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  1. Book ; Online: Exploratory fact-finding scoping study on "digital sequence information" on genetic resources for food and agriculture

    Heinemann, Jack A. / Coray, Dorien S. / Thaler, David S.

    (Background study paper / FAO, Commission on Genetic Resources for Food and Agriculture ; no. 68)

    2018  

    Institution FAO / Commission on Genetic Resources for Food and Agriculture
    Author's details by Jack A. Heinemann, Dorien S. Coray and David S. Thaler ; Food and Agriculture Organization of the United Nations, Commission on Genetic Resources for Food and Agriculture
    Series title Background study paper / FAO, Commission on Genetic Resources for Food and Agriculture ; no. 68
    Background study paper
    Collection Background study paper
    Language English
    Size 1 Online-Ressource (86 Seiten), Illustrationen
    Publisher Food and Agriculture Organization of the United Nations
    Publishing place Rome
    Publishing country Italy
    Document type Book ; Online
    Note Open Access
    HBZ-ID HT021146485
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: PyKleeBarcode: Enabling representation of the whole animal kingdom in information space.

    Duchemin, Wandrille / Thaler, David S

    PloS one

    2023  Volume 18, Issue 6, Page(s) e0286314

    Abstract: As biological sequence databases continue growing, so do the insight that they promise to shed on the shape of the genetic diversity of life. However, to fulfil this promise the software must remain usable, be able to accommodate a large amount of data ... ...

    Abstract As biological sequence databases continue growing, so do the insight that they promise to shed on the shape of the genetic diversity of life. However, to fulfil this promise the software must remain usable, be able to accommodate a large amount of data and allow use of modern high performance computing infrastructure. In this study we present a reimplementation as well as an extension of a technique using indicator vectors to compute and visualize similarities between sets of nucleotide sequences. We have a flexible and easy to use python program relying on standard and open-source libraries. Our tool allows analysis of very large complement of sequences using code parallelization, as well as by providing routines to split a computational task in smaller and manageable subtasks whose results are then merged. This implementation also facilitates adding new sequences into an indicator vector-based representation without re-computing the whole set. The efficient synthesis of data into knowledge is no trivial matter given the size and rapid growth of biological sequence databases. Based on previous results regarding the properties of indicator vectors, the open-source approach proposed here efficiently and flexibly supports comparative analysis of genetic diversity at a large scale. Our software is freely available at: https://github.com/WandrilleD/pyKleeBarcode.
    MeSH term(s) Animals ; Software ; Databases, Nucleic Acid
    Language English
    Publishing date 2023-06-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0286314
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: PyKleeBarcode

    Wandrille Duchemin / David S Thaler

    PLoS ONE, Vol 18, Iss 6, p e

    Enabling representation of the whole animal kingdom in information space.

    2023  Volume 0286314

    Abstract: As biological sequence databases continue growing, so do the insight that they promise to shed on the shape of the genetic diversity of life. However, to fulfil this promise the software must remain usable, be able to accommodate a large amount of data ... ...

    Abstract As biological sequence databases continue growing, so do the insight that they promise to shed on the shape of the genetic diversity of life. However, to fulfil this promise the software must remain usable, be able to accommodate a large amount of data and allow use of modern high performance computing infrastructure. In this study we present a reimplementation as well as an extension of a technique using indicator vectors to compute and visualize similarities between sets of nucleotide sequences. We have a flexible and easy to use python program relying on standard and open-source libraries. Our tool allows analysis of very large complement of sequences using code parallelization, as well as by providing routines to split a computational task in smaller and manageable subtasks whose results are then merged. This implementation also facilitates adding new sequences into an indicator vector-based representation without re-computing the whole set. The efficient synthesis of data into knowledge is no trivial matter given the size and rapid growth of biological sequence databases. Based on previous results regarding the properties of indicator vectors, the open-source approach proposed here efficiently and flexibly supports comparative analysis of genetic diversity at a large scale. Our software is freely available at: https://github.com/WandrilleD/pyKleeBarcode.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    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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  4. Article ; Online: Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same?

    David S. Thaler

    Frontiers in Ecology and Evolution, Vol

    2021  Volume 9

    Abstract: ... SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank ...

    Abstract Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.
    Keywords biodiversity ; microbial diversity ; extinction rate ; generation of diversity ; speciation ; bottleneck ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Archiving time series sewage samples as biological records of built environments.

    Thaler, David S / Sakmar, Thomas P

    BMC infectious diseases

    2021  Volume 21, Issue 1, Page(s) 601

    Abstract: This commentary encourages the regular archiving of nucleic-acid-stabilized serial samples of wastewaters and/or sewage. Stabilized samples would facilitate retrospective reconstitution of built environments' biological fluids. Biological time capsules ... ...

    Abstract This commentary encourages the regular archiving of nucleic-acid-stabilized serial samples of wastewaters and/or sewage. Stabilized samples would facilitate retrospective reconstitution of built environments' biological fluids. Biological time capsules would allow retrospective searches for nucleic acids from viruses such as SARS-CoV-2. Current resources for testing need not be diverted if samples are saved in case they become important in the future. Systematic storage would facilitate investigation into the origin and prevalence of viruses and other agents. Comparison of prevalence data from individual and clinical samplings with community wastewater would allow valuable comparison, contrast and correlation among different testing modalities. Current interest is focused on SARS-CoV-2, but archived samples could become valuable in many contexts including surveys for other infectious and chemical agents whose identity is not currently known. Archived time series of wastewater will take their place alongside other biological repositories and records including those from medical facilities, museums, eDNA, living cell and tissue collections. Together these will prove invaluable records of the evolving Anthropocene.
    MeSH term(s) Built Environment ; COVID-19/virology ; Humans ; Retrospective Studies ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Sewage/virology ; Waste Water/virology
    Chemical Substances Sewage ; Waste Water
    Language English
    Publishing date 2021-06-24
    Publishing country England
    Document type Journal Article ; Review
    ISSN 1471-2334
    ISSN (online) 1471-2334
    DOI 10.1186/s12879-021-06268-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: The Next Supreme Leader

    Nader, Alireza / Thaler, David E / Bohandy, S. R

    Succession in the Islamic Republic of Iran

    2011  

    Keywords Asian history ; International relations ; Political Science ; History
    Language English
    Size 1 Online-Ressource
    Publisher RAND Corporation
    Document type Book ; Online
    Note English
    HBZ-ID HT030610216
    ISBN 9780833051332 ; 0833051334
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  7. Article ; Online: Coronavirus: sampling now for future analysis.

    Thaler, David S / Lipsitch, Marc

    Nature

    2020  Volume 580, Issue 7805, Page(s) 590

    MeSH term(s) Animals ; Betacoronavirus/isolation & purification ; COVID-19 ; Coronavirus ; Coronavirus Infections ; DNA ; Mammals ; Pandemics ; Pneumonia, Viral ; RNA ; SARS-CoV-2 ; Specimen Handling
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2)
    Keywords covid19
    Language English
    Publishing date 2020-04-28
    Publishing country England
    Document type News ; Comment
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-020-01267-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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  8. Article ; Online: Human and domesticated animal environmental DNA as bioassays of the Anthropocene

    David S. Thaler / Jesse H. Ausubel / Mark Y. Stoeckle

    The Innovation, Vol 4, Iss 1, Pp 100356- (2023)

    1480  

    Keywords Science (General) ; Q1-390
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Toward a microbial Neolithic revolution in buildings.

    Thaler, David S

    Microbiome

    2016  Volume 4, Page(s) 14

    Abstract: The Neolithic revolution--the transition of our species from hunter and gatherer to cultivator--began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Neolithic in our relationship with microbes ... ...

    Abstract The Neolithic revolution--the transition of our species from hunter and gatherer to cultivator--began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Neolithic in our relationship with microbes but starting with the gut we continue our hundred-year project of approaching the ability to assess and cultivate benign microbiomes in our bodies. Buildings are analogous to the body and it is time to ask what it means to cultivate benign microbiomes in our built environment. A critical distinction is that we have not found, or invented, niches in buildings where healthful microbial metabolism occurs and/or could be cultivated. Key events affecting the health and healthfulness of buildings such as a hurricane leading to a flood or a burst pipe occur only rarely and unpredictably. The cause may be transient but the effects can be long lasting and, e.g., for moisture damage, cumulative. Non-invasive "building tomography" could find moisture and "sentinel microbes" could record the integral of transient growth. "Seed" microbes are metabolically inert cells able to grow when conditions allow. All microbes and their residue present actinic molecules including immunological epitopes (molecular shapes). The fascinating hygiene and microbial biodiversity hypotheses propose that a healthy immune system requires exposure to a set of microbial epitopes that is rich in diversity. A particular conjecture is that measures of the richness of diversity derived from microbiome next-generation sequencing (NGS) can be mechanistically coupled to--rather than merely correlated with some measures of--human health. These hypotheses and conjectures inspire workers and funders but an alternative is also consequent to the first Neolithic revolution: That the genetic uniformity of contemporary foods may also decrease human exposure to molecular biodiversity in a heath-relevant manner. Understanding the consequences--including the unintended consequences of the first Neolithic revolution--will inform and help us benignly implement the second--the microbial--Neolithic revolution.
    MeSH term(s) Air Microbiology ; Architecture/methods ; Biodiversity ; Construction Industry ; Diet/classification ; Environment Design ; Food ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Hygiene ; Microbiota/physiology ; Quality of Life ; Symbiosis/physiology
    Language English
    Publishing date 2016-03-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-016-0157-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Microwave detection and quantification of water hidden in and on building materials: implications for healthy buildings and microbiome studies.

    Horsley, Andrew / Thaler, David S

    BMC infectious diseases

    2019  Volume 19, Issue 1, Page(s) 67

    Abstract: Background: Excess water in all its forms (moisture, dampness, hidden water) in buildings negatively impacts occupant health but is hard to reliably detect and quantify. Recent advances in through-wall imaging recommend microwaves as a tool with a high ... ...

    Abstract Background: Excess water in all its forms (moisture, dampness, hidden water) in buildings negatively impacts occupant health but is hard to reliably detect and quantify. Recent advances in through-wall imaging recommend microwaves as a tool with a high potential to noninvasively detect and quantify water throughout buildings.
    Methods: Microwaves in both transmission and reflection (radar) modes were used to perform a simple demonstration of the detection of water both on and hidden within building materials.
    Results: We used both transmission and reflection modes to detect as little as 1 mL of water between two 7 cm thicknesses of concrete. The reflection mode was also used to detect 1 mL of water on a metal surface. We observed oscillations in transmitted and reflected microwave amplitude as a function of microwave wavelength and water layer thickness, which we attribute to thin-film interference effects.
    Conclusions: Improving the detection of water in buildings could help design, maintenance, and remediation become more efficient and effective and perhaps increase the value of microbiome sequence data. Microwave characterization of all forms of water throughout buildings is possible; its practical development would require new collaborations among microwave physicists or engineers, architects, building engineers, remediation practitioners, epidemiologists, and microbiologists.
    MeSH term(s) Construction Materials/analysis ; Equipment Design ; Microwaves ; Water/analysis
    Chemical Substances Water (059QF0KO0R)
    Language English
    Publishing date 2019-01-18
    Publishing country England
    Document type Journal Article
    ISSN 1471-2334
    ISSN (online) 1471-2334
    DOI 10.1186/s12879-019-3720-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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