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  1. Book ; Thesis: Clinical probability assessment and biochemical markers in the diagnosis of deep vein thrombosis

    Elf, Johan

    (Doctoral dissertation series ; 2010, 19)

    2010  

    Author's details Johan Elf
    Series title Doctoral dissertation series ; 2010, 19
    Collection
    Language English ; Swedish
    Size Getr. Zählung
    Publishing country Sweden
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Lund, Univ., Diss., 2010
    Note Zsfassung in schwed. Sprache
    HBZ-ID HT016381376
    ISBN 978-91-86443-33-7 ; 91-86443-33-X
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2010 E 2134 order for loan Magazin

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  2. Article ; Online: Antibiotic perseverance increases the risk of resistance development.

    Brandis, Gerrit / Larsson, Jimmy / Elf, Johan

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 2, Page(s) e2216216120

    Abstract: The rise of antibiotic-resistant bacterial infections poses a global threat. Antibiotic resistance development is generally studied in batch cultures which conceals the heterogeneity in cellular responses. Using single-cell imaging, we studied the growth ...

    Abstract The rise of antibiotic-resistant bacterial infections poses a global threat. Antibiotic resistance development is generally studied in batch cultures which conceals the heterogeneity in cellular responses. Using single-cell imaging, we studied the growth response of
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Escherichia coli ; Rifampin/pharmacology ; Mutation ; Bacteria ; Drug Resistance, Bacterial/genetics
    Chemical Substances Anti-Bacterial Agents ; Rifampin (VJT6J7R4TR)
    Language English
    Publishing date 2023-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2216216120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Unreported incidental pulmonary embolism in patients with cancer: Radiologic natural history and risk of recurrent venous thromboembolism and death.

    Wiklund, Peder / Medson, Koshiar / Elf, Johan

    Thrombosis research

    2023  Volume 224, Page(s) 65–72

    Abstract: Purpose: To assess the risk of recurrent venous thromboembolism (VTE) and death in patients with unreported cancer-associated incidental pulmonary embolism (iPE).: Materials and methods: Matched cohort study on cancer patients with a CT study ... ...

    Abstract Purpose: To assess the risk of recurrent venous thromboembolism (VTE) and death in patients with unreported cancer-associated incidental pulmonary embolism (iPE).
    Materials and methods: Matched cohort study on cancer patients with a CT study including the chest between 2014-01-01 and 2019-06-30. Studies were reviewed for unreported iPE, and cases were matched with controls without iPE. Cases and controls were followed for one year, with recurrent VTE and death as outcome events.
    Results: Of the included 2960 patients, 171 patients had unreported and untreated iPE. While controls had a one-year VTE risk of 8.2 events per 100 person-years, cases with a single subsegmental iPE had a recurrent VTE risk of 20.9 events, and between 52.0 and 72.0 events per 100 person-years for multiple subsegmental iPE and more proximal iPE. In multivariable analysis, multiple subsegmental and more proximal iPE were significantly associated with the risk of recurrent VTE, while single subsegmental iPE was not associated with the risk of recurrent VTE (p = 0.13). In the subgroup of patients (n = 47) with cancer not in the highest Khorana VTE risk category, no metastases and up to three involved vessels, recurrent VTE occurred in two patients (4.7 cases per 100 person-years). There were no significant associations between iPE burden and risk of death.
    Conclusion: In cancer patients with unreported iPE, iPE burden was associated with the risk of recurrent VTE. However, having a single subsegmental iPE was not associated with the risk of recurrent VTE. There were no significant associations between iPE burden and risk of death.
    MeSH term(s) Humans ; Venous Thromboembolism/complications ; Cohort Studies ; Anticoagulants ; Pulmonary Embolism/complications ; Pulmonary Embolism/diagnostic imaging ; Neoplasms/complications ; Recurrence
    Chemical Substances Anticoagulants
    Language English
    Publishing date 2023-02-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 121852-9
    ISSN 1879-2472 ; 0049-3848
    ISSN (online) 1879-2472
    ISSN 0049-3848
    DOI 10.1016/j.thromres.2023.02.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 863: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Imaging-based screens of pool-synthesized cell libraries.

    Lawson, Michael / Elf, Johan

    Nature methods

    2021  Volume 18, Issue 4, Page(s) 358–365

    Abstract: Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, ... ...

    Abstract Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these powerful tools to perform live-cell imaging of pool-generated strain libraries for improved biological discovery.
    MeSH term(s) Cell Line ; High-Throughput Screening Assays ; Humans ; Models, Biological ; Mutation ; Open Reading Frames ; Phenotype
    Language English
    Publishing date 2021-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-020-01053-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6022: 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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  5. Article: More Than Just Letters and Chemistry: Genomics Goes Mechanics.

    Deindl, Sebastian / Elf, Johan

    Trends in biochemical sciences

    2021  Volume 46, Issue 6, Page(s) 431–432

    Abstract: Although ubiquitously thought of as a simple string of letters, DNA exhibits complex physicochemical properties. As a result, DNA can store information beyond the extensively studied explicit genetic message. The mechanical code of DNA has not been ... ...

    Abstract Although ubiquitously thought of as a simple string of letters, DNA exhibits complex physicochemical properties. As a result, DNA can store information beyond the extensively studied explicit genetic message. The mechanical code of DNA has not been studied systematically in a genome-wide context until recent groundbreaking work by Basu et al.
    MeSH term(s) Genomics
    Language English
    Publishing date 2021-04-12
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2021.03.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1207: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article: Staying Clear of the Dragons.

    Elf, Johan

    Cell systems

    2016  Volume 2, Issue 4, Page(s) 219–220

    Abstract: A new, game-changing approach makes it possible to rigorously disprove models without making assumptions about the unknown parts of the biological system. ...

    Abstract A new, game-changing approach makes it possible to rigorously disprove models without making assumptions about the unknown parts of the biological system.
    Language English
    Publishing date 2016--27
    Publishing country United States
    Document type Journal Article ; Comment
    ISSN 2405-4712
    ISSN 2405-4712
    DOI 10.1016/j.cels.2016.04.008
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  7. Article: Hypothesis: Homologous Recombination Depends on Parallel Search.

    Elf, Johan

    Cell systems

    2016  Volume 3, Issue 4, Page(s) 325–327

    Abstract: It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose a solution based on freely diffusing molecules that are programmed with sequences corresponding ...

    Abstract It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose a solution based on freely diffusing molecules that are programmed with sequences corresponding to those flanking the break site. In such a process, the target search would be parallelized.
    MeSH term(s) Chromosomes ; DNA ; DNA Damage ; DNA Repair ; Homologous Recombination
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2016-10-26
    Publishing country United States
    Document type Journal Article
    ISSN 2405-4712
    ISSN 2405-4712
    DOI 10.1016/j.cels.2016.10.005
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  8. Article: More Than Just Letters and Chemistry: Genomics Goes Mechanics

    Deindl, Sebastian / Elf, Johan

    Trends in biochemical sciences. 2021 June, v. 46, no. 6

    2021  

    Abstract: Although ubiquitously thought of as a simple string of letters, DNA exhibits complex physicochemical properties. As a result, DNA can store information beyond the extensively studied explicit genetic message. The mechanical code of DNA has not been ... ...

    Abstract Although ubiquitously thought of as a simple string of letters, DNA exhibits complex physicochemical properties. As a result, DNA can store information beyond the extensively studied explicit genetic message. The mechanical code of DNA has not been studied systematically in a genome-wide context until recent groundbreaking work by Basu et al.
    Keywords DNA ; genomics ; mechanics
    Language English
    Dates of publication 2021-06
    Size p. 431-432.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2021.03.004
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 78/716: Show issues

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  9. Article ; Online: Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization.

    Amselem, Elias / Broadwater, Bo / Hävermark, Tora / Johansson, Magnus / Elf, Johan

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 1336

    Abstract: Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the ... ...

    Abstract Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.
    MeSH term(s) Escherichia coli ; Entropy ; Single Molecule Imaging/methods ; Proteins ; Diffusion
    Chemical Substances Proteins
    Language English
    Publishing date 2023-03-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-36879-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy.

    Hallström, Erik / Kandavalli, Vinodh / Ranefall, Petter / Elf, Johan / Wählby, Carolina

    PLoS computational biology

    2023  Volume 19, Issue 11, Page(s) e1011181

    Abstract: Reliable detection and classification of bacteria and other pathogens in the human body, animals, food, and water is crucial for improving and safeguarding public health. For instance, identifying the species and its antibiotic susceptibility is vital ... ...

    Abstract Reliable detection and classification of bacteria and other pathogens in the human body, animals, food, and water is crucial for improving and safeguarding public health. For instance, identifying the species and its antibiotic susceptibility is vital for effective bacterial infection treatment. Here we show that phase contrast time-lapse microscopy combined with deep learning is sufficient to classify four species of bacteria relevant to human health. The classification is performed on living bacteria and does not require fixation or staining, meaning that the bacterial species can be determined as the bacteria reproduce in a microfluidic device, enabling parallel determination of susceptibility to antibiotics. We assess the performance of convolutional neural networks and vision transformers, where the best model attained a class-average accuracy exceeding 98%. Our successful proof-of-principle results suggest that the methods should be challenged with data covering more species and clinically relevant isolates for future clinical use.
    MeSH term(s) Humans ; Deep Learning ; Microscopy, Phase-Contrast ; Neural Networks, Computer ; Bacteria ; Bacterial Infections
    Language English
    Publishing date 2023-11-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011181
    Database MEDical Literature Analysis and Retrieval System OnLINE

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