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  1. Article: Wie kann ich was bewegen? Interview mit Benjamin Schwarz

    Schwarz, Benjamin

    Orthopädie-Technik

    2022  Volume 73, Issue 2, Page(s) 24

    Language German
    Document type Article
    ZDB-ID 207441-2
    ISSN 0340-5591
    Database Current Contents Medicine

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 887: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Frequency Propagation: Multimechanism Learning in Nonlinear Physical Networks.

    Anisetti, Vidyesh Rao / Kandala, Ananth / Scellier, Benjamin / Schwarz, J M

    Neural computation

    2024  Volume 36, Issue 4, Page(s) 596–620

    Abstract: We introduce frequency propagation, a learning algorithm for nonlinear physical networks. In a resistive electrical circuit with variable resistors, an activation current is applied at a set of input nodes at one frequency and an error current is applied ...

    Abstract We introduce frequency propagation, a learning algorithm for nonlinear physical networks. In a resistive electrical circuit with variable resistors, an activation current is applied at a set of input nodes at one frequency and an error current is applied at a set of output nodes at another frequency. The voltage response of the circuit to these boundary currents is the superposition of an activation signal and an error signal whose coefficients can be read in different frequencies of the frequency domain. Each conductance is updated proportionally to the product of the two coefficients. The learning rule is local and proved to perform gradient descent on a loss function. We argue that frequency propagation is an instance of a multimechanism learning strategy for physical networks, be it resistive, elastic, or flow networks. Multimechanism learning strategies incorporate at least two physical quantities, potentially governed by independent physical mechanisms, to act as activation and error signals in the training process. Locally available information about these two signals is then used to update the trainable parameters to perform gradient descent. We demonstrate how earlier work implementing learning via chemical signaling in flow networks (Anisetti, Scellier, et al., 2023) also falls under the rubric of multimechanism learning.
    Language English
    Publishing date 2024-03-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1025692-1
    ISSN 1530-888X ; 0899-7667
    ISSN (online) 1530-888X
    ISSN 0899-7667
    DOI 10.1162/neco_a_01648
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2914: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Chromatin Organization after High-LET Irradiation Revealed by Super-Resolution STED Microscopy.

    Schwarz, Benjamin / Matejka, Nicole / Rudigkeit, Sarah / Sammer, Matthias / Reindl, Judith

    International journal of molecular sciences

    2024  Volume 25, Issue 1

    Abstract: Ion-radiation-induced DNA double-strand breaks can lead to severe cellular damage ranging from mutations up to direct cell death. The interplay between the chromatin surrounding the damage and the proteins responsible for damage recognition and repair ... ...

    Abstract Ion-radiation-induced DNA double-strand breaks can lead to severe cellular damage ranging from mutations up to direct cell death. The interplay between the chromatin surrounding the damage and the proteins responsible for damage recognition and repair determines the efficiency and outcome of DNA repair. The chromatin is organized in three major functional compartments throughout the interphase: the chromatin territories, the interchromatin compartment, and the perichromatin lying in between. In this study, we perform correlation analysis using super-resolution STED images of chromatin; splicing factor SC35, as an interchromatin marker; and the DNA repair factors 53BP1, Rad51, and γH2AX in carbon-ion-irradiated human HeLa cells. Chromatin and interchromatin overlap only in protruding chromatin branches, which is the same for the correlation between chromatin and 53BP1. In contrast, between interchromatin and 53BP1, a gap of (270 ± 40) nm is visible. Rad51 shows overlap with decondensed euchromatic regions located at the borders of condensed heterochromatin with further correlation with γH2AX. We conclude that the DNA damage is repaired in decondensed DNA loops in the perichromatin, located in the periphery of the DNA-dense chromatin compartments containing the heterochromatin. Proteins like γH2AX and 53BP1 serve as supporters of the chromatin structure.
    MeSH term(s) Humans ; Heterochromatin ; HeLa Cells ; Microscopy ; Chromatin ; DNA
    Chemical Substances Heterochromatin ; Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2024-01-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25010628
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Chromatin Organization after High-LET Irradiation Revealed by Super-Resolution STED Microscopy

    Benjamin Schwarz / Nicole Matejka / Sarah Rudigkeit / Matthias Sammer / Judith Reindl

    International Journal of Molecular Sciences, Vol 25, Iss 1, p

    2024  Volume 628

    Abstract: Ion-radiation-induced DNA double-strand breaks can lead to severe cellular damage ranging from mutations up to direct cell death. The interplay between the chromatin surrounding the damage and the proteins responsible for damage recognition and repair ... ...

    Abstract Ion-radiation-induced DNA double-strand breaks can lead to severe cellular damage ranging from mutations up to direct cell death. The interplay between the chromatin surrounding the damage and the proteins responsible for damage recognition and repair determines the efficiency and outcome of DNA repair. The chromatin is organized in three major functional compartments throughout the interphase: the chromatin territories, the interchromatin compartment, and the perichromatin lying in between. In this study, we perform correlation analysis using super-resolution STED images of chromatin; splicing factor SC35, as an interchromatin marker; and the DNA repair factors 53BP1, Rad51, and γH2AX in carbon-ion-irradiated human HeLa cells. Chromatin and interchromatin overlap only in protruding chromatin branches, which is the same for the correlation between chromatin and 53BP1. In contrast, between interchromatin and 53BP1, a gap of (270 ± 40) nm is visible. Rad51 shows overlap with decondensed euchromatic regions located at the borders of condensed heterochromatin with further correlation with γH2AX. We conclude that the DNA damage is repaired in decondensed DNA loops in the perichromatin, located in the periphery of the DNA-dense chromatin compartments containing the heterochromatin. Proteins like γH2AX and 53BP1 serve as supporters of the chromatin structure.
    Keywords chromatin organization ; DNA repair ; super-resolution microscopy ; interchromatin ; perichromatin ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 571
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 107.

    Schwarz, Joshua C / Chan, Benjamin K / Turner, Paul E / Burmeister, Alita R

    Microbiology resource announcements

    2023  Volume 12, Issue 6, Page(s) e0010623

    Abstract: We present the annotated genome sequence of Escherichia coli bacteriophage 107, a T4-like bacteriophage. Phage 107 has a genome length of 167,509 bp and 287 predicted genes. ...

    Abstract We present the annotated genome sequence of Escherichia coli bacteriophage 107, a T4-like bacteriophage. Phage 107 has a genome length of 167,509 bp and 287 predicted genes.
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00106-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Route of Francisella tularensis infection informs spatiotemporal metabolic reprogramming and inflammation in mice

    Forrest Jessop / Benjamin Schwarz / Eric Bohrnsen / Catharine M. Bosio

    PLoS ONE, Vol 18, Iss

    2023  Volume 10

    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Route of Francisella tularensis infection informs spatiotemporal metabolic reprogramming and inflammation in mice.

    Jessop, Forrest / Schwarz, Benjamin / Bohrnsen, Eric / Bosio, Catharine M

    PloS one

    2023  Volume 18, Issue 10, Page(s) e0293450

    Abstract: Route of exposure to pathogens can inform divergent disease pathogenesis and mortality rates. However, the features that contribute to these differences are not well established. Host metabolism has emerged as a critical element governing susceptibility ... ...

    Abstract Route of exposure to pathogens can inform divergent disease pathogenesis and mortality rates. However, the features that contribute to these differences are not well established. Host metabolism has emerged as a critical element governing susceptibility and the metabolism of tissue exposure sites are unique. Therefore, specific metabolic niches may contribute to the course and outcome of infection depending on route of infection. In the current study, we utilized a combination of imaging and systems metabolomics to map the spatiotemporal dynamics of the host response to intranasal (i.n.) or intradermal (i.d.) infection of mice using the bacterium Francisella tularensis subsp tularensis (FTT). FTT causes lethal disease through these infection routes with similar inoculation doses and replication kinetics, which allowed for isolation of host outcomes independent of bacterial burden. We observed metabolic modifications that were both route dependent and independent. Specifically, i.d. infection resulted in early metabolic reprogramming at the site of infection and draining lymph nodes, whereas the lungs and associated draining lymph nodes were refractory to metabolic reprogramming following i.n. infection. Irrespective of exposure route, FTT promoted metabolic changes in systemic organs prior to colonization, and caused massive dysregulation of host metabolism in these tissues prior to onset of morbidity. Preconditioning infection sites towards a more glycolytic and pro-inflammatory state prior to infection exacerbated FTT replication within the lungs but not intradermal tissue. This enhancement of replication in the lungs was associated with the ability of FTT to limit redox imbalance and alter the pentose phosphate pathway. Together, these studies identify central metabolic features of the lung and dermal compartments that contribute to disease progression and identify potential tissue specific targets that may be exploited for novel therapeutic approaches.
    MeSH term(s) Mice ; Animals ; Tularemia/metabolism ; Francisella tularensis ; Mice, Inbred C57BL ; Inflammation ; Lung/metabolism
    Language English
    Publishing date 2023-10-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0293450
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Invasive earthworms modulate native plant trait expression and competition

    Schwarz, Rike / Eisenhauer, Nico / Ferlian, Olga / Maestre, Fernando T. / Rosenbaum, Benjamin / Uthe, Henriette / Thouvenot, Lise

    Oikos. 2024 Jan., v. 2024, no. 1 p.e10008-

    2024  

    Abstract: Biological invasions have major impacts on a variety of ecosystems and threaten native biodiversity. Earthworms have been absent from northern parts of North America since the last ice age, but non‐native earthworms were recently introduced there and are ...

    Abstract Biological invasions have major impacts on a variety of ecosystems and threaten native biodiversity. Earthworms have been absent from northern parts of North America since the last ice age, but non‐native earthworms were recently introduced there and are now being spread by human activities. While past work has shown that plant communities in earthworm‐invaded areas change towards a lower diversity mainly dominated by grasses, the underlying mechanisms related to changes in the biotic interactions of the plants are not well understood. Here, we used a trait‐based approach to study the effect of earthworms on interspecific plant competition and aboveground herbivory. We conducted a microcosm experiment in a growth chamber with a full‐factorial design using three plant species native to northern North American deciduous forests, Poa palustris (grass), Symphyotrichum laeve (herb) and Vicia americana (legume), either growing in monoculture or in a mixture of three. These plant community treatments were crossed with earthworm (presence or absence) and herbivore (presence or absence) treatments. Eight out of the fourteen above‐ and belowground plant functional traits studied were significantly affected by earthworms, either by a general effect or in interaction with plant species identity, plant diversity level and/or herbivore presence. Earthworms increased the aboveground productivity and the number of inflorescences of the grass P. palustris. Further, earthworms and herbivores together affected root tissue density of P. palustris and the specific leaf area of V. americana. In this study, earthworm presence gave a competitive advantage to the grass species P. palustris by inducing changes in plant functional traits. Our results suggest that invasive earthworms can alter competitive and multitrophic interactions of plants, shedding light on some of the mechanisms behind invasive earthworm‐induced plant community changes in northern North America forests.
    Keywords Poa palustris ; Symphyotrichum laeve ; Vicia ; earthworms ; grasses ; growth chambers ; herbivores ; humans ; indigenous species ; legumes ; plant communities ; plant competition ; primary productivity ; species diversity ; specific leaf area ; North America
    Language English
    Dates of publication 2024-01
    Publishing place Blackwell Publishing Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 207359-6
    ISSN 0030-1299
    ISSN 0030-1299
    DOI 10.1111/oik.10008
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 4824: Show issues

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  9. Article ; Online: Route of Francisella tularensis infection informs spatiotemporal metabolic reprogramming and inflammation in mice.

    Forrest Jessop / Benjamin Schwarz / Eric Bohrnsen / Catharine M Bosio

    PLoS ONE, Vol 18, Iss 10, p e

    2023  Volume 0293450

    Abstract: Route of exposure to pathogens can inform divergent disease pathogenesis and mortality rates. However, the features that contribute to these differences are not well established. Host metabolism has emerged as a critical element governing susceptibility ... ...

    Abstract Route of exposure to pathogens can inform divergent disease pathogenesis and mortality rates. However, the features that contribute to these differences are not well established. Host metabolism has emerged as a critical element governing susceptibility and the metabolism of tissue exposure sites are unique. Therefore, specific metabolic niches may contribute to the course and outcome of infection depending on route of infection. In the current study, we utilized a combination of imaging and systems metabolomics to map the spatiotemporal dynamics of the host response to intranasal (i.n.) or intradermal (i.d.) infection of mice using the bacterium Francisella tularensis subsp tularensis (FTT). FTT causes lethal disease through these infection routes with similar inoculation doses and replication kinetics, which allowed for isolation of host outcomes independent of bacterial burden. We observed metabolic modifications that were both route dependent and independent. Specifically, i.d. infection resulted in early metabolic reprogramming at the site of infection and draining lymph nodes, whereas the lungs and associated draining lymph nodes were refractory to metabolic reprogramming following i.n. infection. Irrespective of exposure route, FTT promoted metabolic changes in systemic organs prior to colonization, and caused massive dysregulation of host metabolism in these tissues prior to onset of morbidity. Preconditioning infection sites towards a more glycolytic and pro-inflammatory state prior to infection exacerbated FTT replication within the lungs but not intradermal tissue. This enhancement of replication in the lungs was associated with the ability of FTT to limit redox imbalance and alter the pentose phosphate pathway. Together, these studies identify central metabolic features of the lung and dermal compartments that contribute to disease progression and identify potential tissue specific targets that may be exploited for novel therapeutic approaches.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  10. Book ; Thesis: Moveout and geometry

    Schwarz, Benjamin

    2015  

    Author's details vorgelegt von Benjamin Schwarz
    Language English
    Size IX, 152 S., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Univ., FB Geowiss., Diss.--Hamburg, 2015
    Note Zsfassung in dt. und engl. Sprache
    Database Former special subject collection: coastal and deep sea fishing

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