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  1. Article ; Online: Pooled testing of traced contacts under superspreading dynamics.

    Stratis Tsirtsis / Abir De / Lars Lorch / Manuel Gomez-Rodriguez

    PLoS Computational Biology, Vol 18, Iss 3, p e

    2022  Volume 1010008

    Abstract: Testing is recommended for all close contacts of confirmed COVID-19 patients. However, existing pooled testing methods are oblivious to the circumstances of contagion provided by contact tracing. Here, we build upon a well-known semi-adaptive pooled ... ...

    Abstract Testing is recommended for all close contacts of confirmed COVID-19 patients. However, existing pooled testing methods are oblivious to the circumstances of contagion provided by contact tracing. Here, we build upon a well-known semi-adaptive pooled testing method, Dorfman's method with imperfect tests, and derive a simple pooled testing method based on dynamic programming that is specifically designed to use information provided by contact tracing. Experiments using a variety of reproduction numbers and dispersion levels, including those estimated in the context of the COVID-19 pandemic, show that the pools found using our method result in a significantly lower number of tests than those found using Dorfman's method. Our method provides the greatest competitive advantage when the number of contacts of an infected individual is small, or the distribution of secondary infections is highly overdispersed. Moreover, it maintains this competitive advantage under imperfect contact tracing and significant levels of dilution.
    Keywords Biology (General) ; QH301-705.5
    Subject code 000
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Listening to bluetooth beacons for epidemic risk mitigation

    Gilles Barthe / Roberta De Viti / Peter Druschel / Deepak Garg / Manuel Gomez-Rodriguez / Pierfrancesco Ingo / Heiner Kremer / Matthew Lentz / Lars Lorch / Aastha Mehta / Bernhard Schölkopf

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 14

    Abstract: Abstract The ongoing COVID-19 pandemic let to efforts to develop and deploy digital contact tracing systems to expedite contact tracing and risk notification. Unfortunately, the success of these systems has been limited, partly owing to poor ... ...

    Abstract Abstract The ongoing COVID-19 pandemic let to efforts to develop and deploy digital contact tracing systems to expedite contact tracing and risk notification. Unfortunately, the success of these systems has been limited, partly owing to poor interoperability with manual contact tracing, low adoption rates, and a societally sensitive trade-off between utility and privacy. In this work, we introduce a new privacy-preserving and inclusive system for epidemic risk assessment and notification that aims to address these limitations. Rather than capturing pairwise encounters between user devices as done by existing systems, our system captures encounters between user devices and beacons placed in strategic locations where infection clusters may originate. Epidemiological simulations using an agent-based model demonstrate that, by utilizing location and environmental information and interoperating with manual contact tracing, our system can increase the accuracy of contact tracing actions and may help reduce epidemic spread already at low adoption.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Tracking progress towards malaria elimination in China

    Isobel Routledge / Shengjie Lai / Katherine E Battle / Azra C Ghani / Manuel Gomez-Rodriguez / Kyle B Gustafson / Swapnil Mishra / Juliette Unwin / Joshua L Proctor / Andrew J Tatem / Zhongjie Li / Samir Bhatt

    PLoS Computational Biology, Vol 16, Iss 3, p e

    Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach.

    2020  Volume 1007707

    Abstract: In order to monitor progress towards malaria elimination, it is crucial to be able to measure changes in spatio-temporal transmission. However, common metrics of malaria transmission such as parasite prevalence are under powered in elimination contexts. ... ...

    Abstract In order to monitor progress towards malaria elimination, it is crucial to be able to measure changes in spatio-temporal transmission. However, common metrics of malaria transmission such as parasite prevalence are under powered in elimination contexts. China has achieved major reductions in malaria incidence and is on track to eliminate, having reporting zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we introduce a novel Bayesian framework to model a latent diffusion process and estimate the joint likelihood of transmission between cases and the number of cases with unobserved sources of infection. This is used to estimate the case reproduction number, Rc. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. We estimate the mean Rc between 2011 and 2016 to be 0.171 (95% CI = 0.165, 0.178) for P. vivax cases and 0.089 (95% CI = 0.076, 0.103) for P. falciparum cases. From 2014 onwards, no cases were estimated to have a Rc value above one. An unobserved source of infection was estimated to be moderately likely (p>0.5) for 19/ 611 cases and high (p>0.8) for 2 cases, suggesting very high levels of case ascertainment. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean of 0.005 projected up to 2020, locally-acquired cases are possible due to high levels of importation.
    Keywords Biology (General) ; QH301-705.5
    Subject code 333
    Language English
    Publishing date 2020-03-01T00:00:00Z
    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: Inferring Networks of Diffusion and Influence

    Manuel Gomez-Rodriguez / Jure Leskovec / Andreas Krause

    Abstract: Information diffusion and virus propagation are fundamental processes taking place in networks. While it is often possible to directly observe when nodes become infected with a virus or adopt the information, observing individual transmissions (i.e., who ...

    Abstract Information diffusion and virus propagation are fundamental processes taking place in networks. While it is often possible to directly observe when nodes become infected with a virus or adopt the information, observing individual transmissions (i.e., who infects whom, or who influences whom) is typically very difficult. Furthermore, in many applications, the underlying network over which the diffusions and propagations spread is actually unobserved. We tackle these challenges by developing a method for tracing paths of diffusion and influence through networks and inferring the networks over which contagions propagate. Given the times when nodes adopt pieces of information or become infected, we identify the optimal network that best explains the observed infection times. Since the optimization problem is NP-hard to solve exactly, we develop an efficient approximation algorithm that scales to large datasets and finds provably near-optimal networks. We demonstrate the effectiveness of our approach by tracing information diffusion in a set of 170 million blogs and news articles over a one year period to infer how information flows through the online media space. We find that the diffusion network of news for the top 1,000 media sites and blogs tends to have a core-periphery structure with a small set of core media sites that diffuse information to the rest of the Web. These sites tend to have stable circles of influence with more general news media sites acting as connectors between them.
    Keywords covid19
    Publisher arxiv
    Document type Article
    Database COVID19

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  5. Article ; Online: Tracking progress towards malaria elimination in China: estimates of reproduction numbers and their spatiotemporal variation

    Isobel Routledge / Shengjie Lai / Katherine E Battle / Azra C Ghani / Manuel Gomez-Rodriguez / Kyle B Gustafson / Swapnil Mishra / Joshua L Proctor / Andrew J Tatem / Zhongjie Li / Samir Bhatt

    Abstract: AbstractChina reported zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain ... ...

    Abstract AbstractChina reported zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we jointly estimate the case reproduction number, Rc, and the number of unobserved sources of infection. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean Rc of 0.005 projected for the year 2019, locally-acquired cases are possible due to high levels of importation.
    Keywords covid19
    Publisher biorxiv
    Document type Article ; Online
    DOI 10.1101/628842
    Database COVID19

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  6. Article ; Online: The marketing management of cities and metropolitan areas

    PEDRO MANUEL GÓMEZ RODRÍGUEZ

    Cuadernos de Gestión, Vol 3, Iss 1, Pp 11-

    from product orientation to marketing orientation

    2003  Volume 25

    Abstract: The application of marketing principles in the administration of cities has been usually reduced to the use of the communication tools to try to diffuse the city’s image among the different target publics. At the same time, the development of cities has ... ...

    Abstract The application of marketing principles in the administration of cities has been usually reduced to the use of the communication tools to try to diffuse the city’s image among the different target publics. At the same time, the development of cities has habitually been based on the endowment of infrastructures and singular buildings, by means of relatively opaque strategic planning processes. From a marketing vision, we consider indispensable to base the development of cities on the active citizenship participation, as well as in the empowerment of the tangible and intangible aspects. In the case of the Metropolitan Bilbao, the strategic plan that has been developed in the last decade was centred on tangible elements, while the new plan puts a special emphasis on the intangible aspects and civic participation.
    Keywords Urban marketing ; city marketing ; strategic planning ; citizenship ; Economic theory. Demography ; HB1-3840 ; Social Sciences ; H ; DOAJ:Economics ; DOAJ:Business and Economics ; Business ; HF5001-6182 ; Commerce ; HF1-6182 ; DOAJ:Business and Management
    Subject code 910
    Language Spanish
    Publishing date 2003-06-01T00:00:00Z
    Publisher Instituto de Economía Aplicada a la Empresa
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Physical mapping of 5S and 18S ribosomal DNA in three species of Agave (Asparagales, Asparagaceae)

    Victor Manuel Gomez-Rodriguez / Benjamin Rodriguez-Garay / Guadalupe Palomino / Javier Martínez / Rodrigo Barba-Gonzalez

    Comparative Cytogenetics, Vol 7, Iss 3, Pp 191-

    2013  Volume 203

    Abstract: Agave Linnaeus, 1753 is endemic of America and is considered one of the most important crops in Mexico due to its key role in the country’s economy. Cytogenetic analysis was carried out in A. tequilana Weber, 1902 ‘Azul’, A. cupreata Trelease et Berger, ... ...

    Abstract Agave Linnaeus, 1753 is endemic of America and is considered one of the most important crops in Mexico due to its key role in the country’s economy. Cytogenetic analysis was carried out in A. tequilana Weber, 1902 ‘Azul’, A. cupreata Trelease et Berger, 1915 and A. angustifolia Haworth, 1812. The analysis showed that in all species the diploid chromosome number was 2n = 60, with bimodal karyotypes composed of five pairs of large chromosomes and 25 pairs of small chromosomes. Furthermore, different karyotypical formulae as well as a secondary constriction in a large chromosome pair were found in all species. Fluorescent in situ hybridization (FISH) was used for physical mapping of 5S and 18S ribosomal DNA (rDNA). All species analyzed showed that 5S rDNA was located in both arms of a small chromosome pair, while 18S rDNA was associated with the secondary constriction of a large chromosome pair. Data of FISH analysis provides new information about the position and number of rDNA loci and helps for detection of hybrids in breeding programs as well as evolutionary studies.
    Keywords Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2013-08-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting

    Isobel Routledge / José Eduardo Romero Chevéz / Zulma M. Cucunubá / Manuel Gomez Rodriguez / Caterina Guinovart / Kyle B. Gustafson / Kammerle Schneider / Patrick G.T. Walker / Azra C. Ghani / Samir Bhatt

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 8

    Abstract: Twenty one countries have been identified for malaria elimination by 2020 and their progress needs to be constantly evaluated. Here, the authors present a method that estimates individual reproduction numbers and their variation through time and space ... ...

    Abstract Twenty one countries have been identified for malaria elimination by 2020 and their progress needs to be constantly evaluated. Here, the authors present a method that estimates individual reproduction numbers and their variation through time and space and use it to monitor elimination success in El Salvador between 2010 and 2016.
    Keywords Science ; Q
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting

    Isobel Routledge / José Eduardo Romero Chevéz / Zulma M. Cucunubá / Manuel Gomez Rodriguez / Caterina Guinovart / Kyle B. Gustafson / Kammerle Schneider / Patrick G.T. Walker / Azra C. Ghani / Samir Bhatt

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 8

    Abstract: Twenty one countries have been identified for malaria elimination by 2020 and their progress needs to be constantly evaluated. Here, the authors present a method that estimates individual reproduction numbers and their variation through time and space ... ...

    Abstract Twenty one countries have been identified for malaria elimination by 2020 and their progress needs to be constantly evaluated. Here, the authors present a method that estimates individual reproduction numbers and their variation through time and space and use it to monitor elimination success in El Salvador between 2010 and 2016.
    Keywords Science ; Q
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Solar Radiation Stress in Natural Acidophilic Biofilms of Euglena mutabilis Revealed by Metatranscriptomics and PAM Fluorometry

    Puente-Sánchez, Fernando / Angeles Aguilera / Manuel Gómez-Rodriguez / Maria Altamirano-Jeschke / Ricardo Amils / Sanna Olsson / Victor Parro / Virginia Souza-Egipsy

    Protist. 2016 Feb., v. 167, no. 1

    2016  

    Abstract: The daily photosynthetic performance of a natural biofilm of the extreme acidophilic Euglena mutabilis from Río Tinto (SW, Spain) under full solar radiation was analyzed by means of pulse amplitude-modulated (PAM) fluorescence measurements and ... ...

    Abstract The daily photosynthetic performance of a natural biofilm of the extreme acidophilic Euglena mutabilis from Río Tinto (SW, Spain) under full solar radiation was analyzed by means of pulse amplitude-modulated (PAM) fluorescence measurements and metatrascriptomic analysis. Natural E. mutabilis biofilms undergo large-scale transcriptomic reprogramming during midday due to a dynamic photoinhibition and solar radiation stress. Photoinhibition is due to UV radiation and not to light intensity, as revealed by PAM fluorometry analysis. In order to minimize the negative effects of solar radiation, our data supports the presence of a circadian rhythm in this euglenophyte that increases their opportunity to survive. Differential gene expression throughout the day (at 12:00, 20:00 and night) was monitored by massive Illumina parallel sequencing of metatranscriptomic libraries. The transcription pattern was altered in genes involved in Photosystem II stability and repair, UV damaged DNA repair, non-photochemical quenching and oxidative stress, supporting the photoinhibition detected by PAM fluorometry at midday.
    Keywords adverse effects ; biofilm ; circadian rhythm ; DNA repair ; Euglena ; fluorescence ; fluorometry ; gene expression regulation ; genes ; light intensity ; oxidative stress ; photoinhibition ; photosystem II ; solar radiation ; transcriptomics ; ultraviolet radiation ; Spain
    Language English
    Dates of publication 2016-02
    Size p. 67-81.
    Publishing place Elsevier GmbH
    Document type Article
    ZDB-ID 2036014-9
    ISSN 1618-0941 ; 1434-4610
    ISSN (online) 1618-0941
    ISSN 1434-4610
    DOI 10.1016/j.protis.2015.12.003
    Database NAL-Catalogue (AGRICOLA)

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