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Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Hendriksen, Rene S. ; Munk, Patrick ; Njage, Patrick ; [weitere]

Springer Science and Business Media LLC ; 2019

In: Nature Communications Vol. 10, No. 1 ( 2019-03-08)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2019-03-08)

Kurzfassung: Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.

Materialart: Online-Ressource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-019-08853-3

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2019

ZDB Id: 2553671-0

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A generic method for assignment of reliability scores applied to solvent accessibility predictions

Petersen, Bent ; Petersen, Thomas Nordahl ; Andersen, Pernille ; [weitere]

Springer Science and Business Media LLC ; 2009

In: BMC Structural Biology Vol. 9, No. 1 ( 2009-12)

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In: BMC Structural Biology, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2009-12)

Kurzfassung: Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score. Results An ensemble of artificial neural networks has been trained on a set of experimentally solved protein structures to predict the relative exposure of the amino acids. The method assigns a reliability score to each surface accessibility prediction as an inherent part of the training process. This is in contrast to the most commonly used procedures where reliabilities are obtained by post-processing the output. Conclusion The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20% of predictions sorted according to reliability. For this subset, values of 0.79 and 0.74 are obtained using our and the compared method, respectively. This tendency is true for any selected subset.

Materialart: Online-Ressource

ISSN: 1472-6807

URL: Article

DOI: 10.1186/1472-6807-9-51

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2009

ZDB Id: 2050440-8

SSG: 12

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NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

Petersen, Bent ; Lundegaard, Claus ; Petersen, Thomas Nordahl ; [weitere]

Public Library of Science (PLoS) ; 2010

In: PLoS ONE Vol. 5, No. 11 ( 2010-11-30), p. e15079-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 5, No. 11 ( 2010-11-30), p. e15079-

Materialart: Online-Ressource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0015079

DOI: 10.1371/journal.pone.0015079.g001

DOI: 10.1371/journal.pone.0015079.g002

DOI: 10.1371/journal.pone.0015079.g003

DOI: 10.1371/journal.pone.0015079.g004

DOI: 10.1371/journal.pone.0015079.g005

DOI: 10.1371/journal.pone.0015079.g006

DOI: 10.1371/journal.pone.0015079.t001

DOI: 10.1371/journal.pone.0015079.t002

DOI: 10.1371/journal.pone.0015079.t003

DOI: 10.1371/journal.pone.0015079.s001

DOI: 10.1371/journal.pone.0015079.s002

DOI: 10.1371/journal.pone.0015079.s003

DOI: 10.1371/journal.pone.0015079.s004

DOI: 10.1371/journal.pone.0015079.s005

DOI: 10.1371/journal.pone.0015079.s006

Sprache: Englisch

Verlag: Public Library of Science (PLoS)

Publikationsdatum: 2010

ZDB Id: 2267670-3

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Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Munk, Patrick ; Knudsen, Berith Elkær ; Lukjancenko, Oksana ; [weitere]

Springer Science and Business Media LLC ; 2018

In: Nature Microbiology Vol. 3, No. 8 ( 2018-07-23), p. 898-908

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In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 3, No. 8 ( 2018-07-23), p. 898-908

Materialart: Online-Ressource

ISSN: 2058-5276

URL: Article

DOI: 10.1038/s41564-018-0192-9

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2018

ZDB Id: 2845610-5

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MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

Petersen, Thomas Nordahl ; Lukjancenko, Oksana ; Thomsen, Martin Christen Frølund ; [weitere]

Public Library of Science (PLoS) ; 2017

In: PLOS ONE Vol. 12, No. 5 ( 2017-5-3), p. e0176469-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 12, No. 5 ( 2017-5-3), p. e0176469-

Materialart: Online-Ressource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0176469

DOI: 10.1371/journal.pone.0176469.g001

DOI: 10.1371/journal.pone.0176469.t001

DOI: 10.1371/journal.pone.0176469.t002

DOI: 10.1371/journal.pone.0176469.t003

DOI: 10.1371/journal.pone.0176469.t004

DOI: 10.1371/journal.pone.0176469.t005

DOI: 10.1371/journal.pone.0176469.t006

DOI: 10.1371/journal.pone.0176469.s001

DOI: 10.1371/journal.pone.0176469.s002

DOI: 10.1371/journal.pone.0176469.s003

DOI: 10.1371/journal.pone.0176469.s004

DOI: 10.1371/journal.pone.0176469.s005

DOI: 10.1371/journal.pone.0176469.s006

DOI: 10.1371/journal.pone.0176469.s007

DOI: 10.1371/journal.pone.0176469.s008

DOI: 10.1371/journal.pone.0176469.s009

DOI: 10.1371/journal.pone.0176469.s010

Sprache: Englisch

Verlag: Public Library of Science (PLoS)

Publikationsdatum: 2017

ZDB Id: 2267670-3

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Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

Al-Nakeeb, Kosai ; Petersen, Thomas Nordahl ; Sicheritz-Pontén, Thomas

Springer Science and Business Media LLC ; 2017

In: BMC Bioinformatics Vol. 18, No. 1 ( 2017-12)

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In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 18, No. 1 ( 2017-12)

Materialart: Online-Ressource

ISSN: 1471-2105

URL: Article

DOI: 10.1186/s12859-017-1927-y

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2017

ZDB Id: 2041484-5

SSG: 12

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Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

Petersen, Thomas Nordahl ; Lukjancenko, Oksana ; Thomsen, Martin Christen Frølund ; [weitere]

Public Library of Science (PLoS) ; 2017

In: PLOS ONE Vol. 12, No. 6 ( 2017-6-12), p. e0179778-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 12, No. 6 ( 2017-6-12), p. e0179778-

Materialart: Online-Ressource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0179778

Sprache: Englisch

Verlag: Public Library of Science (PLoS)

Publikationsdatum: 2017

ZDB Id: 2267670-3

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Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Munk, Patrick ; Knudsen, Berith Elkær ; Lukjancenko, Oksana ; [weitere]

Springer Science and Business Media LLC ; 2018

In: Nature Microbiology Vol. 3, No. 10 ( 2018-08-21), p. 1186-1186

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In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 3, No. 10 ( 2018-08-21), p. 1186-1186

Materialart: Online-Ressource

ISSN: 2058-5276

URL: Article

DOI: 10.1038/s41564-018-0241-4

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2018

ZDB Id: 2845610-5

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Improved metagenome binning and assembly using deep variational autoencoders

Nissen, Jakob Nybo ; Johansen, Joachim ; Allesøe, Rosa Lundbye ; [weitere]

Springer Science and Business Media LLC ; 2021

In: Nature Biotechnology Vol. 39, No. 5 ( 2021-05), p. 555-560

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In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 39, No. 5 ( 2021-05), p. 555-560

Materialart: Online-Ressource

ISSN: 1087-0156 , 1546-1696

URL: Article

DOI: 10.1038/s41587-020-00777-4

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2021

ZDB Id: 1494943-X

ZDB Id: 1311932-1

SSG: 12

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Identification of novel genes regulated in the developing human ventral mesencephalon

Jørgensen, Jesper Roland ; Juliusson, Bengt ; Henriksen, Karen Friis ; [weitere]

Elsevier BV ; 2006

In: Experimental Neurology Vol. 198, No. 2 ( 2006-4), p. 427-437

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In: Experimental Neurology, Elsevier BV, Vol. 198, No. 2 ( 2006-4), p. 427-437

Materialart: Online-Ressource

ISSN: 0014-4886

URL: Article

DOI: 10.1016/j.expneurol.2005.12.023

RVK:

XA 10000

Sprache: Englisch

Verlag: Elsevier BV

Publikationsdatum: 2006

ZDB Id: 1466932-8

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