IYTE GCRIS Database (Izmir Institute of Technology)
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Compiler-Managed Replication of Cuda Kernels for Reliable Execution of Gpgpu Applications
No full textAs Graphics Processing Units (GPUs) evolve for general-purpose computations besides inherently fault-tolerant graphics programs, soft error reliability becomes a first-class citizen in program design. Especially, safety-critical systems utilizing GPU devices need to employ fault-tolerance techniques to recover from errors in hardware components. While software-level redundancy approaches, based on the replication of the application code, offer high reliability for safe program execution, it is essential to perform redundancy by utilizing parallel execution units in the target architecture not to hurt performance with redundant computations. In this work, we propose redundancy approaches using the parallel GPU cores and implement a compiler-level redundancy framework that enables the programmer to configure the target GPGPU program for redundant execution. We run redundant executions for GPGPU programs from the PolyBench benchmark suite by applying our kernel-level redundancy approaches and evaluate their performance by considering the parallelism level of the programs. Our results reveal that redundancy approaches utilizing parallelism offered by GPU cores yield higher performance for redundant executions, while the programs that already make use of parallel GPU cores in their original form suffer from overhead caused by contention among redundant threads. © World Scientific Publishing Company
Socio-Economic and Development Disparities Over the Long-Run: Exploring Spatial Heterogeneities in the Case of Turkey
No full textThe aim of this paper is to explore the evolution of socioeconomic development and income disparities and convergence patterns across Turkish provinces, emphasizing the impact of spatial heterogeneities. We propose two types of contributions to the literature. First, most of the studies that apply the β-convergence method presume a unique β parameter, assuming that all regions homogenously converge to the steady state at the same pace. However, we argue that relaxing this assumption by way of considering spatial heterogeneities might be more informative. Second, we provide a simple solution to a severe problem: The neoclassical model assumes a monotonic saddle path along which economic fluctuations are not considered, which might be particularly influential with regard to convergence when the time span is too short to capture long-term evolution. Many empirical studies cover only short periods, which may be easily dominated by recessions or expansions, significantly biasing the results. To overcome this problem, we look into two datasets covering long periods (1963–2017 and 1975–2021). Having applied various empirical methods, such as spatial regressions, GWR and nonparametric regressions, we obtain several results. First, at the country level, there is empirical evidence of regional convergence and decreasing development inequalities. Second, however, this convergence process is not valid in all areas. We conclude that there is nonnegligible spatial heterogeneity that should be taken into account in such analyses. © (2023), (Hungarian Central Statistical Office). All Rights Reserved
Efficient Photon Pair Generation for Quantum Information Technologies
No full textBu tez, dört dalga karışım (FWM) süreci yoluyla görünür dalga boylarında foton çiftleri üretmek için kullanılan dalga kılavuzu ve halka rezonatörün tasarım parametreler- ine odaklanmaktadır. Tezin amacı, görünür dalga boylarında foton çiftleri üretmektir ve bu fotonları algılamak için görünür dalga boyunda çalışan fotodedektörler kullanılmak- tadır. Bu dedektörler, telekomünikasyon muadillerine kıyasla daha iyi foton algılama ar- alıgı, daha düşük karanlık sayım ve hızlı tepki süresi sunmaktadır. Ayrıca, görünür dalga boyundaki fotonlar serbest uzay iletişiminde daha etkilidir. Foton çift üretimi için Si3N4 dalga kılavuzu veya SiO2 tabakası üzerindeki halka rezonatör gibi bir fotonik platform tercih edilmektedir. Bu platformlar, CMOS teknolo- jilerini kullanma ve oda sıcaklıgında çalışma gibi avantajlar sağlar. Si3N4 malzemesinin tercih edilme nedeni, iki foton emilim sürecinden kaçınmaktır. Si bazlı kaynaklar, bant enerjileri nedeniyle iki foton emilim süreci sergilerken, Si3N4 kullanımı bu sorunu ortadan kaldırır. Tezde, dalga kılavuzunun boyutları faz uyumu koşulunu sağlamak amacıyla tasar- lanmış ve dispersiyon özellikleri incelenmiştir. Belirlenen boyutlara göre tasarlanan halka rezonatör, spektral özellikleri açısından verimli foton çift üretimi için analiz edilmiştir.This thesis focuses on the design parameters of waveguides and ring resonators to generate photon pairs through the four-wave mixing process. The goal was to design these components specifically for generating visible-range photon pairs with the intention of using visible-range photodetectors. These detectors offer a better photon detection range, lower dark count, and faster response time compared to their telecom-range counterparts. Additionally, visible wavelength photons are more effective in free-space communication. A photonic platform, such as a Si3N4 waveguide or a ring resonator on a SiO2 layer is utilized for photon pair generation due to several advantages. These advantages include the ability to leverage CMOS technologies and operate at room temperature. The choice of Si3 N4 material aims to avoid a two-photon absorption process. Compared to Si-based sources, which exhibit a two-photon absorption process due to their band energy, utilizing Si3 N4 helps circumvent this issue. In this thesis, the dimensions of the waveguide are tailored to satisfy the phase- matching condition and its dispersion properties are studied. A ring resonator is con- structured based on determined dimensions, and its spectral characteristics are analyzed for efficient photon pair generation
Tunable Magnetism in 2d Organic-Ion Mnpssub>3/Sub> Via Molecule-Dependent Vacancy Generation
No full textThe magnetic properties of van der Waals materials are profoundly influenced by structural defects. The layered antiferromagnet MnPS3 offers a unique opportunity to explore defect-related magnetism, as Mn2+ vacancies can be generated by the intercalation of specific guest molecules. However, the effectiveness of this process in atomically thin flakes and the extent of the magnetic tunability remain unclear. Here, it is shown that the magnetic properties of MnPS3 can be tailored through the intercalation of different guest molecules. Notably, the insertion of four alkylammonium ions introduces different populations of Mn2+ vacancies, leading to a transition from the pristine antiferromagnetic state to more complex magnetic textures, including a ferrimagnetic state displaying a magnetic saturation of 1 mu B per atom. Moreover, it is shown that the intercalation of few-nm-thick flakes also leads to the emergence of a ferrimagnetic response. This in-flake intercalation, which can be monitored in real time using optical microscopy, can be interrupted before completion, generating lateral heterostructures between pristine and intercalated areas. This approach opens the way to the use of partial intercalation to define regions with distinct magnetic properties within a single flake
L-Arginine Treatment Corrects Impaired Autophagy in Gm2 Gangliosidosis Ab-Variant Mouse Cells
No full text[No Abstract Available
Development and Functionalization of Electrospun Fiber Coated Thin Film Microextraction Devices for Rapid Mass Spectrometric Determination of Biologically Important Polar Molecules
No full textRapid diagnosis of diseases is one of the challenging areas in clinical research. From the analytical chemist's perspective, the main challenges are isolating the compounds from the bio-specimen and lengthy analysis times. In this regard, solid phase microextraction offers a platform to address the abovementioned challenges. Moreover, its sharp tip-thin film geometry, known as coated blade spray (CBS), can enhance the extraction and act as an ionization source in direct mass spectrometric analysis. In this study, a new CBS device specifically designed for polar analytes was prepared and optimized to determine urinary metabolites. For this purpose, polyacrylonitrile (PAN) was selected as a base polymer as it can be electrospun to form a nanofibrous structure, and it can be modified with weak ion exchange moieties to interact with polar analytes. Following the electrospinning of PAN, hydrolysis was optimized, and conditions leading to sufficient extraction enhancement without dissolving the polymer were obtained when probes were treated with 5.0 M of NaOH for 2.5 h. Using the coated blades prepared as explained, the evaluation of various extraction conditions showed that 5 min is sufficient for equilibrium extraction. In addition, the solution's ionic strength and pH significantly affect the extraction. Optimum sorption was obtained at no salt added and pH 7.0 conditions. The CBS-MS optimization showed that 10.0 µL of ACN/MeOH/H2O (40:40:20, v/v/v) with formic acid kept for 15 seconds on the blade before voltage application leads to the highest signal. The limits of quantification of the analytes are between 50 and 100 ng/mL. © 2024 Elsevier B.V
Dynamic Frequent Subgraph Mining Algorithms Over Evolving Graphs: a Survey
No full textFrequent subgraph mining (FSM) is an essential and challenging graph mining task used in several applications of the modern data science. Some of the FSM algorithms have the objective of finding all frequent subgraphs whereas some of the algorithms focus on discovering frequent subgraphs approximately. On the other hand, modern applications employ evolving graphs where the increments are small graphs or stream of nodes and edges. In such cases, FSM task becomes more challenging due to growing data size and complexity of the base algorithms. Recently we see frequent subgraph mining algorithms designed for dynamic graph data. However, there is no comparative review of the dynamic subgraph mining algorithms focusing on the discovery of frequent subgraphs over evolving graph data. This article focuses on the characteristics of dynamic frequent subgraph mining algorithms over evolving graphs. We first introduce and compare dynamic frequent subgraph mining algorithms; trying to highlight their attributes as increment type, graph type, graph representation, internal data structure, algorithmic approach, programming approach, base algorithm and output type. Secondly, we introduce and compare the approximate frequent subgraph mining algorithms for dynamic graphs with additional attributes as their sampling strategy, data in the sample, statistical guarantees on the sample and their main objective. Finally, we highlight research opportunities in this specific domain from our perspective. Overall, we aim to introduce the research area of frequent subgraph mining over evolving graphs with the hope that this can serve as a reference and inspiration for the researchers of the field
Enhancement of Ultraviolet Resistance of Polyaspartics
No full textThe degradation of polyaspartic ester (PAE) resins under ultraviolet (UV) exposure poses significant challenges for their long-term use in outdoor applications. This study investigates the enhancement of UV resistance of PAE resins through the incorporation of metal oxide particles as UV absorbers. The research aims to determine the efficacy of metal oxide particles in improving the UV protective properties of PAE resins. Experimental results demonstrate that the UV absorption values of resin dispersions containing metal oxide particles significantly increased compared to pure PAE resin. This enhancement may be attributed to the metal oxides' ability to absorb and scatter UV light, thereby reducing the transmission of harmful UV rays through the resin matrix. Various concentrations of metal oxide particles were tested, and the findings underscore the importance of achieving a homogeneous dispersion within the resin for optimal UV protection. The study concludes that the incorporation of metal oxide particles into PAE resins can remarkably enhance the UV resistance of PAE. The improved UV absorption characteristics make these modified resins more suitable for applications exposed to prolonged UV radiation. This research provides a foundation for further exploration into optimizing particle concentrations and dispersion techniques to maximize the UV resistance of polyaspartic ester resins while maintaining their transparency over visible region of the optical spectrum.Poliaspartik ester (PAE) reçinelerinin ultraviyole (UV) ışınlarına maruz kalması, açık hava uygulamalarında uzun ömürlü kullanımlarında önemli zorluklar yaratmaktadır. Bu çalışma, UV soğurucu olarak metal oksit tanecikleri eklenerek PAE reçinelerinin UV direncinin artırılmasını araştırmaktadır. Araştırmanın amacı, metal oksit taneciklerin PAE reçinelerinin UV koruma özelliklerini iyileştirmedeki etkinliğini belirlemektir. Deneysel sonuçlar, metal oksit tanecikleri içeren reçine dispersiyonlarının UV absorpsiyon değerlerinin saf PAE reçinesine kıyasla önemli ölçüde arttığını göstermektedir. Bu iyileşme, metal oksitlerin UV ışığını absorbe etme ve saçma yeteneklerine bağlanmaktadır; böylece zararlı UV ışınlarının reçine matrisi içinden geçişi azalır. Çeşitli metal oksit tanecik konsantrasyonları test edilmiş ve optimal UV koruması için reçine içinde homojen bir dağılımın önemini vurgulamaktadır. Çalışma, metal oksit taneciklerinin PAE reçinelerine eklenmesinin, reçinelerin UV direncini etkili bir şekilde artırdığını sonucuna varmıştır. Gelişmiş UV absorpsiyon özellikleri, bu modifiye edilmiş reçineleri, uzun süreli UV ışınımına maruz kalan uygulamalar için daha uygun hale getirmektedir. Bu araştırma, poliaspartik ester reçinelerinin UV direncini maksimize etmek ve görünüt bölgede saydamlığını korumak için tanecik derişimini ve dispersiyon tekniklerinin optimize edilmesine yönelik çalışmalara temel oluşturmaktadır
Targeting the Panoptosome Using Necrostatin-1 Reduces Panoptosis and Protects the Kidney Against Ischemia-Reperfusion Injury in a Rat Model of Controlled Experimental Nonheart-Beating Donor
No full textPurpose. Reducing renal ischemia is crucial for the function and survival of grafts from non- heartbeat donors, as it leads to inflammatory responses and tubulointerstitial damage. The primary concern with organs from nonheartbeat donors is the long warm ischemia period and reperfusion injury following renal transplantation. This study had two main goals; one goal is to determine how Necrostatin-1 targeting the PANoptosome affects PANoptosis in the nonheartbeating donor rat model. The other goal is to fi nd out if Necrostatin-1 can protect the kidney from ischemic injury for renal transplantation surgery. Methods. Twenty-four rats were grouped randomly as control and Necrostatin-1 in this experimental animal study, and we administered 1.65 mg/kg of Necrostatin-1 intraperitoneally to the experimental group for 30 minutes before cardiac arrest. We removed the rats' left kidneys and measured various oxidative stress marker measures such as malondialdehyde, superoxide dismutase, catalase, GPx, and 8-hydroxy-2-deoxyguanosine levels. We then subjected the tissues to immunohistochemical analysis, electron microscopy, and histopathological analysis. Findings. The Necrostatin-1 group had a lower total tubular injury score (P .001) and less Caspase-3, gasdermin D, and mixed lineage kinase domain-like protein expression. Additionally, the apoptotic index of the study group was lower (P .001). Furthermore, the study group had higher levels of superoxide dismutase and GPx (P .05), whereas malondialdehyde levels were reduced (P = .009). Electron microscopy also revealed a significant improvement in tissue structure in the Necrostatin-1 group. Conclusion. Necrostatin-1 protects against ischemic acute kidney injury in nonheart-beating donor rats by inhibiting PANoptosis via the blockade of RIPK1. As a result of this, Necrostatin1 may offer novel opportunities for protecting donor kidneys from renal ischemia-reperfusion injury during transplantation in patients with end-stage kidney disease requiring a renal transplantation
Expression, Purification and Preliminary Functional Characterization of the Acidianus Two-Tailed Virus Tnpb Endonucleases
No full textTnpB is an RNA-guided endonuclease encoded in the IS200/605 transposon family. It forms a complex with a self-encoded ωRNA that directs TnpB to an appropriate target DNA sequence for activity. DNA cleavage at the target site promotes homologous recombination thus ensuring propagation of IS200/605 elements. Although IS200/605 elements are abundant in prokaryotic genomes, they are rarely found in viruses. However, the Acidianus two-tailed virus (ATV), which possesses 72 genes, encodes four TnpB proteins (gp10, gp40, gp43 and gp68). In this study, bioinformatics analysis of all ATV tnpB genes demonstrated that they were all solo tnpB genes and therefore could be classified as part of the IS1341 group. TnpB proteins are characterized by having a DED catalytic site motif and a C-terminal C4 zinc finger motif. Although the ATV gp10 protein retains the DED active site motif found in most TnpB proteins, the other ATV TnpB proteins possess a different amino acid instead of the Glu residue. Additionally, the ATV TnpB proteins possess the C4 zinc finger motif except for ATV gp40, which possesses three cysteine residues. All four ATV tnpB genes were cloned and expressed in the heterologous Escherichia coli host. The gp40 and gp68 proteins were purified using Ni2+ -NTA and gel filtration chromatography. Although gp68 appears to bind to DNA, there is insufficient evidence for RNA binding. Cleavage assays revealed that gp68 demonstrated nonspecific DNA nickase and cleavage activities. The significance of this study and the broader implications regarding the possible role of TnpB in virus survival are discussed.TnpB, IS200/605 transpozon ailesinde kodlanan bir RNA kılavuzlu endonükleazdır. TnpB, kendisi tarafından kodlanan bir ωRNA ile kompleks oluşturur ve bu RNA, TnpB'yi aktivite için uygun hedef DNA dizisine yönlendirir. Hedef DNA'nın bölgesinin kesilmesi homolog rekombinasyonu teşvik eder ve böylece IS200/605 elementlerinin yayılmasını sağlar. IS200/605 elementleri prokaryot genomlarında yaygın olsa da virüslerde nadiren bulunur. Bununla birlikte, 72 geni bulunan Acidianus iki kuyruklu virüsü (ATV), dört TnpB proteini kodlar (gp10, gp40, gp43 ve gp68). Bu çalışmada, tüm ATV tnpB genlerinin biyoinformatik analizi, bunların yalnızca tnpB genleri olduğunu gösterdi ve dolayısıyla IS1341 grubunun bir parçası olarak sınıflandırılabildi. TnpB proteinleri, bir DED katalitik bölge motifine ve bir C-terminal C4 çinko parmak motifine sahiptir. ATV gp10 proteini çoğu TnpB proteini gibi DED aktif bölge motifini korurken, diğer ATV TnpB proteinleri Glu kalıntısının yerine farklı bir amino asit taşır. Ayrıca, ATV TnpB proteinleri ATV gp40 dışında C4 çinko parmak motifine sahiptir; ATV gp40 üç sistein kalıntısına sahiptir. Dört ATV tnpB geni de heterolog Escherichia coli konak hücresinde klonlandı ve ekprese edildi. Gp40 ve gp68 proteinleri Ni2+-NTA ve jel filtrasyon kromatografisi kullanılarak saflaştırıldı. Gp68'in DNA'ya bağlandığı, ancak RNA bağlamak için yeterli kanıt olmadığı görüldü. Kesim deneyleri, gp68'in spesifik olmayan DNA nikaz ve kesim aktiviteleri gösterdi. Bu çalışmanın önemi ve TnpB'nin virüslerin hayatta kalmasındaki olası rolü ile ilgili geniş çaplı etkileri tartışılmıştır