A Novel Approach to Accessing Large Images in the Database

Abstract. This paper describes several ways to achieve access to images in a database and on the field of application of these methods have drawbacks as well as a detailed comparison, we propose a feasible implementation. Finally, this approach will be promoted, making it suitable for a variety of media file format

ItsBlue: A Distributed Bluetooth-Based Framework for Intelligent Transportation Systems

Inefficiency in transportation networks is having an expanding impact, at a variety of levels. Transportation authorities expect increases in delay hours and in fuel consumption and, consequently, the total cost of congestion. Nowadays, Intelligent Transportation Systems (ITS) have become a necessity in order to alleviate the expensive consequences of the rapid demand on transportation networks. Since the middle of last century, ITS have played a significant role in road safety and comfort enhancements. However, the majority of state of the art ITS are suffering from several drawbacks, among them high deployment costs and complexity of maintenance. Over the last decade, wireless technologies have reached a wide range of daily users. Today\u27s Mobile devices and vehicles are now heavily equipped with wireless communication technologies. Bluetooth is one of the most widely spread wireless technologies in current use. Bluetooth technology has been well studied and is broadly employed to address a variety of challenges due to its cost-effectiveness, data richness, and privacy perverseness, yet Bluetooth utilization in ITS is limited to certain applications. However, Bluetooth technology has a potential far beyond today\u27s ITS applications. In this dissertation, we introduce itsBlue, a novel Bluetooth-based framework that can be used to provide ITS researchers and engineers with desired information. In the itsBlue framework, we utilize Bluetooth technology advantages to collect road user data from unmodified Bluetooth devices, and we extract a variety of traffic statistics and information to satisfy ITS application requirements in an efficient and cost-effective way. The itsBlue framework consists of data collection units and a central computing unit. The itsBlue data collection unit features a compact design that allows for stationary or mobile deployment in order to extend the data collection area. Central computing units aggregate obtained road user data and extract a number of Bluetooth spatial and temporal features. Road users’ Bluetooth features are utilized in a novel way to determine traffic-related information, such as road user context, appearance time, vehicle location and direction, etc. Extracted information is provided to ITS applications to generate the desired transportation services. Applying such a passive approach involves addressing several challenges, like discovering on-board devices, filtering out data received from vehicles out of the target location, or revealing vehicle status and direction. Traffic information provided by the itsBlue framework opens a wide to the development of a wide range of ITS applications. Hence, on top of the itsBlue framework, we develop a pack of intersection management applications that includes pedestrians’ volume and waiting times, as well as vehicle queue lengths and waiting times. Also, we develop a vehicle trajectory reconstruction application. The itsBlue framework and applications are thoroughly evaluated by experiments and simulations. In order to evaluate our work, we develop an enhanced version of the UCBT Network Simulator 2 (NS-2). According to evaluation outcomes, itsBlue framework and applications evaluations show promising results. For instance, the evaluation results show that the itsBlue framework has the ability to reveal road user context with accuracy exceeding 95% in 25s

A Web GIS-based Integration of 3D Digital Models with Linked Open Data for Cultural Heritage Exploration

This PhD project explores how geospatial semantic web concepts, 3D web-based visualisation, digital interactive map, and cloud computing concepts could be integrated to enhance digital cultural heritage exploration; to offer long-term archiving and dissemination of 3D digital cultural heritage models; to better interlink heterogeneous and sparse cultural heritage data. The research findings were disseminated via four peer-reviewed journal articles and a conference article presented at GISTAM 2020 conference (which received the ‘Best Student Paper Award’)

Evolving IoT honeypots

The Internet of Things (IoT) is the emerging world where arbitrary objects from our everyday lives gain basic computational and networking capabilities to become part of the Internet. Researchers are estimating between 25 and 35 billion devices will be part of Internet by 2022. Unlike conventional computers where one hardware platform (Intel x86) and three operating systems (Windows, Linux and OS X) dominate the market, the IoT landscape is far more heterogeneous. To meet the growth demand the number of The System-on-Chip (SoC) manufacturers has seen a corresponding exponential growth making embedded platforms based on ARM, MIPS or SH4 processors abundant. The pursuit for market share is further leading to a price war and cost-cutting ultimately resulting in cheap systems with limited hardware resources and capabilities. The frugality of IoT hardware has a domino effect. Due to resource constraints vendors are packaging devices with custom, stripped-down Linux-based firmwares optimized for performing the device’s primary function. Device management, monitoring and security features are by and far absent from IoT devices. This created an asymmetry favouring attackers and disadvantaging defenders. This research sets out to reduce the opacity and identify a viable strategy, tactics and tooling for gaining insight into the IoT threat landscape by leveraging honeypots to build and deploy an evolving world-wide Observatory, based on cloud platforms, to help with studying attacker behaviour and collecting IoT malware samples. The research produces useful tools and techniques for identifying behavioural differences between Medium-Interaction honeypots and real devices by replaying interactive attacker sessions collected from the Honeypot Network. The behavioural delta is used to evolve the Honeypot Network and improve its collection capabilities. Positive results are obtained with respect to effectiveness of the above technique. Findings by other researchers in the field are also replicated. The complete dataset and source code used for this research is made publicly available on the Open Science Framework website at https://osf.io/vkcrn/.Thesis (MSc) -- Faculty of Science, Computer Science, 202

EdgeX: Edge Replication for Web Applications

Global web applications face the problem of high network latency due to their need to communicate with distant data centers. Many applications use edge networks for caching images, CSS, javascript, and other static content in order to avoid some of this network latency. However, for updates and for anything other than static content, communication with the data center is still required, and can dominate application request latencies. One way to address this problem is to push more of the web application, as well the database on which it depends, from the remote data center towards the edge of the network. This thesis presents preliminary work in this direction. Speci cally, it presents an edge-aware dynamic data replication architecture for relational database systems supporting web applications. The objective is to allow dynamic content to be served from the edge of the network, with low latency

Autonomous Database Management at Scale: Automated Tuning, Performance Diagnosis, and Resource Decentralization

Database administration has always been a challenging task, and is becoming even more difficult with the rise of public and private clouds. Today, many enterprises outsource their database operation to cloud service providers (CSPs) in order to reduce operating costs. CSPs, now tasked with managing an extremely large number of database instances, cannot simply rely on database administrators. In fact, humans have become a bottleneck in the scalability and profitability of cloud offerings. This has created a massive demand for building autonomous databases—systems that operate with little or zero human supervision. While autonomous databases have gained much attention in recent years in both academia and industry, many of the existing techniques remain limited to automating parameter tuning, backup/recovery, and monitoring. Consequently, there is much to be done before realizing a fully autonomous database. This dissertation examines and offers new automation techniques for three specific areas of modern database management. 1. Automated Tuning – We propose a new generation of physical database designers that are robust against uncertainty in future workloads. Given the rising popularity of approximate databases, we also develop an optimal, hybrid sampling strategy that enables efficient join processing on offline samples, a long-standing open problem in approximate query processing. 2. Performance Diagnosis – We design practical tools and algorithms for assisting database administrators in quickly and reliably diagnosing performance problems in their transactional databases. 3. Resource Decentralization – To achieve autonomy among database components in a shared environment, we propose a highly efficient, starvation-free, and fully decentralized distributed lock manager for distributed database clusters.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/153349/1/dyoon_1.pd

Biosynthesis of penilactones and peniphenones in Penicillium crustosum

Secondary metabolites originated from plants, bacteria and fungi constitute a large group of compounds, which are not essential for the growth, development and reproduction of the organism, but necessary for protection, competition and species interactions. Microbes, e.g. fungi and bacteria, have been more important sources of natural products since the discovery of penicillin in 1928. With advanced isolation and characterization techniques for secondary metabolites from crude biological samples, diverse compounds from different groups including polyketides, nonribosomal peptides, alkaloids and terpenes have been identified. Producing organisms utilize a limited set of primary metabolic building blocks to produce different natural product skeletons, which are further modified by a number of tailoring enzymes to form a variety of end products. For example, a core structure of polyketide can be derived from acyl-CoAs by polyketide synthase(s) (PKS(s)) and catalyzed by a series of tailoring enzymes such as nonheme FeII/2-OG-dependent oxygenases, flavin-containing oxidoreductases, cytochrome P450s and prenyltransferases to create an amazing diversity of natural product architectures. To facilitate the biosynthetic mechanism, advanced bioinformatics, biological technologies and biochemical tools have been utilized to investigate the coding genes of these enzymes, which are usually located together as a biosynthetic gene cluster (BGC). However, post-biosynthetic non-enzymatic events can also be involved in natural product formation. In this thesis, biosynthesis of secondary metabolites from a fungal strain, Penicillium crustosum PRB-2, was investigated in cooperation with Ge Liao. Penilactones A, B and D, as well as peniphenone D, structurally comprising clavatol and r-butyrolactone moieties, were identified from the wild type. Two separate gene clusters were functionally characterized as building blocks of the complex penilactone and peniphenone structures by gene disruption in the native PRB-2 strain, heterologous expression in Aspergillus nidulans and precursor feeding experiment in the available deletion mutants. A non-reducing (NR) PKS ClaF from the clavatol cluster is responsible for the formation of clavatol. A hybrid PKS-NRPS TraA from the terrestric acid cluster is involved in the biosynthesis of crustosic acid and terrestric acid, which undergo C-C bond cleavage to give r-butyrolactone moieties in penilactones and peniphenones. Oxidation of clavatol to hydroxyclavatol by a nonheme FeII/2-OG-dependent oxygenase ClaD and its spontaneous dehydration to an intermediate ortho-quinone methide initiate the non-enzymatic 1,4-Michael additions with r-butyrolactones. Therefore, the cross-coupling of two moieties from two separate gene clusters leads to the formation of peniphenone D and penilactone D, which undergo a second Michael addition with ortho-quinone methide to give penilactones A and B. Our findings represent rare examples of complex structures derived from two separate clusters and formed through enzymatic and non-enzymatic approaches. Afterwards, the investigation on terrestric acid formation was extended by using similar strategies. The hybrid PKS-NRPS TraA and the enoyl reductase TraG were demonstrated to be responsible for the accumulation of the tetronate core structure carboxylcrustic acid and viridicatic acid as precursors of crustosic acid in PRB-2. Biochemical characterizations proved that the conversion of crustosic acid to terrestric acid was achieved via oxidative decarboxylation catalyzed by a nonheme FeII/2-OG-dependent oxygenase TraH and subsequent stereospecific C-C double bond reduction by a flavin-containing oxidoreductase TraD. Among the two-step oxidative decarboxylation and stereospecific reduction, the mechanism with FeIV=O species as important intermediates was postulated for TraH-catalyzed olefination with or without CO2 elimination. Results on the biosynthesis of terrestric acid also provide a valid experimental basis for understanding the formation of the fungal acyltetronates with different stereochemistry involving sequential redox-assisted decarboxylation and stereoisomerization. In addition to penilactones and peniphenones, there are more clavatol-containing natural products from fungi. We wondered that these compounds are very likely synthesized from different precursors by nucleophilic attacking ortho-quinone methide derived from hydroxyclavatol. This hypothesis triggered our interest to screen the reactivity of ortho-quinone methide with diverse natural products or natural product-like compounds. Coincubation of 102 selected reactants with hydroxyclavatol under mild conditions (in nearly pH neutral aqueous solution) led to the detection of clavatol coupling products in 86 cases. As a result, 32 new clavatol-containing compounds were identified after isolation and structural elucidation. The conjugation between clavatol and the nucleophiles occurs mainly with the C-C bond formation at para- or ortho-positions of hydroxyl/amino group at the benzene ring and C-2 position of the indole skeleton. This study confirmed the activity of the ortho-quinone methide which is spontaneously derived from hydroxyclavatol in an aqueous system and increased significantly the diversity of clavatol-containing products in nature

Increasing structural diversity of natural products by enzymatic or nonenzymatic reactions

Secondary metabolites are generally low-molecule-mass compounds, also known as natural products. So far, millions of natural products with remarkably structural diversity have been found in nature. These include, but are not limited to, polyketides, nonribosomal peptides, alkaloids, and terpenoids. The structural divergence of natural products begins with the formation of basic skeletons by different backbone enzymes using fundamental building blocks derived from primary metabolism. Following modifications of the pre-matured scaffolds are catalyzed by tailoring enzymes such as oxidoreductases and transferases, thus completing the biosynthesis of end products with vast diversity and complexity. Enzymes from natural product biosynthetic pathways are versatile biocatalysts due to the merits of high efficiency and specificity. Harnessing biocatalytic potential of enzymes through chemoenzymatic synthesis has proven to be a useful tool for enriching chemical libraries. In addition to enzymatic catalysis, the occurrence of nonenzymatic events has also been found during the post-biosynthetic processing of natural products. These nonenzymatic reactions often occur with the involvement of reactive biosynthetic intermediates. Full exploitation of these intermediates for chemical synthesis can be used as an updated strategy to expand the chemical variety of natural products. In a cooperation project with Dr. Peter Mai, five prenyltransferases (PTs) of the dimethylallyltryptophan synthase (DMATS) family, i.e. FtmPT1, BrePT, CdpC2PT, CdpNPT, and CdpC3PT, were selected for protein engineering. These PTs catalyze a regular or reverse transfer of the dimethylallyl residue (C5) from dimethylallyl diphosphate (DMAPP) to the C-2 or C-3 position of indolyl residues in cyclic dipeptides (CDPs). To switch their prenyl donor specificity from DMAPP to geranyl diphosphate (GPP), protein sequence alignments of the five PTs with those of AtaPT and FgaPT2 led to the identification of the gatekeeping residues at Met364 in FtmPT1, Ile337 in BrePT, Thr351 in CdpC2PT, Met349 in CdpNPT, and Phe335 in CdpC3PT. Replacing the respective key amino acids by glycine resulted in the construction of FtmPT1_M364G, BrePT_I337G, CdpC2PT_T351G, CdpNPT_M349G, and CdpC3PT_F335G. These mutants showed clearly improved activity toward GPP but reduced activity toward DMAPP. As a result, 42 geranylated derivatives were obtained from the incubation mixtures of the generated mutants with 15 tested CDPs in the presence of GPP and their structures were elucidated by NMR and MS analyses. When using cyclo-L-Trp-L-Trp as the acceptor and GPP as the donor, the transfer of geranyl moieties to all seven possible positions of the indole nucleus can be achieved by the engineered enzymes. Prior to our study, only limited numbers of geranylated indole derivatives have been reported. This study significantly increased the structural diversity of geranylated products by structure-based protein engineering of available dimethylallyl transferases. In a cooperation study with Dr. Jie Fan, the biosynthesis of peniphenone and penilactones in Penicillium crustosum PRB-2 was elucidated, which revealed occurrence of both enzymatic and nonenzymatic reactions during their formation. The hybrid PKS-NRPS TraA from the terrestric acid pathway is involved in the formation of crustosic acid, which undergoes decarboxylation by the nonheme FeII/2-OG-dependent oxygenase TraH and subsequent reduction by the flavin-containing oxidoreductase TraD to afford terrestric acid. Both acids are precursors of the r-butyrolactones. The nonreducing PKS ClaF from the clavatol pathway is responsible for the formation of clavatol, which is then oxidized to hydroxyclavatol by the nonheme FeII/2-OG-dependent oxygenase ClaD. Alongside with spontaneous dehydration of hydroxyclavatol to the reactive intermediate ortho-quinone methide (QM), nonenzymatic 1,4-Michael additions were initiated by the nucleophilic attack from the r-butyrolactones to the ortho-QMs, leading to the sequential formation of peniphenone D and penilactone A as well as penilactones D and B. In addition to utilizing enzymes from the natural biosynthetic machinery, an alternative strategy was used for structural diversification by taking advantage of reactive intermediates from the biosynthetic pathway of natural products. As mentioned above, the ortho-QM involved in the formation of peniphenone and penilactones was proven to be highly reactive and capable of reacting with r-butyrolactones spontaneously under very mild conditions. As a following work, the reactivity of the ortho-QM derived from hydroxyclavatol was tested with 101 natural products or natural product-like compounds. These include flavonoids, hydroxynaphthalenes, coumarins, xanthones, anthraquinones, phloroglucinols, phenolic acids, indole derivatives, tyrosine analogues, and quinolines. LC-MS analysis revealed product formation in the incubation mixtures of 85 tested reactants. 32 clavatol-containing products were isolated from 23 selected incubations and identified by NMR and MS analyses. The cross-coupling between the tested nucleophiles and the ortho-QM from hydroxyclavatol occurs preferentially via C-C bonds at the ortho- or para-position of phenolic hydroxyl groups and the C-2 position of the indole ring. The obtained products were also tested for their biological activities. This study proved the ortho-QM as an excellent Michael acceptor for a variety of substances, suggesting the utilization of the reactive biosynthetic intermediate for accessing chemical diversity of natural products

Biosynthesis of penilactones and peniphenones in Penicillium crustosum

Secondary metabolites originated from plants, bacteria and fungi constitute a large group of compounds, which are not essential for the growth, development and reproduction of the organism, but necessary for protection, competition and species interactions. Microbes, e.g. fungi and bacteria, have been more important sources of natural products since the discovery of penicillin in 1928. With advanced isolation and characterization techniques for secondary metabolites from crude biological samples, diverse compounds from different groups including polyketides, nonribosomal peptides, alkaloids and terpenes have been identified. Producing organisms utilize a limited set of primary metabolic building blocks to produce different natural product skeletons, which are further modified by a number of tailoring enzymes to form a variety of end products. For example, a core structure of polyketide can be derived from acyl-CoAs by polyketide synthase(s) (PKS(s)) and catalyzed by a series of tailoring enzymes such as nonheme FeII/2-OG-dependent oxygenases, flavin-containing oxidoreductases, cytochrome P450s and prenyltransferases to create an amazing diversity of natural product architectures. To facilitate the biosynthetic mechanism, advanced bioinformatics, biological technologies and biochemical tools have been utilized to investigate the coding genes of these enzymes, which are usually located together as a biosynthetic gene cluster (BGC). However, post-biosynthetic non-enzymatic events can also be involved in natural product formation. In this thesis, biosynthesis of secondary metabolites from a fungal strain, Penicillium crustosum PRB-2, was investigated in cooperation with Ge Liao. Penilactones A, B and D, as well as peniphenone D, structurally comprising clavatol and r-butyrolactone moieties, were identified from the wild type. Two separate gene clusters were functionally characterized as building blocks of the complex penilactone and peniphenone structures by gene disruption in the native PRB-2 strain, heterologous expression in Aspergillus nidulans and precursor feeding experiment in the available deletion mutants. A non-reducing (NR) PKS ClaF from the clavatol cluster is responsible for the formation of clavatol. A hybrid PKS-NRPS TraA from the terrestric acid cluster is involved in the biosynthesis of crustosic acid and terrestric acid, which undergo C-C bond cleavage to give r-butyrolactone moieties in penilactones and peniphenones. Oxidation of clavatol to hydroxyclavatol by a nonheme FeII/2-OG-dependent oxygenase ClaD and its spontaneous dehydration to an intermediate ortho-quinone methide initiate the non-enzymatic 1,4-Michael additions with r-butyrolactones. Therefore, the cross-coupling of two moieties from two separate gene clusters leads to the formation of peniphenone D and penilactone D, which undergo a second Michael addition with ortho-quinone methide to give penilactones A and B. Our findings represent rare examples of complex structures derived from two separate clusters and formed through enzymatic and non-enzymatic approaches. Afterwards, the investigation on terrestric acid formation was extended by using similar strategies. The hybrid PKS-NRPS TraA and the enoyl reductase TraG were demonstrated to be responsible for the accumulation of the tetronate core structure carboxylcrustic acid and viridicatic acid as precursors of crustosic acid in PRB-2. Biochemical characterizations proved that the conversion of crustosic acid to terrestric acid was achieved via oxidative decarboxylation catalyzed by a nonheme FeII/2-OG-dependent oxygenase TraH and subsequent stereospecific C-C double bond reduction by a flavin-containing oxidoreductase TraD. Among the two-step oxidative decarboxylation and stereospecific reduction, the mechanism with FeIV=O species as important intermediates was postulated for TraH-catalyzed olefination with or without CO2 elimination. Results on the biosynthesis of terrestric acid also provide a valid experimental basis for understanding the formation of the fungal acyltetronates with different stereochemistry involving sequential redox-assisted decarboxylation and stereoisomerization. In addition to penilactones and peniphenones, there are more clavatol-containing natural products from fungi. We wondered that these compounds are very likely synthesized from different precursors by nucleophilic attacking ortho-quinone methide derived from hydroxyclavatol. This hypothesis triggered our interest to screen the reactivity of ortho-quinone methide with diverse natural products or natural product-like compounds. Coincubation of 102 selected reactants with hydroxyclavatol under mild conditions (in nearly pH neutral aqueous solution) led to the detection of clavatol coupling products in 86 cases. As a result, 32 new clavatol-containing compounds were identified after isolation and structural elucidation. The conjugation between clavatol and the nucleophiles occurs mainly with the C-C bond formation at para- or ortho-positions of hydroxyl/amino group at the benzene ring and C-2 position of the indole skeleton. This study confirmed the activity of the ortho-quinone methide which is spontaneously derived from hydroxyclavatol in an aqueous system and increased significantly the diversity of clavatol-containing products in nature