bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective assessment of rapid outbreak investigation for gastrointestinal diseases using only cases and background exposure data
Authors: Kafatos G. , Mook P. , Charlett A. , Rees E. , Elson R. , Inns T. , Kanagarajah S. , Andrews N. J. 
Published: February 2020

Abstract
For outbreaks of gastrointestinal disease, rapid identification of the source is crucial to enable public health intervention and prevent further cases. Outbreak investigation comprises analyses of exposure information from cases and, if required, undertaking analytical epidemiological studies. Hypothesis generation has been reliant on empirical knowledge of exposures historically associated with a given pathogen. Epidemiology studies are resource-intensive and prone to bias, one of the reasons being the difficulties in recruiting appropriate controls. For this paper, the information from cases was compared against pre-defined background exposure information. As exemplars, three past outbreaks were used, one of common and two of rare exposures. Information from historical case trawling questionnaires was used to define background exposure having removed any exposures implicated with the outbreak. The case-background approach showed good sensitivity and specificity, identifying correctly all outbreak-related exposures. One additional exposure related to a retailer was identified and four food items where all cases had been exposed. In conclusion, the case-background method, a development of the case-case design, can be used to assist with hypothesis generation or when a case-control study may not be possible to carry out.
Seasonality in carriage of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in the general population: a pooled analysis of nationwide cross-sectional studies
Authors: Wielders C. C. H. , Van Duijkeren E. , Van Den Bunt G. , Meijs A. P. , Dierikx C. M. , Bonten M. J. M. , Van Pelt W. , Franz E. , De Greeff S. C. 
Published: February 2020

Abstract
Infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are often preceded by asymptomatic carriage. Higher incidences in enteric infectious diseases during summer have been reported. Here, we assessed whether the presence of seasonality in intestinal ESBL-Escherichia coli/Klebsiella pneumoniae (ESBL-E/K) carriage in the general Dutch population exists. From 2014 to 2017, the faecal carriage of ESBL-E/K in healthy individuals was determined in three cross-sectional studies in the Netherlands, including 5985 subjects. Results were pooled to identify seasonal trends in prevalence (by month of sampling). Multivariate logistic regression analysis was used to calculate pooled odds ratios and 95% confidence intervals. Results were adjusted for age, sex, antibiotic use and travel. Overall prevalence of ESBL-E/K carriage was 4.3% (n = 260 ESBL-E/K-positive), with differences between months ranging from 2.6% to 7.4%. Compared to January, the monthly prevalence of ESBL-E carriage was highest in August (OR 1.88, 95% CI 1.02–3.49) and September (OR 2.25, 95% CI 1.30–3.89). The observed monthly differences in ESBL-E/K carriage rates suggest that there is seasonal variation in exposure to ESBL-E/K other than due to travelling and antibiotic use. This should be taken into account in designing future ESBL-E prevalence studies in temperate regions.
Low temperature stimulates spatial molecular reprogramming of theArabidopsisseed germination programme
Authors: Mitchell Jack , Mukhtar Nur K. , Bassel George W. 
Published: February 2020

AbstractThe timing of the germination of seeds is highly responsive to inputs from the environment. Temperature plays a key role in the control of germination, with low temperatures acting to stimulate this developmental transition in many species. InArabidopsis, extensive gene expression changes have been reported at the whole seed level in response to cold, while much less is known about their spatial distribution across the diverse cell types of the embryo. In this study we examined the spatiotemporal patterns of promoter activity and protein abundance for key gibberellic acid (GA) and abscisic acid (ABA) factors which regulate the decision to germinate both during a time course of germination and in response to cold. Low temperature stimulated the spatial relocalization of these factors to the vasculature. The response of these seeds to dormancy-breaking stratification treatments therefore stimulates the distribution of both positive (GA) and negatively acting (ABA) components to this same cell type. This altered spatial pattern persisted following the transfer of seeds to 22°C, as well as after their rehydration, indicating that this alteration is persistent. These observations suggest that the vasculature plays a role in the low temperature-mediated stimulation of germination in this species, while novel cell types are recruited to promote germination in response to stratification.
Comparative efficacy of antimicrobial treatments in dairy cows at dry-off to prevent new intramammary infections during the dry period or clinical mastitis during early lactation: a systematic review and network meta-analysis
Authors: Winder C. B. , Sargeant J. M. , Hu D. , Wang C. , Kelton D. F. , Leblanc S. J. , Duffield T. F. , Glanville J. , Wood H. , Churchill K. J. , Dunn J. , Bergevin M. D. , Dawkins K. , Meadows S. , Deb B. , Reist M. , Moody C. , O'Connor A. M. 
Published: February 2020

AbstractA systematic review and network meta-analysis were conducted to assess the relative efficacy of antimicrobial therapy given to dairy cows at dry-off. Eligible studies were controlled trials assessing the use of antimicrobials compared to no treatment or an alternative treatment, and assessed one or more of the following outcomes: incidence of intramammary infection (IMI) at calving, incidence of IMI during the first 30 days in milk (DIM), or incidence of clinical mastitis during the first 30 DIM. Databases and conference proceedings were searched for relevant articles. The potential for bias was assessed using the Cochrane Risk of Bias 2.0 algorithm. From 3480 initially identified records, 45 trials had data extracted for one or more outcomes. Network meta-analysis was conducted for IMI at calving. The use of cephalosporins, cloxacillin, or penicillin with aminoglycoside significantly reduced the risk of new IMI at calving compared to non-treated controls (cephalosporins, RR = 0.37, 95% CI 0.23–0.65; cloxacillin, RR = 0.55, 95% CI 0.38–0.79; penicillin with aminoglycoside, RR = 0.42, 95% CI 0.26–0.72). Synthesis revealed challenges with a comparability of outcomes, replication of interventions, definitions of outcomes, and quality of reporting. The use of reporting guidelines, replication among interventions, and standardization of outcome definitions would increase the utility of primary research in this area.
The efficacy of antibiotics to control colibacillosis in broiler poultry: a systematic review
Authors: Sargeant Jan M. , Bergevin Michele D. , Churchill Katheryn , Dawkins Kaitlyn , Deb Bhumika , Dunn Jennifer , Logue Catherine M. , Novy Anastasia , O'Connor Annette M. , Reist Mark , Winder Charlotte B. 
Published: February 2020

AbstractThe objective of this systematic review was to evaluate the efficacy of antibiotics to prevent or control colibacillosis in broilers. Studies found eligible were conducted controlled trials in broilers that evaluated an antibiotic intervention, with at least one of the following outcomes: mortality, feed conversion ratio (FCR), condemnations at slaughter, or total antibiotic use. Four electronic databases plus the gray literature were searched. Abstracts were screened for eligibility and data were extracted from eligible trials. Risk of bias was evaluated.Seven trials reported eligible outcomes in a format that allowed data extraction; all reported results for FCR and one also reported mortality. Due to the heterogeneity in the interventions and outcomes evaluated, it was not feasible to conduct meta-analysis.Qualitatively, for FCR, comparisons between an antibiotic and an alternative product did not show a significant benefit for either. Some of the comparisons between an antibiotic and a no-treatment placebo showed a numerical benefit to antibiotics, but with wide confidence intervals. The risk-of-bias assessment revealed concerns with reporting of key trial features.The results of this review do not provide compelling evidence for or against the efficacy of antibiotics for the control of colibacillosis.
Comparative efficacy of antimicrobials for treatment of clinical mastitis in lactating dairy cattle: a systematic review and network meta-analysis
Authors: Winder C. B. , Sargeant J. M. , Hu D. , Wang C. , Kelton D. F. , Godkin M. A. , Churchill K. J. , O'Connor A. M. 
Published: February 2020

AbstractA systematic review and network meta-analysis were conducted to assess the relative efficacy of antimicrobial therapy for clinical mastitis in lactating dairy cattle. Controlled trials in lactating dairy cattle with natural disease exposure were eligible if they compared an antimicrobial treatment to a non-treated control, placebo, or a different antimicrobial, for the treatment of clinical mastitis, and assessed clinical or bacteriologic cure. Potential for bias was assessed using a modified Cochrane Risk of Bias 2.0 tool. From 14775 initially identified records, 54 trials were assessed as eligible. Networks were established for bacteriologic cure by bacterial species group, and clinical cure. Disparate networks among bacteriologic cures precluded meta-analysis. Network meta-analysis was conducted for trials assessing clinical cure, but lack of precision of point estimates resulted in wide credibility intervals for all treatments, with no definitive conclusions regarding relative efficacy. Consideration of network geometry can inform future research to increase the utility of current and previous work. Replication of intervention arms and consideration of connection to existing networks would improve the future ability to determine relative efficacy. Challenges in the evaluation of bias in primary research stemmed from a lack of reporting. Consideration of reporting guidelines would also improve the utility of future research.
Use your power for good: plural valuation of nature – the Oaxaca statement
Authors: Jacobs Sander , Zafra-Calvo Noelia , Gonzalez-Jimenez David , Guibrunet Louise , Benessaiah Karina , Berghöfer Augustin , Chaves-Chaparro Juliana , Díaz Sandra , Gomez-Baggethun Erik , Lele Sharachchandra , Martín-López Berta , Masterson Vanessa Anne , Merçon Juliana , Moersberger Hannah , Muraca Barbara , Norström Albert , O'Farrell Patrick , Ordonez Jenny C. , Prieur-Richard Anne-Hélène , Rincón-Ruiz Alexander , Sitas Nadia , Subramanian Suneetha M. , Tadesse Wubalem , van Noordwijk Meine , Pascual Unai , Balvanera Patricia 
Published: February 2020

Non-technical abstract
Decisions on the use of nature reflect the values and rights of individuals, communities and society at large. The values of nature are expressed through cultural norms, rules and legislation, and they can be elicited using a wide range of tools, including those of economics. None of the approaches to elicit peoples’ values are neutral. Unequal power relations influence valuation and decision-making and are at the core of most environmental conflicts. As actors in sustainability thinking, environmental scientists and practitioners are becoming more aware of their own posture, normative stance, responsibility and relative power in society. Based on a transdisciplinary workshop, our perspective paper provides a normative basis for this new community of scientists and practitioners engaged in the plural valuation of nature.
High‐Resolution Numerical Modeling of Heat and Volatile Transfer from Basalt to Wall Rock: Application to the Crustal Column beneath Long Valley Caldera, CA
Authors: Calogero M. A. , Hetland E. A. , Lange R. A. 
Published: February 2020

AbstractWe present a high‐resolution numerical model of the thermal evolution of the crustal column beneath Long Valley caldera, California, from which >800 km3 rhyolite erupted over the last 2.2 Myr. We examine how randomly emplaced basaltic sills of variable thickness (10, 50, or 100 m) at various depth intervals (10–25 km) and at variable emplacement rates (5–50 m/kyr) gradually heat the crust and lead to a variably mixed crustal lithology (solidified mafic sills and preexisting granitoid). We additionally explore the time scales over which dissolved water (~3 wt%) in a newly emplaced basaltic sill exsolves during crystallization and is transferred to adjacent wall rock that is undergoing partial melting. We employ a finite‐difference‐based technique, with variable spatial (≥1 m to ≥10 km) and temporal (<100 and > 106 years) resolution, that enables dense analysis within and directly adjacent to a newly emplaced sill. Our results show that once ambient crustal temperatures reach ~500–600 °C, subsequent injections of basaltic sills lead to significant partial melting of adjacent wall rock (granitoid and solidified mafic sills) on time scales (101–102 years) that match those of exsolution of H2O‐rich fluid from basaltic sills. Large volumes of fusion (>10%) during fluid‐undersaturated partial melting, combined with the preexisting occurrence of aplite dikes, facilitates the development of melt‐filled fractures that exceed the critical length for self‐propagation. The advection of wall‐rock partial melts (with a combined mantle‐derived and crustal geochemical signature) to shallower depths will alter both the thermal and compositional profile of the middle‐upper crust.
The Complex Vertical Motion of Intraplate Oceanic Islands Assessed in Santiago Island, Cape Verde
Authors: Marques F. O. , Hildenbrand A. , Zeyen H. , Cunha C. , Victória S. S. 
Published: February 2020

AbstractDated paleosea level markers and eustatic sea level changes are necessary but not sufficient information to calculate vertical motion rates on oceanic islands. Therefore, we use a procedure in which we work progressively back in time to incorporate the more recent vertical motion rates implied by the youngest paleoshorelines into the vertical motion history of all older shorelines. Specifically, we calculate the time‐averaged vertical motion rates required to explain the present‐day elevations of the dated sequence of paleoshorelines on Santiago volcanic island (Cape Verde). We thus obtain a vertical motion history consisting of time‐averaged vertical motion rates spanning the five intervening periods between paleoshoreline formation and the present day: (1) 5.06 to 3.29 Ma—seamount growth or island subsidence because all the rocks in this period are submarine; (2) fast uplift (approximately 0.96 mm/a) from 3.29 to 2.87 Ma, mostly responsible for putting submarine lavas currently close to 410 m altitude; (3) relatively fast subsidence (approximately −0.11 mm/a) between 2.87 and 2.18 Ma; (4) stagnation from 2.18 to 0.811 Ma; and (5) relatively fast uplift (approximately 0.14 mm/a) between 0.811 and 0 Ma. We numerically tested top‐down (volcanic loading) and bottom‐up (lithosphere thinning, underplating, and mantle plume) mechanisms to explain the inferred vertical movements, and we conclude that volcanic loading and crustal underplating are capable of producing the observed subsidence and uplift, respectively.
Eddy‐Driven Cross‐Shelf Transport in the East Australian Current Separation Zone
Authors: Malan Neil , Archer Matthew , Roughan Moninya , Cetina‐Heredia Paulina , Hemming Michael , Rocha Carlos , Schaeffer Amandine , Suthers Iain , Queiroz Eduardo 
Published: February 2020

AbstractIn western boundary current systems, sharp velocity gradients between the poleward flowing jet and coastal waters generally act to inhibit cross‐shelf exchange. Downstream of jet separation, dynamic mesoscale eddies dominate the flow. In the East Australian Current System, counter‐rotating eddy dipoles are often present which, in the appropriate configuration, have potential to drive cross‐shelf transport. However, this eddy dipole mode is poorly understood in the framework of cross‐shelf exchange and the effect of these structures on shelf waters is uncertain. Using 25 years of satellite altimetry, as well as in situ sampling of a typical dipole event, we investigate the characteristics of eddy‐driven cross‐shelf exchange. We show that the maximum onshore velocity is driven by an eddy dipole structure and occurs in a defined latitudinal band between 33°S and 34°S more than 50% of the time. We sample a typical eddy dipole and find a strong onshore jet, 37 km wide, with velocities up to 1.78 m s
and a transport of at least 16 Sv. Hydrographic data from an autonomous underwater glider show that this jet manifests on the shelf as a subsurface intrusion of warm salty water extending from offshore up onto the midshelf. In the light of climatic changes in western boundary current transport and the increase in their eddy kinetic energy, understanding eddy‐driven cross‐shelf exchange is important to predict future changes to the shelf water mass.
Time Scale Dependence of the Meridional Coherence of the Atlantic Meridional Overturning Circulation
Authors: Gu Sifan , Liu Zhengyu , Wu Lixin 
Published: February 2020

AbstractThe Atlantic Meridional Overturning Circulation (AMOC) variability is suggested to be incoherent between the subpolar and subtropical gyres in the Atlantic on interannual and even decadal time scales, questioning the representativeness of AMOC variability at a single latitude in modern observation and paleoreconstruction. Paleoreconstructions of the Florida Current transport suggest that Florida Current variability is associated with the AMOC on the millennial time scale, but the Rapid Climate Change (RAPID) mooring array suggests a weak correlation between the Florida Current and the AMOC. In this study, we investigate the meridional coherence of AMOC variability and the relationship between the Florida Current variability and the AMOC variability on different time scales in a transient 20,000‐year simulation. We find that with the increase of time scales, the meridional coherence of the AMOC increases. On decadal and longer time scales, the coherent subtropical and subpolar AMOC is caused by the coherent buoyancy forcing in the subpolar gyre. Also, the Florida Current transport is highly correlated with AMOC variability on decadal and longer time scales, suggesting that observations of the Florida Current can be used to indicate AMOC variability on long time scales.
Predicting Internal Solitary Waves in the Gulf of Maine
Authors: Shen Hui , Perrie Will , Johnson Catherine L. 
Published: February 2020

AbstractInternal solitary waves (ISWs) are important physical processes in the Gulf of Maine (GoM), which is one of the most productive ecosystems of the Northwest Atlantic. In order to understand the roles that ISWs play, it is necessary to have synthesized knowledge of their timing and distributions. We detail the ISW spatial distribution patterns in the GoM using modern high‐resolution satellite imagery. A prediction methodology is suggested based on the speed of mode‐1 ISWs, which is cross validated using three methods: Remote sensing based on positional displacements of ISWs strips in continuous images, theoretical analysis based on climatological ocean stratification, and an empirical method based on bathymetry. Prediction accuracy is further validated by independently collected high spatial resolution satellite images from multiple sensors. We found a new‐generation site for ISWs near Grand Manan, with wave crests extending over the entire GoM. Interference of ISWs originating from the new‐generation site and the well‐known generation location on Georges Bank, plus local‐scale ISW generation sites, creates cross‐sea conditions within the water column, resulting in complex ISWs. We find that the background barotropic currents do not significantly influence the ISW spatial distributions, which simplifies the prediction of ISWs; we also consider the influence of tidal currents, general circulation, and stratification. This methodology is potentially useful for additional studies, for example, linking ISWs, energy and nutrient budgets, mixing, and primary production in the Gulf of Maine.
The Magnitude and Drivers of Methane Ebullition and Diffusion Vary on a Longitudinal Gradient in a Small Freshwater Reservoir
Authors: McClure R. P. , Lofton M. E. , Chen S. , Krueger K. M. , Little J. C. , Carey C. C. 
Published: February 2020

Key Points

CH4 ebullition rates decreased by 98% and CH4 diffusion decreased by 32% on a longitudinal gradient from reservoir inflow to dam
Ebullition was driven by physical variables upstream and phytoplankton downstream; diffusion was most related to phytoplankton
Despite large variation in CH4 emissions longitudinally, time series models well captured the dynamics of emissions from a small reservoir
MHD Modeling of the Background Solar Wind in the Inner Heliosphere From 0.1 to 5.5 AU: Comparison With In Situ Observations
Authors: Wang Y. X. , Guo X. C. , Wang C. , Florinski V. , Shen F. , Li H. , Blanc M. 
Published: February 2020

AbstractThe accurate prediction of solar wind conditions in the interplanetary space is crucial in the context of both scientific research and technical applications. In this study, we simulate the solar wind throughout the heliosphere from 0.1 to 5.5 astronomical units (AU) with our improved heliospheric magnetohydrodynamics (MHD) model during the time period from 2007 to 2017. The model uses synoptic magnetogram maps as input to derive the inner boundary conditions based on a series of empirical relations such as the Wang‐Sheeley‐Arge (WSA) relation. To test the performance of this model, we compare the simulation results with in situ measurements from multiple spacecraft including ACE/WIND, Solar TErrestrial Relations Observatory, Ulysses, Juno, and MErcury Surface, Space ENvironment, GEochemistry, and Ranging at different latitudes and heliocentric distances. There is an overall agreement between the model results and solar wind observations at different latitudes and heliocentric distances. Statistical analysis for Year 2007 reveals that our model can predict most of the corotation interaction regions, high‐speed streams, and magnetic sector boundaries at 1 AU. In addition, the bimodal structure of the solar wind for different latitudes is well reproduced by the model which is consistent with Ulysses data. This study demonstrates the capabilities of our heliosphere model in the prediction of the large‐scale structures of the solar wind in the inner heliosphere, and the model can be used to predict the ambient solar wind at locations of planets in the solar system such as Earth and Jupiter.