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  • SDSN - Greece
  • 2018-2022
  • Publications
  • Aurora Universities Network

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carolina dos S Ribeiro; Martine van Roode; Elmoubasher Farag; Mohamed Nour; +5 Authors

    Background Epidemics are a constant threat in the 21st century, particularly disease outbreaks following spillover of an animal virus to humans. Timeliness, a key metric in epidemic response, can be examined to identify critical steps and delays in public health action. Aim To examine timeliness, we analysed the response to the Middle East respiratory syndrome (MERS) epidemic, with a focus on the international and One Health response efforts. Methods We performed a historical review of the MERS epidemic between September 2012 and January 2019 in three steps: (i) the construction of a timeline identifying critical events in the global response, (ii) the performance of a critical path analysis to define outbreak milestones and (iii) a time gap analysis to measure timeliness in the execution of these milestones. Results We proposed 14 MERS-specific milestones at different phases of the epidemic, assessing timeliness of the public health response as well as at the animal–human interface, where we identified the most significant delays. Conclusions When comparing timeliness across three coronavirus epidemics, i.e. MERS (2012), SARS (2002) and COVID-19 (2019), we identified clear improvements over time for certain milestones including laboratory confirmation and diagnostics development, while this was not as apparent for others, as the identification of zoonotic hosts. To more efficiently respond to emerging threats, the global health community should widely assess and tackle specific delays in implementing response interventions by addressing challenges in the sharing of information, data and resources, as well as efficiency, quality, transparency and reliability of reporting events.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Eurosurveillancearrow_drop_down
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    https://hdl.handle.net/1871.1/...
    Other literature type . 2022
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    Article . 2023
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    Eurosurveillance
    Other literature type . Article . 2022 . Peer-reviewed
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    Eurosurveillance
    Article . 2023
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Eurosurveillancearrow_drop_down
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      https://hdl.handle.net/1871.1/...
      Other literature type . 2022
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      Eurosurveillance
      Other literature type . Article . 2022 . Peer-reviewed
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      Eurosurveillance
      Article . 2023
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    Authors: Lincke, Daniel; Hinkel, Jochen; Mengel, Matthias; Nicholls, Robert J.;

    AbstractGlobal coastal flood exposure (population and assets) has been growing since the beginning of the industrial age and is likely to continue to grow through 21st century. Three main drivers are responsible: (a) climate‐related mean sea‐level change, (b) vertical land movement contributing to relative sea‐level rise, and (c) socio‐economic development. This paper attributes growing coastal exposure and flood risk from 1860 to 2100 to these three drivers. For historic flood exposure (1860–2005) we find that the roughly six‐fold increase in population exposure and 53‐fold increase in asset exposure are almost completely explained by socio‐economic development (>97% for population and >99% for assets). For future exposure (2005–2100), assuming a middle‐of‐the‐road regionalized socio‐economic scenario (SSP2) without coastal migration and sea‐level rise according to RCP2.6 and RCP6.0, climate‐change induced sea‐level rise will become the most important driver for the growth in population exposure, while growth in asset exposure will still be mainly determined by socio‐economic development.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Earth's Futurearrow_drop_down
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    Earth's Future
    Article . 2022 . Peer-reviewed
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    Earth's Future
    Article . 2022
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Earth's Futurearrow_drop_down
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      Earth's Future
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      Earth's Future
      Article . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Ruggiero, Alessandra; Punzo, Paola; Van Oosten, Michael James; Cirillo, Valerio; +5 Authors

    Tomato is a horticultural crop of high economic and nutritional value. Suboptimal environmental conditions, such as limited water and nutrient availability, cause severe yield reductions. Thus, selection of genotypes requiring lower inputs is a goal for the tomato breeding sector. We screened 10 tomato varieties exposed to water deficit, low nitrate or a combination of both. Biometric, physiological and molecular analyses revealed different stress responses among genotypes, identifying T270 as severely affected, and T250 as tolerant to the stresses applied. Investigation of transcriptome changes caused by combined stress in roots and leaves of these two genotypes yielded a low number of differentially expressed genes (DEGs) in T250 compared to T270, suggesting that T250 tailors changes in gene expression to efficiently respond to combined stress. By contrast, the susceptible tomato activated approximately one thousand and two thousand genes in leaves and roots respectively, indicating a more generalized stress response in this genotype. In particular, developmental and stress-related genes were differentially expressed, such as hormone responsive factors and transcription factors. Analysis of differential alternative splicing (DAS) events showed that combined stress greatly affects the splicing landscape in both genotypes, highlighting the important role of AS in stress response mechanisms. In particular, several stress and growth-related genes as well as transcription and splicing factors were differentially spliced in both tissues. Taken together, these results reveal important insights into the transcriptional and post-transcriptional mechanisms regulating tomato adaptation to growth under reduced water and nitrogen inputs.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Plant S...arrow_drop_down
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    Frontiers in Plant Science
    Article . 2022
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Plant S...arrow_drop_down
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      Frontiers in Plant Science
      Article . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: E. E. Aalbers; E. E. Aalbers; E. van Meijgaard; G. Lenderink; +3 Authors

    Projections of changes in extreme droughts under future climate conditions are associated with large uncertainties, owing to the complex genesis of droughts and large model uncertainty in the atmospheric dynamics. In this study we investigate the impact of global warming on soil moisture drought severity in west-central Europe by employing pseudo global warming (PGW) experiments, which project the 1980–2020 period in a globally warmer world. The future analogues of present-day drought episodes allow for investigation of changes in drought severity conditional on the historic day-to-day evolution of the atmospheric circulation. The 2018 west-central European drought is the most severe drought in the 1980–2020 reference period in this region. Under 1.5, 2 and 3 ∘C global warming, this drought episode experiences strongly enhanced summer temperatures but a fairly modest soil moisture drying response compared to the change in climatology. This is primarily because evaporation is already strongly moisture-constrained during present-day conditions, limiting the increase in evaporation and thus the modulation of the temperature response under PGW. Increasing precipitation in winter, spring and autumn limits or prevents an earlier drought onset and duration. Nevertheless, the drought severity, defined as the cumulative soil moisture deficit volume, increases considerably, with 20 % to 39 % under 2 ∘C warming. The extreme drought frequency in the 1980–2020 period strongly increases under 2 ∘C warming. Several years without noticeable droughts under present-day conditions show very strong drying and warming. This results in an increase in 2003-like drought occurrences, compounding with local summer temperature increases considerably above 2 ∘C. Even without taking into account a (potentially large) dynamical response to climate change, drought risk in west-central Europe is strongly enhanced under global warming. Owing to increases in drought frequency, severity and compounding heat, a reduction in recovery times between drought episodes is expected to occur. Our physical climate storyline provides evidence complementing conventional large-ensemble approaches and is intended to contribute to the formulation of effective adaptation strategies.

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    Natural Hazards and Earth System Sciences
    Article . 2023 . Peer-reviewed
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    https://doi.org/10.5194/egusph...
    Preprint . 2022 . Peer-reviewed
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    Copernicus Publications
    Other literature type . 2023 . 2022
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Vrije Universiteit A...arrow_drop_down
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      Natural Hazards and Earth System Sciences
      Article . 2023 . Peer-reviewed
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      https://doi.org/10.5194/egusph...
      Preprint . 2022 . Peer-reviewed
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  • Authors: Gozde S. Demirer; Donald J. Gibson; Xiaoyan Yue; Kelly Pan; +9 Authors

    AbstractPhosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate fertilizer, on the other hand, leads to eutrophication and has a negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. Here, we show that Solanum pennellii, a wild relative of tomato, is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response, which is dependent on zinc over-accumulation. Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation.

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    Authors: Glaubitz, Lina; Stumme, Johanna; Lucht, Sarah; Moebus, Susanne; +4 Authors

    BACKGROUND: Older adults show a high variability in cognitive performance that cannot be explained by aging alone. Although research has linked air pollution and noise to cognitive impairment and structural brain alterations, the potential impact of air pollution and noise on functional brain organization is unknown. OBJECTIVE: This study examined the associations between long-term air pollution and traffic noise with measures of functional brain organization in older adults. We hypothesize that exposures to high air pollution and noise levels are associated with age-like changes in functional brain organization, shown by less segregated brain networks. METHODS: Data from 574 participants (44.1% female, 56-85 years of age) in the German 1000BRAINS study (2011-2015) were analyzed. Exposure to particulate matter (formula presented , and formula presented absorbance), accumulation mode particle number (formula presented ), and nitrogen dioxide (formula presented ) was estimated applying land-use regression and chemistry transport models. Noise exposures were assessed as weighted 24-h (formula presented ) and nighttime (formula presented ) means. Functional brain organization of seven established brain networks (visual, sensorimotor, dorsal and ventral attention, limbic, frontoparietal and default network) was assessed using resting-state functional brain imaging data. To assess functional brain organization, we determined the degree of segregation between networks by comparing the strength of functional connections within and between networks. We estimated associations between air pollution and noise exposure with network segregation, applying multiple linear regression models adjusted for age, sex, socioeconomic status, and lifestyle variables. RESULTS: Overall, small associations of high exposures with lesser segregated networks were visible. For the sensorimotor networks, we observed small associations between high air pollution and noise and lower network segregation, which had a similar effect size as a 1-y increase in age [e.g., in sensorimotor network, formula presented (95% CI: formula presented , 0.009) per 0.3 formula presented increase in formula presented absorbance and formula presented (95% CI: formula presented ) per 1-y age increase]. CONCLUSION: High exposure to air pollution and noise was associated with less segregated functional brain networks. https://doi.org/10.1289/EHP9737.

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    Urban sustainability has often been accused of tending mostly to its environmental and economic dimensions, neglecting or marginalising issues of justice. Simultaneously, the European Union has been increasingly funding research explicitly focused on the intersection of justice, sustainability and the city. The role of such research in furthering or jeopardising just urban sustainability objectives and outcomes so far remains underexplored. We conducted a discourse analysis on 27 selected research projects funded by the EU FP7 and Horizon 2020 schemes and which focus on the themes of urban sustainability and justice, supplemented by qualitative interviews with core researchers in those projects, to examine their potential in (re-)politicising or depoliticising urban sustainability. Our findings indicate that justice is often loosely defined through terms such as "stakeholder participation," "inclusion," or "diversity" in urban sustainability interventions, and research projects fail to pay attention to structural and historical drivers of injustice within a broader context of political economy, society and culture. We find this trend mostly in international collaborative projects that are implementation-oriented and promise to fast track inter- or trans-disciplinarity within a context of precarious research contracts and limited timescales for researchers. We build on earlier critiques of the ecological modernist character of EU research and policy priorities and contribute further by demonstrating how the academic entrepreneurial system perpetrated by EU-funded projects can undermine the politicising possibilities of research. To overcome funding constraints, we urge funders to allow for broader methods and timescales to examine and reflect on what are, or could be, just urban sustainabilities. Unidad de excelencia María de Maeztu CEX2019-000940-M Altres ajuts: Maria de Maeztu MDM-2021

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    Authors: Janes, Victoria A.; Matamoros, S. bastien; Munk, Patrick; Clausen, Philip T. L. C.; +11 Authors

    BackgroundSemi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine. MethodsIn this proof-of-concept study, we prospectively included consecutive urine samples from a clinical diagnostic laboratory in Amsterdam. Urine samples were screened by DNA concentration, followed by PCR-free metagenomic sequencing of randomly selected samples with a high concentration of DNA (culture positive and negative). A diagnostic index was calculated as the product of DNA concentration and fraction of pathogen reads. We compared results with semi-quantitative culture using area under the receiver operating characteristic curve (AUROC) analyses. We used ResFinder and PointFinder for resistance gene detection and compared results to phenotypic antimicrobial susceptibility testing for six antibiotics commonly used for urinary tract infection treatment: nitrofurantoin, ciprofloxacin, fosfomycin, cotrimoxazole, ceftazidime, and ceftriaxone. FindingsWe screened 529 urine samples of which 86 were sequenced (43 culture positive and 43 culture negative). The AUROC of the DNA concentration-based screening was 0·85 (95% CI 0·81-0·89). At a cutoff value of 6·0 ng/mL, culture positivity was ruled out with a negative predictive value of 91% (95% CI 87-93; 26 of 297 samples), reducing the number of samples requiring sequencing by 56% (297 of 529 samples). The AUROC of the diagnostic index was 0·87 (95% CI 0·79-0·95). A diagnostic index cutoff value of 17·2 yielded a positive predictive value of 93% (95% CI 85-97) and a negative predictive value of 69% (55-80), correcting for a culture-positive prevalence of 66%. Gram-positive pathogens explained eight (89%) of the nine false-negative metagenomic test results. Agreement of phenotypic and genotypic antimicrobial susceptibility testing varied between 71% (22 of 31 samples) and 100% (six of six samples), depending on the antibiotic tested. InterpretationThis study provides proof-of-concept of metagenomic semi-quantitative pathogen and resistome detection for the diagnosis of urinary tract infection. The findings warrant prospective clinical validation of the value of this approach in informing patient management and care. FundingEU Horizon 2020 Research and Innovation Programme.

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    Authors: Anna Boqué Ciurana; Melisa Ménendez; María Suárez Bilbao; Enric Aguilar;

    Surfing is one of the most popular activities in coastal tourism resorts. However, the sport depends strongly on the met-ocean weather conditions, particularly on the surface wind-generated waves that reach the coast. This study provides examples of how users? needs and user perspectives are considered by climate data specialists to develop needed, highly useful information addressing human and social needs. In this vein, the climate analysis of such data can provide input on the expected length of a surfing season, according to the surfer?s level of expertise. In addition, other water sports, such as SUP Wave and windsurfing, among others, might be indicated when surfing conditions are not optimal. Finally, the safety of surfers and other tourists who venture into the sea is also dependent on those conditions. We collaborated with the surfing community to define a series of indices for quantifying surfing days (SD), surfing days stratified by surfers? skills (SDS), alternate offers (AOs), and surfers? and swimmers? safety (SuS and SwS). These are of general applications but require wind and wave data at a very fine scale as the input. To illustrate the potential of our indices, we applied them to the Somo beach (Cantabria, Spain). We downscaled a global wave hindcast dataset covering a 30-year period to a spatial resolution of 100 m to obtain wave-surfing information at Somo?s surf spot. The results confirmed Somo?s status as a year-round surf spot, with SD values of 229.5 days/year and monthly values between 22 days/month and 16 days/month. SDS showed different seasonal peaks according to the surfers? skills. Beginners? conditions occurred more often in the summer (18.1 days/month in July), intermediate surfers? conditions appeared in the transitional seasons (14.1 days/month in April), and advanced and big-wave riders in the winter (15.1 days/month in January and 0.7 days/month, respectively). The AO index identified the SUP wave values of 216 days/year. Wind water sports presented values of 141.6 days/year; conversely, SUP sports were possible on only 7.4 days/year. SuS and SwS identified different seasonal hazard values, decreasing from the winter, autumn, and spring to minimum values in the summer. This research is within the INDECIS project (INDECIS is part of ERA4CS, an ERA-NET initiated by JPI Climate and funded by FORMAS (SE), DLR (DE), BMWFW (AT), IFD (DK), MINECO (ES), and ANR (FR) with co-funding by the European Union Grant 690462). This article publication was possible with the support of the Secretaria d’Universitats i Recerca del Departament d’Empresa i Coneixement de la Generalitat de Catalunya, the European Union (UE), and the European Social Fund (ESF) (Doctoral Research Grant 2021FI_B2 00147—Formació personal investigador novell).

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    Sustainability
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    Authors: Giulia I. Corsi; Swapnil Tichkule; Anna Rosa Sannella; Paolo Vatta; +5 Authors

    AbstractCryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human‐ and ruminant‐derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long‐term evolutionary consequences of these events. Our results suggest that increased globalization and close human‐animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host–parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carolina dos S Ribeiro; Martine van Roode; Elmoubasher Farag; Mohamed Nour; +5 Authors

    Background Epidemics are a constant threat in the 21st century, particularly disease outbreaks following spillover of an animal virus to humans. Timeliness, a key metric in epidemic response, can be examined to identify critical steps and delays in public health action. Aim To examine timeliness, we analysed the response to the Middle East respiratory syndrome (MERS) epidemic, with a focus on the international and One Health response efforts. Methods We performed a historical review of the MERS epidemic between September 2012 and January 2019 in three steps: (i) the construction of a timeline identifying critical events in the global response, (ii) the performance of a critical path analysis to define outbreak milestones and (iii) a time gap analysis to measure timeliness in the execution of these milestones. Results We proposed 14 MERS-specific milestones at different phases of the epidemic, assessing timeliness of the public health response as well as at the animal–human interface, where we identified the most significant delays. Conclusions When comparing timeliness across three coronavirus epidemics, i.e. MERS (2012), SARS (2002) and COVID-19 (2019), we identified clear improvements over time for certain milestones including laboratory confirmation and diagnostics development, while this was not as apparent for others, as the identification of zoonotic hosts. To more efficiently respond to emerging threats, the global health community should widely assess and tackle specific delays in implementing response interventions by addressing challenges in the sharing of information, data and resources, as well as efficiency, quality, transparency and reliability of reporting events.

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      Eurosurveillance
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    Authors: Lincke, Daniel; Hinkel, Jochen; Mengel, Matthias; Nicholls, Robert J.;

    AbstractGlobal coastal flood exposure (population and assets) has been growing since the beginning of the industrial age and is likely to continue to grow through 21st century. Three main drivers are responsible: (a) climate‐related mean sea‐level change, (b) vertical land movement contributing to relative sea‐level rise, and (c) socio‐economic development. This paper attributes growing coastal exposure and flood risk from 1860 to 2100 to these three drivers. For historic flood exposure (1860–2005) we find that the roughly six‐fold increase in population exposure and 53‐fold increase in asset exposure are almost completely explained by socio‐economic development (>97% for population and >99% for assets). For future exposure (2005–2100), assuming a middle‐of‐the‐road regionalized socio‐economic scenario (SSP2) without coastal migration and sea‐level rise according to RCP2.6 and RCP6.0, climate‐change induced sea‐level rise will become the most important driver for the growth in population exposure, while growth in asset exposure will still be mainly determined by socio‐economic development.

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    Earth's Future
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    Authors: Ruggiero, Alessandra; Punzo, Paola; Van Oosten, Michael James; Cirillo, Valerio; +5 Authors

    Tomato is a horticultural crop of high economic and nutritional value. Suboptimal environmental conditions, such as limited water and nutrient availability, cause severe yield reductions. Thus, selection of genotypes requiring lower inputs is a goal for the tomato breeding sector. We screened 10 tomato varieties exposed to water deficit, low nitrate or a combination of both. Biometric, physiological and molecular analyses revealed different stress responses among genotypes, identifying T270 as severely affected, and T250 as tolerant to the stresses applied. Investigation of transcriptome changes caused by combined stress in roots and leaves of these two genotypes yielded a low number of differentially expressed genes (DEGs) in T250 compared to T270, suggesting that T250 tailors changes in gene expression to efficiently respond to combined stress. By contrast, the susceptible tomato activated approximately one thousand and two thousand genes in leaves and roots respectively, indicating a more generalized stress response in this genotype. In particular, developmental and stress-related genes were differentially expressed, such as hormone responsive factors and transcription factors. Analysis of differential alternative splicing (DAS) events showed that combined stress greatly affects the splicing landscape in both genotypes, highlighting the important role of AS in stress response mechanisms. In particular, several stress and growth-related genes as well as transcription and splicing factors were differentially spliced in both tissues. Taken together, these results reveal important insights into the transcriptional and post-transcriptional mechanisms regulating tomato adaptation to growth under reduced water and nitrogen inputs.

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    Frontiers in Plant Science
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      Frontiers in Plant Science
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    Authors: E. E. Aalbers; E. E. Aalbers; E. van Meijgaard; G. Lenderink; +3 Authors

    Projections of changes in extreme droughts under future climate conditions are associated with large uncertainties, owing to the complex genesis of droughts and large model uncertainty in the atmospheric dynamics. In this study we investigate the impact of global warming on soil moisture drought severity in west-central Europe by employing pseudo global warming (PGW) experiments, which project the 1980–2020 period in a globally warmer world. The future analogues of present-day drought episodes allow for investigation of changes in drought severity conditional on the historic day-to-day evolution of the atmospheric circulation. The 2018 west-central European drought is the most severe drought in the 1980–2020 reference period in this region. Under 1.5, 2 and 3 ∘C global warming, this drought episode experiences strongly enhanced summer temperatures but a fairly modest soil moisture drying response compared to the change in climatology. This is primarily because evaporation is already strongly moisture-constrained during present-day conditions, limiting the increase in evaporation and thus the modulation of the temperature response under PGW. Increasing precipitation in winter, spring and autumn limits or prevents an earlier drought onset and duration. Nevertheless, the drought severity, defined as the cumulative soil moisture deficit volume, increases considerably, with 20 % to 39 % under 2 ∘C warming. The extreme drought frequency in the 1980–2020 period strongly increases under 2 ∘C warming. Several years without noticeable droughts under present-day conditions show very strong drying and warming. This results in an increase in 2003-like drought occurrences, compounding with local summer temperature increases considerably above 2 ∘C. Even without taking into account a (potentially large) dynamical response to climate change, drought risk in west-central Europe is strongly enhanced under global warming. Owing to increases in drought frequency, severity and compounding heat, a reduction in recovery times between drought episodes is expected to occur. Our physical climate storyline provides evidence complementing conventional large-ensemble approaches and is intended to contribute to the formulation of effective adaptation strategies.

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    Natural Hazards and Earth System Sciences
    Article . 2023 . Peer-reviewed
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    https://doi.org/10.5194/egusph...
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    Copernicus Publications
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  • Authors: Gozde S. Demirer; Donald J. Gibson; Xiaoyan Yue; Kelly Pan; +9 Authors

    AbstractPhosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate fertilizer, on the other hand, leads to eutrophication and has a negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. Here, we show that Solanum pennellii, a wild relative of tomato, is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response, which is dependent on zinc over-accumulation. Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation.

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    Authors: Glaubitz, Lina; Stumme, Johanna; Lucht, Sarah; Moebus, Susanne; +4 Authors

    BACKGROUND: Older adults show a high variability in cognitive performance that cannot be explained by aging alone. Although research has linked air pollution and noise to cognitive impairment and structural brain alterations, the potential impact of air pollution and noise on functional brain organization is unknown. OBJECTIVE: This study examined the associations between long-term air pollution and traffic noise with measures of functional brain organization in older adults. We hypothesize that exposures to high air pollution and noise levels are associated with age-like changes in functional brain organization, shown by less segregated brain networks. METHODS: Data from 574 participants (44.1% female, 56-85 years of age) in the German 1000BRAINS study (2011-2015) were analyzed. Exposure to particulate matter (formula presented , and formula presented absorbance), accumulation mode particle number (formula presented ), and nitrogen dioxide (formula presented ) was estimated applying land-use regression and chemistry transport models. Noise exposures were assessed as weighted 24-h (formula presented ) and nighttime (formula presented ) means. Functional brain organization of seven established brain networks (visual, sensorimotor, dorsal and ventral attention, limbic, frontoparietal and default network) was assessed using resting-state functional brain imaging data. To assess functional brain organization, we determined the degree of segregation between networks by comparing the strength of functional connections within and between networks. We estimated associations between air pollution and noise exposure with network segregation, applying multiple linear regression models adjusted for age, sex, socioeconomic status, and lifestyle variables. RESULTS: Overall, small associations of high exposures with lesser segregated networks were visible. For the sensorimotor networks, we observed small associations between high air pollution and noise and lower network segregation, which had a similar effect size as a 1-y increase in age [e.g., in sensorimotor network, formula presented (95% CI: formula presented , 0.009) per 0.3 formula presented increase in formula presented absorbance and formula presented (95% CI: formula presented ) per 1-y age increase]. CONCLUSION: High exposure to air pollution and noise was associated with less segregated functional brain networks. https://doi.org/10.1289/EHP9737.

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    Urban sustainability has often been accused of tending mostly to its environmental and economic dimensions, neglecting or marginalising issues of justice. Simultaneously, the European Union has been increasingly funding research explicitly focused on the intersection of justice, sustainability and the city. The role of such research in furthering or jeopardising just urban sustainability objectives and outcomes so far remains underexplored. We conducted a discourse analysis on 27 selected research projects funded by the EU FP7 and Horizon 2020 schemes and which focus on the themes of urban sustainability and justice, supplemented by qualitative interviews with core researchers in those projects, to examine their potential in (re-)politicising or depoliticising urban sustainability. Our findings indicate that justice is often loosely defined through terms such as "stakeholder participation," "inclusion," or "diversity" in urban sustainability interventions, and research projects fail to pay attention to structural and historical drivers of injustice within a broader context of political economy, society and culture. We find this trend mostly in international collaborative projects that are implementation-oriented and promise to fast track inter- or trans-disciplinarity within a context of precarious research contracts and limited timescales for researchers. We build on earlier critiques of the ecological modernist character of EU research and policy priorities and contribute further by demonstrating how the academic entrepreneurial system perpetrated by EU-funded projects can undermine the politicising possibilities of research. To overcome funding constraints, we urge funders to allow for broader methods and timescales to examine and reflect on what are, or could be, just urban sustainabilities. Unidad de excelencia María de Maeztu CEX2019-000940-M Altres ajuts: Maria de Maeztu MDM-2021

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    Authors: Janes, Victoria A.; Matamoros, S. bastien; Munk, Patrick; Clausen, Philip T. L. C.; +11 Authors

    BackgroundSemi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine. MethodsIn this proof-of-concept study, we prospectively included consecutive urine samples from a clinical diagnostic laboratory in Amsterdam. Urine samples were screened by DNA concentration, followed by PCR-free metagenomic sequencing of randomly selected samples with a high concentration of DNA (culture positive and negative). A diagnostic index was calculated as the product of DNA concentration and fraction of pathogen reads. We compared results with semi-quantitative culture using area under the receiver operating characteristic curve (AUROC) analyses. We used ResFinder and PointFinder for resistance gene detection and compared results to phenotypic antimicrobial susceptibility testing for six antibiotics commonly used for urinary tract infection treatment: nitrofurantoin, ciprofloxacin, fosfomycin, cotrimoxazole, ceftazidime, and ceftriaxone. FindingsWe screened 529 urine samples of which 86 were sequenced (43 culture positive and 43 culture negative). The AUROC of the DNA concentration-based screening was 0·85 (95% CI 0·81-0·89). At a cutoff value of 6·0 ng/mL, culture positivity was ruled out with a negative predictive value of 91% (95% CI 87-93; 26 of 297 samples), reducing the number of samples requiring sequencing by 56% (297 of 529 samples). The AUROC of the diagnostic index was 0·87 (95% CI 0·79-0·95). A diagnostic index cutoff value of 17·2 yielded a positive predictive value of 93% (95% CI 85-97) and a negative predictive value of 69% (55-80), correcting for a culture-positive prevalence of 66%. Gram-positive pathogens explained eight (89%) of the nine false-negative metagenomic test results. Agreement of phenotypic and genotypic antimicrobial susceptibility testing varied between 71% (22 of 31 samples) and 100% (six of six samples), depending on the antibiotic tested. InterpretationThis study provides proof-of-concept of metagenomic semi-quantitative pathogen and resistome detection for the diagnosis of urinary tract infection. The findings warrant prospective clinical validation of the value of this approach in informing patient management and care. FundingEU Horizon 2020 Research and Innovation Programme.

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    The Lancet Microbe
    Article . 2022 . Peer-reviewed
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      The Lancet Microbe
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    Authors: Anna Boqué Ciurana; Melisa Ménendez; María Suárez Bilbao; Enric Aguilar;

    Surfing is one of the most popular activities in coastal tourism resorts. However, the sport depends strongly on the met-ocean weather conditions, particularly on the surface wind-generated waves that reach the coast. This study provides examples of how users? needs and user perspectives are considered by climate data specialists to develop needed, highly useful information addressing human and social needs. In this vein, the climate analysis of such data can provide input on the expected length of a surfing season, according to the surfer?s level of expertise. In addition, other water sports, such as SUP Wave and windsurfing, among others, might be indicated when surfing conditions are not optimal. Finally, the safety of surfers and other tourists who venture into the sea is also dependent on those conditions. We collaborated with the surfing community to define a series of indices for quantifying surfing days (SD), surfing days stratified by surfers? skills (SDS), alternate offers (AOs), and surfers? and swimmers? safety (SuS and SwS). These are of general applications but require wind and wave data at a very fine scale as the input. To illustrate the potential of our indices, we applied them to the Somo beach (Cantabria, Spain). We downscaled a global wave hindcast dataset covering a 30-year period to a spatial resolution of 100 m to obtain wave-surfing information at Somo?s surf spot. The results confirmed Somo?s status as a year-round surf spot, with SD values of 229.5 days/year and monthly values between 22 days/month and 16 days/month. SDS showed different seasonal peaks according to the surfers? skills. Beginners? conditions occurred more often in the summer (18.1 days/month in July), intermediate surfers? conditions appeared in the transitional seasons (14.1 days/month in April), and advanced and big-wave riders in the winter (15.1 days/month in January and 0.7 days/month, respectively). The AO index identified the SUP wave values of 216 days/year. Wind water sports presented values of 141.6 days/year; conversely, SUP sports were possible on only 7.4 days/year. SuS and SwS identified different seasonal hazard values, decreasing from the winter, autumn, and spring to minimum values in the summer. This research is within the INDECIS project (INDECIS is part of ERA4CS, an ERA-NET initiated by JPI Climate and funded by FORMAS (SE), DLR (DE), BMWFW (AT), IFD (DK), MINECO (ES), and ANR (FR) with co-funding by the European Union Grant 690462). This article publication was possible with the support of the Secretaria d’Universitats i Recerca del Departament d’Empresa i Coneixement de la Generalitat de Catalunya, the European Union (UE), and the European Social Fund (ESF) (Doctoral Research Grant 2021FI_B2 00147—Formació personal investigador novell).

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    Other literature type . Article . 2022 . Peer-reviewed
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      Other literature type . Article . 2022 . Peer-reviewed
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    Authors: Giulia I. Corsi; Swapnil Tichkule; Anna Rosa Sannella; Paolo Vatta; +5 Authors

    AbstractCryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human‐ and ruminant‐derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long‐term evolutionary consequences of these events. Our results suggest that increased globalization and close human‐animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host–parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

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