Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different ...vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact.
Abstract
We invoke a Gaussian mixture model (GMM) to jointly analyse two traditional emission-line classification schemes of galaxy ionization sources: the Baldwin–Phillips–Terlevich (BPT) and W
H α ...versus N ii/H α (WHAN) diagrams, using spectroscopic data from the Sloan Digital Sky Survey Data Release 7 and SEAGal/STARLIGHT data sets. We apply a GMM to empirically define classes of galaxies in a three-dimensional space spanned by the log O iii/H β, log N ii/H α and log EW(H α) optical parameters. The best-fitting GMM based on several statistical criteria suggests a solution around four Gaussian components (GCs), which are capable to explain up to 97 per cent of the data variance. Using elements of information theory, we compare each GC to their respective astronomical counterpart. GC1 and GC4 are associated with star-forming galaxies, suggesting the need to define a new starburst subgroup. GC2 is associated with BPT's active galactic nuclei (AGN) class and WHAN's weak AGN class. GC3 is associated with BPT's composite class and WHAN's strong AGN class. Conversely, there is no statistical evidence – based on four GCs – for the existence of a Seyfert/low-ionization nuclear emission-line region (LINER) dichotomy in our sample. Notwithstanding, the inclusion of an additional GC5 unravels it. The GC5 appears associated with the LINER and passive galaxies on the BPT and WHAN diagrams, respectively. This indicates that if the Seyfert/LINER dichotomy is there, it does not account significantly to the global data variance and may be overlooked by standard metrics of goodness of fit. Subtleties aside, we demonstrate the potential of our methodology to recover/unravel different objects inside the wilderness of astronomical data sets, without lacking the ability to convey physically interpretable results. The probabilistic classifications from the GMM analysis are publicly available within the COINtoolbox at https://cointoolbox.github.io/GMM_Catalogue/.
Climate change, alteration of atmospheric composition, land abandonment in some areas and land use intensification in others, wildfires and biological invasions threaten forests, shrublands and ...pastures all over the world. However, the impacts of the combinations between global change factors are not well understood despite its pressing importance. Here we posit that reviewing global change factors combination in an exemplary region can highlight the necessary aspects in order to better understand the challenges we face, warning about the consequences, and showing the challenges ahead of us. The forests, shrublands and pastures of the Mediterranean Basin are an ideal scenario for the study of these combinations due to its spatial and temporal heterogeneity, increasing and diverse human population and the historical legacy of land use transformations. The combination of multiple global change factors in the Basin shows different ecological effects. Some interactions alter the effects of a single factor, as drought enhances or decreases the effects of atmospheric components on plant ecophysiology. Several interactions generate new impacts: drought and land use changes, among others, alter water resources and lead to land degradation, vegetation regeneration decline, and expansion of forest diseases. Finally, different factors can occur alone or simultaneously leading to further increases in the risk of fires and biological invasions. The transitional nature of the Basin between temperate and arid climates involves a risk of irreversible ecosystem change towards more arid states. However, combinations between factors lead to unpredictable ecosystem alteration that goes beyond the particular consequences of drought. Complex global change scenarios should be studied in the Mediterranean and other regions of the world, including interregional studies. Here we show the inherent uncertainty of this complexity, which should be included in any management strategy.
•Different global change factors combine causing unprecedented ecological effects.•Much more complex interactions arise when combinations occur together.•Drought should be considered when designing and applying management policies.•Conserving Mediterranean terrestrial ecosystems is a collective effort.
1. Plants exhibit a wide variety in traits at different organizational levels. Intraspecific and interspecific studies have potential to demonstrate functional relationships and trade-offs amongst ...traits, with potential consequences for growth. However, the distinction between the correlative and functional nature of trait covariation presents a challenge because traits interact in complex ways. 2. We present an intraspecific study on Scots pine branches and use functional multi-trait concepts to organize and understand trait interactions and their impacts on growth. Branch-level traits were assessed for 97 branches from 12 Scots pine sites across Europe. 3. To test alternative hypotheses on cause-effect relationships between anatomical traits, hydraulic traits and branch growth, we measured for each branch: the tracheid hydraulic diameter, double cell wall thickness, cell lumen span area, wood density, cavitation vulnerability, wood-specific hydraulic conductivity, the leaf area to sapwood area ratio and branch growth. We used mixed linear effect models and path models to show how anatomical traits determine hydraulic traits and, in turn, how those traits influence growth. 4. Tracheid hydraulic diameter was the best predictor of cavitation vulnerability (R₂ = 0-09 explained by path model) and specific conductivity (R₂ = 0-19) amongst anatomical traits. Leaf area to sapwood area ratio had the strongest direct effect on branch growth (R₂ = 0-19) and was positively associated with the tracheid hydraulic diameter (R₂ = 0-22). A number of bivariate correlations between traits could be explained by these functional relationships amongst traits. 5. The plasticity in tracheid hydraulic diameter (10.0-15.1 um) and leaf area to sapwood area ratio (600-6051 cm₂ cm⁻₂) and the maintenance of a minimum leaf water potential (between -2 and -2.5 MPa) appear to drive the anatomical and hydraulic traits of Scots pine across Europe. These properties are major drivers of the functional trait network underlying the growth variation amongst pine branches and thus possibly contribute to the ecological success of pines at a local and continental scale.
The stay-at-home restrictions to control the spread of COVID-19 led to unparalleled sudden change in daily life, but it is unclear how they affected urban crime globally. We collected data on daily ...counts of crime in 27 cities across 23 countries in the Americas, Europe, the Middle East and Asia. We conducted interrupted time series analyses to assess the impact of stay-at-home restrictions on different types of crime in each city. Our findings show that the stay-at-home policies were associated with a considerable drop in urban crime, but with substantial variation across cities and types of crime. Meta-regression results showed that more stringent restrictions over movement in public space were predictive of larger declines in crime.
Slow paramagnetic relaxation was observed at low temperatures from ac susceptibility measurements in the form of a frequency‐dependent out‐of‐phase (χ$\rm{{{\prime \prime \hfill \atop {\rm ...m}\hfill}}}$) signal for the title complex (see picture). This provides compelling evidence that this cluster is a rare example of a cyanide‐bridged single‐molecule magnet.
Widespread tree species must show physiological and structural plasticity to deal with contrasting water balance conditions. To investigate these plasticity mechanisms, a meta-analysis of Pinus ...sylvestris L. sap flow and its response to environmental variables was conducted using datasets from across its whole geographical range. For each site, a Jarvis-type, multiplicative model was used to fit the relationship between sap flow and photosynthetically active radiation, vapour pressure deficit (D) and soil moisture deficit (SMD); and a logarithmic function was used to characterize the response of stomatal conductance (G s) to D. The fitted parameters of those models were regressed against climatic variables to study the acclimation of Scots pine to dry/warm conditions. The absolute value of sap flow and its sensitivity to D and SMD increased with the average summer evaporative demand. However, relative sensitivity of G s to D (m/G s,ref, where m is the slope and G s,ref is reference G s at D = 1 kPa) did not increase with evaporative demand across populations, and transpiration per unit leaf area at a given D increased accordingly in drier/warmer climates. This physiological plasticity was linked to the previously reported climate- and size-related structural acclimation of leaf to sapwood area ratios. G s,ref, and its absolute sensitivity to D (m), tended to decrease with age/height of the trees as previously reported for other pine species. It is unclear why Scots pines have higher transpiration rates at drier/warmer sites, at the expense of lower water-use efficiency. In any case, our results suggest that these structural adjustments may not be enough to prevent lower xylem tensions at the driest sites.
To deal with the challenging requirements of metropolitan area networks (MANs), it is essential to design cost-effective systems that can support high capacity and dynamic adaptation, as well as a ...synergy of programmability and efficient photonic technologies. This becomes crucial for very large MANs that support 5G, where multihop connections will need to be dynamically established at target capacities beyond Tb/s. Programmability, automation, and modularity of network elements are key desired features. In this work, a modular photonic system, programmable via a software-defined networking platform, designed for dynamic 5G-supportive MANs, is described and analyzed. We consider modular sliceable bandwidth/bit rate variable transceivers (S-BVTs) based on vertical-cavity surface-emitting laser (VCSEL) technology and dense photonic integration. The proposed system and its programmability are experimentally assessed using a VCSEL with 10 GHz bandwidth. The experiments are performed over connections as long as six-hop and 160 km, from low-level aggregation nodes to metro-core nodes, thereby enabling IP off-loading. Furthermore, a numerical model is derived to estimate the performance when adopting higher bandwidth VCSELs ({\ge} {18}\;{\rm GHz}≥18GHz) and integrated coherent receivers, as targeted in the proposed system. The analysis is performed for both 50 GHz and 25 GHz granularities. In the former case, 50 Gb/s capacity per flow can be supported over the targeted connections, for optical signal-to-noise ratio values above 26 dB. When the granularity is 25 GHz, the filter narrowing effect severely impacts the performance. Nevertheless, 1.2 Tb/s capacity (scalable to higher values if spectral/spatial dimensions are exploited) can be achieved when configuring the S-BVT to enable 40 VCSEL flows. This confirms that the system is promising to support Tb/s connections in future agile MANs.
To assess the quality of antifungal use, to propose a point score for this evaluation and to estimate the potential economic savings of an antifungal stewardship programme.
From December 2010 to ...January 2011, we identified 100 adult inpatients receiving systemic antifungals. Antifungal use was evaluated by means of a predefined score that considered indication, drug selection, dosage, adjustments after microbiology results, switching to an oral agent and length of treatment. Total antifungal prescriptions in defined daily doses (DDDs) and days of therapy (DOTs) and potential cost savings were calculated.
Overall, 43% of prescriptions came from medical departments, 25% from haematology/oncology and 17% from intensive care units. The main reasons for starting antifungals were empirical (42%), pre-emptive (20%) and targeted treatment (20%). Antifungals were unnecessary in 16% of cases. Inadequacies in other aspects of antifungal prescription were: drug selection, 31%; dosing, 16%; no switch from intravenous to oral administration, 20%; no adjustment after microbiological results, 35%; and length of therapy, 27%. The number of antifungal DDDs per 1000 patient-days was 65.1. The total number of DOTs was 1556, which added a direct cost of €219 364. Only 51.3% of DOTs were considered optimal. The potential estimated savings would be €50 536.
Major efforts should be made to improve the selection and duration of antifungal therapy. Our study demonstrated the potential cost savings that could be achieved by optimizing antifungal therapy. A stewardship programme should include an instrument to objectively evaluate the adequacy of antifungal use.
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