Nest survival of Tricolored Blackbirds in California\u27s Central Valley

The Tricolored Blackbird (Agelaius tricolor), almost entirely restricted to California, USA, has recently been proposed for listing under the U.S. Endangered Species Act. Tricolored Blackbirds historically nested in wetlands, but a large proportion of the population now nests in agricultural grain fields where the crop is ready to harvest before the young have fledged. Since 1991, federal agencies have paid farmers to delay harvesting in an effort to increase nesting productivity. However, the relative nesting success of Tricolored Blackbirds breeding in agricultural fields versus wetlands is unknown. Our objectives were to estimate daily survival rate (DSR) of nests, identify habitat covariates that influence nest survival, and estimate the number of young produced per nest. During 2011–2012, we monitored 1,323 Tricolored Blackbird nests in 12 colonies using small temperature data loggers. We modeled DSR using Program RMark with combinations of the following variables: site, habitat type, nest initiation date, nest height, water depth, nest density, colony population size, year, and the proportion of nearby nests that failed. Nest survival varied greatly (range: 0.024–0.719) but was not explained by habitat type. Nest height and nest density were positively associated with DSR. DSR was lowest midway through the breeding season and declined with colony population size. Number of young produced per nest varied by site, was lowest in intermediate-sized colonies of 1,000–5,000 birds, and was highest in 2011. DSR and number of young fledged per nest were similar in agricultural fields and in wetlands. Our results suggest that Tricolored Blackbirds benefit from policies that allow them to complete their nesting cycle in agricultural fields

Comparing Bird Population Trends in the Badlands and Prairies Using BBS and IMBCR Data

We compared the direction and precision of trend estimates of bird species in the Badlands and Prairie Bird Conservation Region (BCR 17) from 2009-2015 using Breeding Bird Survey (BBS) and Integrated Monitoring in Bird Conservation Regions (IMBCR) data. We used Bayesian modeling estimates provided by the BBS and newly developed Bayesian estimates of IMBCR data. Trend estimates often differed between the two data sets and estimates of precision were generally smaller for IMBCR than for BBS data. In addition, because the BBS estimates do not correct for detection probability, the BBS estimates measure the trend on an index rather than the detection corrected abundance. If the relationship between the BBS index and true abundance is not linear and 1:1, the interpretation of the BBS trend is unclear. Finally, because BBS counts are conducted along roads, species that are attracted to or avoid roads may be over or under counted, respectively. BBS trends can be helpful for examining long-term trends (greater than 20 years) in bird abundance across large regions but only IMBCR trends provide sufficient precision to examine trends at shorter time intervals. IMBCR trends, therefore, are more useful for identifying current factors influencing bird population trends

Gold substrate-induced single-mode lasing of GaN nanowires

We demonstrate a method for mode-selection by coupling a GaN nanowire laser to an underlying gold substrate. Multimode lasing of GaN nanowires is converted to single-mode behavior following placement onto a gold film. A mode-dependent loss is generated by the absorbing substrate to suppress multiple transverse-mode operation with a concomitant increase in lasing threshold of only ∼13%. This method provides greater flexibility in realizing practical single-mode nanowire lasers and offers insight into the design of metal-contacted nanoscale optoelectronics

Network substrates of cognitive impairment in Alzheimer's Disease

This is the final version. Available on open access from Elsevier via the DOI in this recordObjectives: Functional and structural disconnection of the brain is a prevailing hypothesis to explain cognitive impairment in Alzheimer's Disease (AD). We aim to understand the link between alterations to networks and cognitive impairment using functional connectivity analysis and modelling. Methods: EEG was recorded from 21 AD patients and 26 controls, mapped into source space using eLORETA, and functional connectivity was calculated using phase locking factor. The mini-mental state exam (MMSE) was used to assess cognitive impairment. A computational model was used to uncover mechanisms of altered functional connectivity. Results: Small-worldness (SW) of functional networks decreased in AD and was positively correlated with MMSE score and the language sub-score. Reduced SW was a result of increased path lengths, predominantly localized to the temporal lobes. Combining observed differences in local oscillation frequency with reduced temporal lobe effective connectivity in the model could account for observed functional network differences. Conclusions: Temporal lobe disconnection plays a key role in cognitive impairment in AD. Significance: We combine electrophysiology, neuropsychological scores, and computational modelling to provide novel insight into the relationships between the disconnection hypothesis and cognitive decline in AD.Engineering and Physical Sciences Research Council (EPSRC)Wellcome TrustAlzheimer's SocietyGarfield Weston FoundationUniversity of Bristo

Isolating the effects of land use and functional variation on Yucatán's forest biomass under global change

Tropical forests hold large stocks of carbon in biomass and face pressures from changing climate and anthropogenic disturbance. Forests' capacity to store biomass under future conditions and accumulate biomass during regrowth after clearance are major knowledge gaps. Here we use chronosequence data, satellite observations and a C-cycle model to diagnose woody C dynamics in two dry forest ecotypes (semi-deciduous and semi-evergreen) in Yucatán, Mexico. Woody biomass differences between mature semi-deciduous (90 MgC ha−1) and semi-evergreen (175 MgC ha−1) forest landscapes are mostly explained by differences in climate (c. 60%), particularly temperature, humidity and soil moisture effects on production. Functional variation in foliar phenology, woody allocation, and wood turnover rate explained c. 40% of biomass differences between ecotypes. Modeling experiments explored varied forest clearance and regrowth cycles, under a range of climate and CO2 change scenarios to 2100. Production and steady state biomass in both ecotypes were reduced by forecast warming and drying (mean biomass 2021–2100 reduced 16–19% compared to 2001–2020), but compensated by fertilisation from rising CO2. Functional analysis indicates that trait adjustments amplify biomass losses by 70%. Experiments with disturbance and recovery across historically reported levels indicate reductions to mean forest biomass stocks over 2021–2100 similar in magnitude to climate impacts (10–19% reductions for disturbance with recovery). Forest disturbance without regrowth amplifies biomass loss by three- or four-fold. We conclude that vegetation functional differences across the Yucatán climate gradient have developed to limit climate risks. Climate change will therefore lead to functional adjustments for all forest types. These adjustments are likely to magnify biomass reductions caused directly by climate change over the coming century. However, the range of impacts of land use and land use change are as, or more, substantive than the totality of direct and indirect climate impacts. Thus the carbon storage of Yucatan's forests is highly vulnerable both to climate and land use and land use change. Our results here should be used to test and enhance land surface models use for dry forest carbon cycle assessment regionally and globally. A single plant functional type approach for modeling Yucatán's forests is not justified

Sustainability appraisal: Jack of all trades, master of none?

Sustainable development is a commonly quoted goal for decision making and supports a large number of other discourses. Sustainability appraisal has a stated goal of supporting decision making for sustainable development. We suggest that the inherent flexibility of sustainability appraisal facilitates outcomes that often do not adhere to the three goals enshrined in most definitions of sustainable development: economic growth, environmental protection and enhancement, and the wellbeing of the human population. Current practice is for sustainable development to be disenfranchised through the interpretation of sustainability, whereby the best alternative is good enough even when unsustainable. Practitioners must carefully and transparently review the frameworks applied during sustainability appraisal to ensure that outcomes will meet the three goals, rather than focusing on a discourse that emphasises one or more goals at the expense of the other(s)

The Asteroseismic Poltential of TESS: Exoplanet-Host Stars

New insights on stellar evolution and stellar interior physics are being made possible by asteroseismology. Throughout the course of the Kepler mission, asteroseismology has also played an important role in the characterization of exoplanet-host stars and their planetary systems. The upcoming NASA Transiting Exoplanet Survey Satellite (TESS) will be performing a near all-sky survey for planets that transit bright nearby stars. In addition, its excellent photometric precision, combined with its fine time sampling and long intervals of uninterrupted observations, will enable asteroseismology of solar-type and red-giant stars. Here we develop a simple test to estimate the detectability of solar-like oscillations in TESS photometry of any given star. Based on an all-sky stellar and planetary synthetic population, we go on to predict the asteroseismic yield of the TESS mission, placing emphasis on the yield of exoplanet-host stars for which we expect to detect solar-like oscillations. This is done for both the target stars (observed at a 2-minute cadence) and the full-frame-image stars (observed at a 30-minute cadence). A similar exercise is also conducted based on a compilation of known host stars. We predict that TESS will detect solar-like oscillations in a few dozen target hosts (mainly subgiant stars but also in a smaller number of F dwarfs), in up to 200 low-luminosity red-giant hosts, and in over 100 solar-type and red-giant known hosts, thereby leading to a threefold improvement in the asteroseismic yield of exoplanet-host stars when compared to Kepler's.Science and Technology Facilities Council (Great Britain

Three-dimensional CFD simulations with large displacement of the geometries using a connectivity-change moving mesh approach

This paper deals with three-dimensional (3D) numerical simulations involving 3D moving geometries with large displacements on unstructured meshes. Such simulations are of great value to industry, but remain very time-consuming. A robust moving mesh algorithm coupling an elasticity-like mesh deformation solution and mesh optimizations was proposed in previous works, which removes the need for global remeshing when performing large displacements. The optimizations, and in particular generalized edge/face swapping, preserve the initial quality of the mesh throughout the simulation. We propose to integrate an Arbitrary Lagrangian Eulerian compressible flow solver into this process to demonstrate its capabilities in a full CFD computation context. This solver relies on a local enforcement of the discrete geometric conservation law to preserve the order of accuracy of the time integration. The displacement of the geometries is either imposed, or driven by fluid–structure interaction (FSI). In the latter case, the six degrees of freedom approach for rigid bodies is considered. Finally, several 3D imposed-motion and FSI examples are given to validate the proposed approach, both in academic and industrial configurations

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types