Testate amoebae as a hydrological proxy for reconstructing water-table depth in the mires of south-eastern Australia

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordAlthough it is well established that moisture availability in south-eastern Australia has been decreasing through time recently, the driver(s) of this trend are contentious, and our understanding of any drivers is limited by a relatively short historic record. Testate amoebae have been widely used to reconstruct peatland hydrology in the Northern Hemisphere, but in the Southern Hemisphere research is still needed to assess their proficiency as a palaeohydrological proxy and to develop robust transfer functions. Here we examine the ecology of testate amoebae in several high altitude mires in south-eastern Australia and present the first transfer function for the continent. Euglypha tuberculata type, Centropyxis platystoma type and Assulina muscorum were the most common taxa in our modern samples. Water-table depth was the primary environmental variable determining testate amoebae assemblages and therefore transfer functions were developed for this ecological factor. We found that the performance of various all-species and species-pruned transfer functions were statistically robust, with R2 values of around 0.8 and Root Mean Squared Error of Prediction (RMSEP) values of about 7 cm. All cross-validation methods (leave-one-out RMSEP, cluster-bootstrap RMSEP, segment-wise RMSEP and leave-one-site-out RMSEP from all-species and species-pruned transfer functions) suggested that the Modern Analogue Technique (MAT) was the best performing transfer function, with negligible bias evident from un-even sampling and spatial autocorrelation. We also used a new approach to evaluate the importance of taxa and the performance of our transfer functions using species-pruned methods. Our results suggest that the all-species MAT, with an RMSEP of 5.73 and R2 of 0.86, provides the best reconstruction of water-table depth across our sites in south-eastern Australia.Australian National Universit

Forecasting GOES 15 >2 MeV Electron Fluxes From Solar Wind Data and Geomagnetic Indices

The flux of > 2 MeV electrons at geosynchronous orbit is used by space weather forecasters as a key indicator of enhanced risk of damage to spacecraft in low, medium or geosynchronous Earth orbits. We present a methodology that uses the amount of time a single input dataset (solar wind data or geomagnetic indices) exceeds a given threshold to produce deterministic and probabilistic forecasts of the > 2 MeV flux at GEO exceeding 1000 or 10000 cm ‐2 s ‐1 sr ‐1 within up to 10 days. By comparing our forecasts with measured fluxes from GOES 15 between 2014 and 2016, we determine the optimum forecast thresholds for deterministic and probabilistic forecasts by maximising the ROC and Brier Skill Scores respectively. The training dataset gives peak ROC scores of 0.71 to 0.87 and peak Brier Skill Scores of ‐0.03 to 0.32. Forecasts from AL give the highest skill scores for forecasts of up to 6‐days. AL, solar wind pressure or SYM‐H give the highest skill scores over 7‐10 days. Hit rates range over 56‐89% with false alarm rates of 11‐53%. Applied to 2012, 2013 and 2017, our best forecasts have hit rates of 56‐83% and false alarm rates of 10‐20%. Further tuning of the forecasts may improve these. Our hit rates are comparable to those from operational fluence forecasts, that incorporate fluence measurements, but our false alarm rates are higher. This proof‐of‐concept shows that the geosynchronous electron flux can be forecast with a degree of success without incorporating a persistence element into the forecasts

Disability quotas: past or future policy?

This article considers the issues associated with the use of quota systems for the employment of workers with a disability. It examines the use and experiences of such quotas in Italy, Russia and the United Kingdom. Italy has a long established quota for the employment of such workers, whilst the modern Russian system it is a more recent innovation. In contrast the UK abandoned its quotas in the 1990s. We draw on the experiences of the three countries to consider generally whether the use of quotas is either an acceptable means of encouraging employers to take on disabled workers, or is necessary to achieve this objective

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Carbon related defects in irradiated silicon revisited

Electronic structure calculations employing hybrid functionals are used to gain insight into the interaction of carbon (C) atoms, oxygen (O) interstitials, and self-interstitials in silicon (Si). We calculate the formation energies of the C related defects C(i)(Si(I)), C(i)O(i), C(i)C(s), and C(i)O(i)(Si(I)) with respect to the Fermi energy for all possible charge states. The C(i)(Si(I))(2+) state dominates in almost the whole Fermi energy range. The unpaired electron in the C(i)O(i)(+) state is mainly localized on the C interstitial so that spin polarization is able to lower the total energy. The three known atomic configurations of the C(i)C(s) pair are reproduced and it is demonstrated that hybrid functionals yield an improved energetic order for both the A and B-types as compared to previous theoretical studies. Different structures of the C(i)O(i)(Si(I)) cluster result for positive charge states in dramatically distinct electronic states around the Fermi energy and formation energies

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

Does urbanization explain differences in interactions between an insect herbivore and its natural enemies and mutualists?

Urbanization can alter the composition of arthropod communities. However, little is known about how urbanization affects ecological interactions. Using experimental colonies of the black bean aphid Aphis fabae Scopoli reared on Vicia faba L, we asked if patterns of predator-prey, host-parasitoid and ant-aphid mutualisms varied along an urbanization gradient across a large town in southern England. We recorded the presence of naturally occurring predators, parasitoid wasps and mutualistic ants together with aphid abundance. We examined how biotic (green areas and plant richness) and abiotic features (impervious surfaces and distance to town center) affected (1) aphid colony size, (2) the likelihood of finding predators, mutualistic ants and aphid mummies (indicating the presence of parasitoids), and (3) how the interplay among these factors affected patterns of parasitoid attack, predator abundance, mutualistic interactions and aphid abundance. The best model to predict aphid abundance was the number of mutualistic ants attending the colonies. Aphid predators responded negatively to both the proportion of impervious surfaces and to the number of mutualistic ants farming the colonies, and positively to aphid population size, whereas parasitized aphids were found in colonies with higher numbers of aphids and ants. The number of mutualistic ants attending was positively associated with aphid colony size and negatively with the number of aphid predators. Our findings suggest that for insect-natural enemy interactions, urbanization may affect some groups, while not influencing others, and that local effects (mutualists, host plant presence) will also be key determinants of how urban ecological communities are formed