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  1. Article ; Online: Facilitating rapid prototyping in the distributed data analytics platform OODIDA via active-code replacement

    Gregor Ulm / Simon Smith / Adrian Nilsson / Emil Gustavsson / Mats Jirstrand

    Array, Vol 8, Iss , Pp 100043- (2020)

    2020  

    Abstract: OODIDA (On-board/Off-board Distributed Data Analytics) is a platform for distributed real-time analytics, targeting fleets of reference vehicles in the automotive industry. Its users are data analysts. The bulk of the data analytics tasks are performed ... ...

    Abstract OODIDA (On-board/Off-board Distributed Data Analytics) is a platform for distributed real-time analytics, targeting fleets of reference vehicles in the automotive industry. Its users are data analysts. The bulk of the data analytics tasks are performed by clients (on-board), while a central cloud server performs supplementary tasks (off-board). OODIDA can be automatically packaged and deployed, which necessitates restarting parts of the system, or all of it. As this is potentially disruptive, we added the ability to execute user-defined Python modules on clients as well as the server. These modules can be replaced without restarting any part of the system; they can even be replaced between iterations of an ongoing assignment. This feature is referred to as active-code replacement. It facilitates use cases such as iterative A/B testing of machine learning algorithms or modifying experimental algorithms on-the-fly. Various safeguards are in place to ensure that custom code does not have harmful consequences, for instance by limiting the allowed types for return values or prohibiting importing of certain modules of the Python standard library. Consistency of results is achieved by majority vote, which prevents tainted state. Our evaluation shows that active-code replacement can be done in less than a second in an idealized setting whereas a standard deployment takes many orders of magnitude more time. The main contribution of this paper is the description of a relatively straightforward approach to active-code replacement that is very user-friendly. It enables a data analyst to quickly execute custom code on the cloud server as well as on client devices. Sensible safeguards and design decisions ensure that this feature can be used by non-specialists who are not familiar with the implementation of OODIDA in general or this feature in particular. As a consequence of adding the active-code replacement feature, OODIDA is now very well-suited for rapid prototyping.
    Keywords Distributed computing ; Concurrent computing ; Distributed data processing ; Hot swapping ; Code replacement ; Erlang ; Computer engineering. Computer hardware ; TK7885-7895 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 004
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: S-RASTER

    Gregor Ulm / Simon Smith / Adrian Nilsson / Emil Gustavsson / Mats Jirstrand

    Journal of Big Data, Vol 7, Iss 1, Pp 1-

    contraction clustering for evolving data streams

    2020  Volume 21

    Abstract: Abstract Contraction Clustering (RASTER) is a single-pass algorithm for density-based clustering of 2D data. It can process arbitrary amounts of data in linear time and in constant memory, quickly identifying approximate clusters. It also exhibits good ... ...

    Abstract Abstract Contraction Clustering (RASTER) is a single-pass algorithm for density-based clustering of 2D data. It can process arbitrary amounts of data in linear time and in constant memory, quickly identifying approximate clusters. It also exhibits good scalability in the presence of multiple CPU cores. RASTER exhibits very competitive performance compared to standard clustering algorithms, but at the cost of decreased precision. Yet, RASTER is limited to batch processing and unable to identify clusters that only exist temporarily. In contrast, S-RASTER is an adaptation of RASTER to the stream processing paradigm that is able to identify clusters in evolving data streams. This algorithm retains the main benefits of its parent algorithm, i.e. single-pass linear time cost and constant memory requirements for each discrete time step within a sliding window. The sliding window is efficiently pruned, and clustering is still performed in linear time. Like RASTER, S-RASTER trades off an often negligible amount of precision for speed. Our evaluation shows that competing algorithms are at least 50% slower. Furthermore, S-RASTER shows good qualitative results, based on standard metrics. It is very well suited to real-world scenarios where clustering does not happen continually but only periodically.
    Keywords Big data ; Stream processing ; Clustering ; Machine learning ; Unsupervised learning ; Big data analytics ; Computer engineering. Computer hardware ; TK7885-7895 ; Information technology ; T58.5-58.64 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher SpringerOpen
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Chromophore–Protein Interplay during the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy

    Ihalainen, Janne A / Emil Gustavsson / Lea Schroeder / Serena Donnini / Heli Lehtivuori / Linnéa Isaksson / Christian Thöing / Vaibhav Modi / Oskar Berntsson / Brigitte Stucki-Buchli / Alli Liukkonen / Heikki Häkkänen / Elina Kalenius / Sebastian Westenhoff / Tilman Kottke

    Journal of the American Chemical Society. 2018 Sept. 05, v. 140, no. 39

    2018  

    Abstract: Phytochrome proteins regulate many photoresponses of plants and microorganisms. Light absorption causes isomerization of the biliverdin chromophore, which triggers a series of structural changes to activate the signaling domains of the protein. However, ... ...

    Abstract Phytochrome proteins regulate many photoresponses of plants and microorganisms. Light absorption causes isomerization of the biliverdin chromophore, which triggers a series of structural changes to activate the signaling domains of the protein. However, the structural changes are elusive, and therefore the molecular mechanism of signal transduction remains poorly understood. Here, we apply two-color step-scan infrared spectroscopy to the bacteriophytochrome from Deinococcus radiodurans. We show by recordings in H₂O and D₂O that the hydrogen bonds to the biliverdin D-ring carbonyl become disordered in the first intermediate (Lumi-R) forming a dynamic microenvironment, then completely detach in the second intermediate (Meta-R), and finally reform in the signaling state (Pfr). The spectra reveal via isotope labeling that the refolding of the conserved “PHY-tongue” region occurs with the last transition between Meta-R and Pfr. Additional changes in the protein backbone are detected already within microseconds in Lumi-R. Aided by molecular dynamics simulations, we find that a strictly conserved salt bridge between an arginine of the PHY tongue and an aspartate of the chromophore binding domains is broken in Lumi-R and the arginine is recruited to the D-ring C═O. This rationalizes how isomerization of the chromophore is linked to the global structural rearrangement in the sensory receptor. Our findings advance the structural understanding of phytochrome photoactivation.
    Keywords Deinococcus radiodurans ; Fourier transform infrared spectroscopy ; absorption ; arginine ; aspartic acid ; deuterium oxide ; hydrogen bonding ; isomerization ; isotope labeling ; microorganisms ; molecular dynamics ; phytochrome ; plants (botany) ; sensory receptors ; signal transduction ; simulation models ; tongue
    Language English
    Dates of publication 2018-0905
    Size p. 12396-12404.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.8b04659
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Sequential conformational transitions and α-helical supercoiling regulate a sensor histidine kinase

    Oskar Berntsson / Ralph P. Diensthuber / Matthijs R. Panman / Alexander Björling / Emil Gustavsson / Maria Hoernke / Ashley J. Hughes / Léocadie Henry / Stephan Niebling / Heikki Takala / Janne A. Ihalainen / Gemma Newby / Silke Kerruth / Joachim Heberle / Marianne Liebi / Andreas Menzel / Robert Henning / Irina Kosheleva / Andreas Möglich /
    Sebastian Westenhoff

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 8

    Abstract: Sensor histidine kinases (SHK) consist of sensor, linker and kinase modules and different models for SHK signal transduction have been proposed. Here the authors present nano- to millisecond time-resolved X-ray scattering measurements, which reveal a ... ...

    Abstract Sensor histidine kinases (SHK) consist of sensor, linker and kinase modules and different models for SHK signal transduction have been proposed. Here the authors present nano- to millisecond time-resolved X-ray scattering measurements, which reveal a structural mechanism for kinase domain activation in SHK.
    Keywords Science ; Q
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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