obtained in order to derive the stellar parameters and projected rotational velocity. From an analysis of the Kepler time series, three independent frequencies and a few hundred combination frequencies are found. The light curve is dominated by two modes with frequencies f(1) = 4.9107 and f(2) = 6.4314 d(-1). The third mode with f(3) = 8.0350 d(-1) has a much lower amplitude. We attempt mode identification by examining the amplitude ratios and phase differences in different wavebands from multicolour photometry and comparing them to calculations for different spherical harmonic degree, l. We find that the theoretical models for f(1) and f(2) are in a best agreement with the observations and lead to value of l = 1 modes, but the mode identification of f(3) is uncertain due to its low amplitude. Non-adiabatic pulsation models show that frequencies below 6 d(-1) are stable, which means that the low frequency of f(1) cannot be reproduced. This is a further confirmation that current models predict a narrower pulsation frequency range than actually observed.Article Citation - WoS: 12Citation - Scopus: 15Effects of Cell-Mediated Osteoprotegerin Gene Transfer and Mesenchymal Stem Cell Applications on Orthodontically Induced Root Resorption of Rat Teeth(Oxford University Press, 2017) Amuk, Nisa Gül; Kurt, Gökmen; Baran, Yusuf; Seyrantepe, Volkan; Kartal Yandım, Melis; Adan, Aysun; Akyıldız Demir, Seçil; Kiraz, Yağmur; Sönmez, Mehmet FatihAim: The aim of this study is to evaluate and compare therapeutic effects of mesenchymal stem cell (MSCs) and osteoprotegerin (OPG) gene transfer applications on inhibition and/or repair of orthodontically induced inflammatory root resorption (OIIRR). Materials and methods: Thirty Wistar rats were divided into four groups as untreated group (negative control), treated with orthodontic appliance group (positive control), MSCs injection group, and OPG transfected MSCs [gene therapy (GT) group]. About 100 g of orthodontic force was applied to upper first molar teeth of rats for 14 days. MSCs and transfected MSC injections were performed at 1st, 6th, and 11th days to the MSC and GT group rats. At the end of experiment, upper first molar teeth were prepared for genetical, scanning electron microscopy (SEM), fluorescent microscopy, and haematoxylin eosin-tartrate resistant acid phosphatase staining histological analyses. Number of total cells, number of osteoclastic cells, number of resorption lacunae, resorption area ratio, SEM resorption ratio, OPG, RANKL, Cox-2 gene expression levels at the periodontal ligament (PDL) were calculated. Paired t-test, Kruskal-Wallis, and chi-square tests were performed. Results: Transferred MSCs showed marked fluorescence in PDL. The results revealed that number of osteoclastic cells, resorption lacunae, resorption area ratio, RANKL, and Cox-2 were reduced after single MSC injections significantly (P < 0.05). GT group showed the lowest number of osteoclastic cells (P < 0.01), number of resorption lacunae, resorption area ratio, and highest OPG expression (P < 0.001). Conclusions: Taken together all these results, MSCs and GT showed marked inhibition and/or repair effects on OIIRR during orthodontic treatment on rats.Article Citation - WoS: 30Citation - Scopus: 28Bianchi I Model: an Alternative Way To Model the Present-Day Universe(Oxford University Press, 2014) Russell, Esra; Kılınç, Can Battal; Pashaev, OktayAlthough the new era of high-precision cosmology of the cosmic microwave background (CMB) radiation improves our knowledge to understand the infant as well as the presentday Universe, it also leads us to question the main assumption of the exact isotropy of the CMB. There are two pieces of observational evidence that hint towards there being no exact isotropy. These are: first, the existence of small anisotropy deviations from isotropy of theCMB radiation and secondly, the presence of large angle anomalies, although the existence of these anomalies is currently a huge matter of debate. These hints are particularly important since isotropy is one of the two main postulates of the Copernican principle on which the Friedmann Robertson Walker (FRW) models are built. This almost-isotropic CMB radiation implies that the universe is almost an FRW universe, as is proved by previous studies. Assuming that the matter component forms the deviations from isotropy in the CMB density fluctuations when matter and radiation decouples, we here attempt to find possible constraints on the FRW-type scale and Hubble parameter by using the Bianchi type I (BI) anisotropic model which is asymptotically equivalent to the standard FRW. To obtain constraints on such an anisotropic model, we derive average and late-time shear values that come from the anisotropy upper limits of the recent Planck data based on a model independent shear parameter of Maartens, Ellis & Stoeger and from the theoretical consistency relation. These constraints lead us to obtain a BI model which becomes an almost-FRWmodel in time, and which is consistent with the latest observational data of the CMB.Article Citation - WoS: 88Citation - Scopus: 92Sur1-Trpm4 Cation Channel Expression in Human Cerebral Infarcts(Oxford University Press, 2015) Mehta, Rupal I.; Tosun, Çiğdem; Ivanova, Svetlana; Tsymbalyuk, Natalia; Famakin, Bolanle M.; Kwon, Min Seong; Castellani, Rudy J.; Gerzanich, Volodymyr; Simard, J. MarcThe nonselective monovalent cation channel transient receptor potential melastatin 4 (Trpm4) is transcriptionally upregulated in neural and vascular cells in animal models of brain infarction. It associates with sulfonylurea receptor 1 (Sur1) to form Sur1-Trpm4 channels, which have critical roles in cytotoxic edema, cell death, blood-brain barrier breakdown, and vasogenic edema. We examined Trpm4 expression in postmortem brain specimens from 15 patients who died within the first 31 days of the onset of focal cerebral ischemia. We found increased Trpm4 protein expression in all cases using immunohistochemistry; transcriptional upregulation was confirmed using in situ hybridization of Trpm4 messenger RNA. Transient receptor potential melastatin 4 colocalized and coassociated with Sur1 within ischemic endothelial cells and neurons. Coexpression of Sur1 and Trpm4 in necrotic endothelial cells was also associated with vasogenic edema indicated by upregulated perivascular tumor necrosis factor, extravasation of serum immunoglobulin G, and associated inflammation. Upregulated Trpm4 protein was present up to 1 month after the onset of cerebral ischemia. In a rat model of middle cerebral artery occlusion stroke, pharmacologic channel blockade by glibenclamide, a selective inhibitor of sulfonylurea receptor, mitigated perivascular tumor necrosis factor labeling. Thus, upregulated Sur1-Trpm4 channels and associated blood-brain barrier disruption and cerebral edema suggest that pharmacologic targeting of this channel may represent a promising therapeutic strategy for the clinical management of patients with cerebral ischemia.Article Citation - WoS: 3Citation - Scopus: 3Extended Void Merging Tree Algorithm for Self-Similar Models(Oxford University Press, 2014) Russell, EsraIn hierarchical evolution, voids exhibit two different behaviours related with their surroundings and environments, they can merge or collapse. These two different types of void processes can be described by the two-barrier excursion set formalism based on Brownian random walks. In this study, the analytical approximate description of the growing void merging algorithm is extended by taking into account the contributions of voids that are embedded into overdense region(s) which are destined to vanish due to gravitational collapse. Following this, to construct a realistic void merging model that consists of both collapse and merging processes, the twobarrier excursion set formalism of the void population is used. Assuming spherical voids in the Einstein-de Sitter Universe, the void merging algorithm which allows us to consider the two main processes of void hierarchy in one formalism is constructed. In addition to this, the merger rates, void survival probabilities, void size distributions in terms of the collapse barrier and finally, the void merging tree algorithm in the self-similar models are defined and derived.Article Citation - WoS: 12Citation - Scopus: 12Short and Long Time-Scale Variability in Magnetic Cataclysmic Variables: Long-Term Monitoring of Polars(Oxford University Press, 2012) Kalomeni, BelindaWe present long-term observations of the magnetic cataclysmic variables AM Her, AN UMa, AR UMa, DP Leo and V1309 Ori. Analyses of both short- and long-period light variations are presented. For the first time, as far as we know, long-period variations of AN UMa and AR UMa have been studied and multiple frequencies obtained. Fourier analysis indicates 170-, 218- and 180-d variations for AM Her, AN UMa and AR UMa, respectively. These periodicities may be due to modulation of the mass-transfer rate resulting from magnetic cycles in the secondary stars. In addition, we collect the physical parameters of polars from the literature and estimate their mass-transfer rates and orbital period variation and give a rough estimation of the donor magnetic fields.