1,181 research outputs found

    SSTRED: A data-processing and metadata-generating pipeline for CHROMIS and CRISP

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    We present a data pipeline for the newly installed SST/CHROMIS imaging spectrometer, as well as for the older SST/CRISP spectropolarimeter. The aim is to provide observers with a user-friendly data pipeline, that delivers science-ready data with the metadata needed for archival. We generalized the CRISPRED data pipeline for multiple instruments and added metadata according to recommendations worked out as part of the SOLARNET project. We made improvements to several steps in the pipeline, including the MOMFBD image restoration. A part of that is a new fork of the MOMFBD program called REDUX, with several new features that are needed in the new pipeline. The CRISPEX data viewer has been updated to accommodate data cubes stored in this format. The pipeline code, as well as REDUX and CRISPEX are all freely available through git repositories or web download. We derive expressions for combining statistics of individual frames into statistics for a set of frames. We define a new extension to the World Coordinate System, that allow us to specify cavity errors as distortions to the spectral coordinate.Comment: Draf

    Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK

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    Shigellosis in men who have sex with men (MSM) is caused by multidrug resistant Shigellae, exhibiting resistance to antimicrobials including azithromycin, ciprofloxacin and more recently the third-generation cephalosporins. We sequenced four bla (CTX-M-27)-positive MSM Shigella isolates (2018–20) using Oxford Nanopore Technologies; three S. sonnei (identified as two MSM clade 2, one MSM clade 5) and one S. flexneri 3a, to explore AMR context. All S. sonnei isolates harboured Tn7/Int2 chromosomal integrons, whereas S. flexneri 3a contained the Shigella Resistance Locus. All strains harboured IncFII pKSR100-like plasmids (67-83kbp); where present bla (CTX-M-27) was located on these plasmids flanked by IS26 and IS903B, however bla (CTX-M-27) was lost in S. flexneri 3a during storage between Illumina and Nanopore sequencing. IncFII AMR regions were mosaic and likely reorganised by IS26; three of the four plasmids contained azithromycin-resistance genes erm(B) and mph(A) and one harboured the pKSR100 integron. Additionally, all S. sonnei isolates possessed a large IncB/O/K/Z plasmid, two of which carried aph(3’)-Ib/aph(6)-Id/sul2 and tet(A). Monitoring the transmission of mobile genetic elements with co-located AMR determinants is necessary to inform empirical treatment guidance and clinical management of MSM-associated shigellosis

    Applications of satellite technology to broadband ISDN networks

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    Two satellite architectures for delivering broadband integrated services digital network (B-ISDN) service are evaluated. The first is assumed integral to an existing terrestrial network, and provides complementary services such as interconnects to remote nodes as well as high-rate multicast and broadcast service. The interconnects are at a 155 Mbs rate and are shown as being met with a nonregenerative multibeam satellite having 10-1.5 degree spots. The second satellite architecture focuses on providing private B-ISDN networks as well as acting as a gateway to the public network. This is conceived as being provided by a regenerative multibeam satellite with on-board ATM (asynchronous transfer mode) processing payload. With up to 800 Mbs offered, higher satellite EIRP is required. This is accomplished with 12-0.4 degree hopping beams, covering a total of 110 dwell positions. It is estimated the space segment capital cost for architecture one would be about 190Mwhereasthesecondarchitecturewouldbeabout190M whereas the second architecture would be about 250M. The net user cost is given for a variety of scenarios, but the cost for 155 Mbs services is shown to be about $15-22/minute for 25 percent system utilization

    MODIFIED MULTI-LEVEL STEGANOGRAPHY TO ENHANCE DATA SECURITY

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    Data-hiding using steganography algorithm becomes an important technique to prevent unauthorized users to have access to a secret data.  In this paper, steganography algorithm has been constructed to hide a secret data in a gray and a color images, this algorithm is named deep hiding/extraction algorithm (DHEA) to modify multi-level steganography (MLS). The suggested hiding algorithm is based on modified least significant bit (MDLSB) to scatter data in a cover-image and it utilizes a number of levels; where each level perform hiding data on a gray image except the last level that applies a color image to keep secret data. Furthermore, proper randomization approach with two layers is implemented; the first layer uses random pixels selection for hiding a secret data at each level, while the second layer implements at the last level to move randomly from segment to the others. In addition, the proposed hiding algorithm implements an effective lossless image compression using DEFLATE algorithm to make it possible to hide data into a next level. Dynamic encryption algorithm based on Advanced Encryption Standard (AES) is applied at each level by changing cipher keys (Ck) from level to the next, this approach has been applied to increase the security and working against attackers. Soft computing using a meta-heuristic approach based on artificial bee colony (ABC) algorithm has been introduced to achieve smoothing on pixels of stego-image, this approach is effective to reduce the noise caused by a hidden large amount of data and to increase a stego-image quality on the last level. The experimental result demonstrates the effectiveness of the proposed algorithm with bee colony DHA-ABC to show high-performing to hide a large amount of data up to four bits per pixel (bpp) with high security in terms of hard extraction of a secret message and noise reduction of the stego-image. Moreover, using deep hiding with unlimited levels is promising to confuse attackers and to compress a deep sequence of images into one image

    An Analysis of Global Gene Expression Resulting from Exposure to Energetic Materials

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    AN ANALYSIS OF GLOBAL GENE EXPRESSION RESULTING FROM EXPOSURE TO ENERGETIC MATERIALS A Dissertation Presented for the Doctor of Philosophy Degree University of Tennessee, Knoxville VERNON LASHAWN MCINTOSH JR. August 2010 Dedication This dissertation is dedicated to my family. My mother and father Debra and Vernon McIntosh instilled in me the respect for academic excellence and the drive maximize my potential. Early on, my younger brother Kyle started showing signs of a shared interest in biology thus my desire to be a positive role model for him kept me motivated. Last but certainly not least, my loving wife and best friend Nichole has been there to offer love and support throughout my entire undergraduate and graduate degrees. It’s difficult to imagine making it this far without her (and that’s not just because she paid the bills). Abstract Characteristic transcriptional biomarkers have been identified for microbial cultures exposed to 2, 4, 6-trinitrotoluene (TNT), 2, 6-dinitrotoluene (DNT), or triacetone-triperoxide (TATP). This study describes the generation of expression profiles for exposure to each compound, the functional significance of each response, and the identification of the characteristic alterations in gene expression associated with exposure to each compound. Expression profiles were generated from a total of three different candidate organisms: Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida. Common to all three organisms, TNT exposure resulted in increased expression of genes involved in toxin resistance and drug efflux systems. The S.cerevisiae and E.coli expression profiles were both characterized by increased expression of genes involved in iron-sulfur cluster assembly, sulfur containing amino acids, sulfate transport and assimilation and the metabolism of nitrogen compounds. Only E.coli and Saccharomyces were used to generate DNT induced expression profiles; both profiles exhibited high degrees of similarity with each organism’s respective TNT profiles. This was especially true of the E.coli profile where 25 of the 30 alterations were also observed after exposure to TNT. A computational discriminant functional analysis was performed to identify characteristic biomarkers for each exposure. For each compound a set of transcriptional biomarkers (10 or less) was developed. An additional set of biomarkers was developed encompassing both TNT and DNT exposure. These sets of genes serve as a transcriptional fingerprint for exposure to each respective compound. The sensitivity and specificity of each transcriptional fingerprint is sufficient to correctly identify exposure to energetic materials against a background of non-energetic compound exposures. This study makes several novel contributions to the greater body of scientific knowledge: • This is the first documented study of the interactions of TATP in any biological system. • This is the first comprehensive gene expression study of the TNT response by P. putida, E.coli or E.coli. • This is the first application of computational class prediction in the development of biomarkers for exposure to energetic material

    Markov models of biomolecular systems

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    The THUMOS Challenge on Action Recognition for Videos "in the Wild"

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    Automatically recognizing and localizing wide ranges of human actions has crucial importance for video understanding. Towards this goal, the THUMOS challenge was introduced in 2013 to serve as a benchmark for action recognition. Until then, video action recognition, including THUMOS challenge, had focused primarily on the classification of pre-segmented (i.e., trimmed) videos, which is an artificial task. In THUMOS 2014, we elevated action recognition to a more practical level by introducing temporally untrimmed videos. These also include `background videos' which share similar scenes and backgrounds as action videos, but are devoid of the specific actions. The three editions of the challenge organized in 2013--2015 have made THUMOS a common benchmark for action classification and detection and the annual challenge is widely attended by teams from around the world. In this paper we describe the THUMOS benchmark in detail and give an overview of data collection and annotation procedures. We present the evaluation protocols used to quantify results in the two THUMOS tasks of action classification and temporal detection. We also present results of submissions to the THUMOS 2015 challenge and review the participating approaches. Additionally, we include a comprehensive empirical study evaluating the differences in action recognition between trimmed and untrimmed videos, and how well methods trained on trimmed videos generalize to untrimmed videos. We conclude by proposing several directions and improvements for future THUMOS challenges.Comment: Preprint submitted to Computer Vision and Image Understandin

    Modelling the trajectories of disease accumulation in multimorbidity

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    Multimorbidity is defined as the co-occurrence of two or more chronic conditions. The prevalence of multimorbidity is closely related to age, and due to population ageing, multimorbidity has become a major burden for healthcare systems. The biggest challenge when modelling multimorbidity is patient heterogeneity since the patients can suffer from a wide variety of disease combinations. Previous work has shown how age, sex, and socioeconomic status are key determinants of multimorbidity prevalence and multimorbidity disease clusters. However, little is known about the order in which patients acquire multiple chronic conditions. This thesis aims to study the trajectories of disease accumulation that multimorbid patients follow. To address this challenge, we present four models that focus on the different aspects of the problem and apply them to an Electronic Health Record (EHR) dataset. First, we group chronic conditions into concordant clinical clusters and use a Multi-state Markov model to micro-simulate patient cohorts. This approach allows us to estimate how sex, socioeconomic status, and different disease clusters affect the trajectories and Life Expectancy. Second, we adapt a previously proposed method to identify the networks of chronic diseases that condense the most significant trajectories observed in the data. In this model, we avoid grouping or clustering diseases, and the resulting networks describe specific disease accumulation sequences. Third, we use a greedy structure learning algorithm to find the Bayesian Networks that better fit our EHR dataset. The results of this model help better understand the conditional dependencies between chronic conditions. Fourth, we present a Bernoulli mixture model to study multimorbid patient subtypes. The models presented in this thesis characterize the temporal patterns that multimorbid patients follow from multiple perspectives and could be used to inform where to focus treatment to prevent or delay the multimorbidity progression

    Compressed Sensing in Resource-Constrained Environments: From Sensing Mechanism Design to Recovery Algorithms

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    Compressed Sensing (CS) is an emerging field based on the revelation that a small collection of linear projections of a sparse signal contains enough information for reconstruction. It is promising that CS can be utilized in environments where the signal acquisition process is extremely difficult or costly, e.g., a resource-constrained environment like the smartphone platform, or a band-limited environment like visual sensor network (VSNs). There are several challenges to perform sensing due to the characteristic of these platforms, including, for example, needing active user involvement, computational and storage limitations and lower transmission capabilities. This dissertation focuses on the study of CS in resource-constrained environments. First, we try to solve the problem on how to design sensing mechanisms that could better adapt to the resource-limited smartphone platform. We propose the compressed phone sensing (CPS) framework where two challenging issues are studied, the energy drainage issue due to continuous sensing which may impede the normal functionality of the smartphones and the requirement of active user inputs for data collection that may place a high burden on the user. Second, we propose a CS reconstruction algorithm to be used in VSNs for recovery of frames/images. An efficient algorithm, NonLocal Douglas-Rachford (NLDR), is developed. NLDR takes advantage of self-similarity in images using nonlocal means (NL) filtering. We further formulate the nonlocal estimation as the low-rank matrix approximation problem and solve the constrained optimization problem using Douglas-Rachford splitting method. Third, we extend the NLDR algorithm to surveillance video processing in VSNs and propose recursive Low-rank and Sparse estimation through Douglas-Rachford splitting (rLSDR) method for recovery of the video frame into a low-rank background component and sparse component that corresponds to the moving object. The spatial and temporal low-rank features of the video frame, e.g., the nonlocal similar patches within the single video frame and the low-rank background component residing in multiple frames, are successfully exploited

    Selected Papers from the First International Symposium on Future ICT (Future-ICT 2019) in Conjunction with 4th International Symposium on Mobile Internet Security (MobiSec 2019)

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    The International Symposium on Future ICT (Future-ICT 2019) in conjunction with the 4th International Symposium on Mobile Internet Security (MobiSec 2019) was held on 17–19 October 2019 in Taichung, Taiwan. The symposium provided academic and industry professionals an opportunity to discuss the latest issues and progress in advancing smart applications based on future ICT and its relative security. The symposium aimed to publish high-quality papers strictly related to the various theories and practical applications concerning advanced smart applications, future ICT, and related communications and networks. It was expected that the symposium and its publications would be a trigger for further related research and technology improvements in this field
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