A nose for trouble: ecotoxicological implications for climate change and disease in Saiga antelope (S. t. tatarica).

In recent decades, Saiga antelope (Saiga t. tatarica) mass die-offs have become more common. The mass die-off of 2015 in central Kazakhstan, recorded 140,000 individual deaths across multiple herds. Previously, research has shown atmospheric humidity, the bacterium Pasteurella multocida serotype B, and resultant haemorrhagic septicaemia, were the primary cause. However, other synergistic factors may have impacted this process. Here we use a multivariate compositional data analysis (CoDA) approach to assess what other factors may have been involved. We show a pollutant linkage mechanism where relative humidity and dewpoint temperature combine with environmental pollutants, potentially toxic elements (e.g., Hg, As), complex carbon compounds (e.g., Acetone, Toluene), and inorganic compounds (e.g., CHx, SO2) which affected the Saiga during the calving season (start and peak) and at the onset of the mass die-off. We suggest a mechanism for this process. Upon arrival at their carving grounds, the Saiga experienced a sudden precipitation event, a spike in temperatures, and resultant high humidity occurs. The infectious bacterium P. multocida serotype B then spreads. Further, environmental pollutants contained within steppe soils are released to the air, forming localised smog events, these synergistically combine, and mass die-off occurs.

Dead-reckoning elucidates fine-scale habitat use by European badgers Meles meles.

Background: Recent developments in both hardware and software of animal-borne data loggers now enable large amounts of data to be collected on both animal movement and behaviour. In particular, the combined use of tri-axial accelerometers, tri-axial magnetometers and GPS loggers enables animal tracks to be elucidated using a procedure of 'dead-reckoning'. Although this approach was first suggested 30 years ago by Wilson et al. (1991), surprisingly few measurements have been made in free-ranging terrestrial animals. The current study examines movements, interactions with habitat features, and home-ranges calculated from just GPS data and also from dead-reckoned data in a model terrestrial mammal, the European badger (Meles meles). Methods: Research was undertaken in farmland in Northern Ireland. Two badgers (one male, one female) were live-trapped and fitted with a GPS logger, a tri-axial accelerometer, and a tri-axial magnetometer. Thereafter, the badgers' movement paths over 2 weeks were elucidated using just GPS data and GPS-enabled dead-reckoned data, respectively. Results: Badgers travelled further using data from dead-reckoned calculations than using the data from only GPS data. Whilst once-hourly GPS data could only be represented by straight-line movements between sequential points, the sub-second resolution dead-reckoned tracks were more tortuous. Although there were no differences in Minimum Convex Polygon determinations between GPS- and dead-reckoned data, Kernel Utilisation Distribution determinations of home-range size were larger using the former method. This was because dead-reckoned data more accurately described the particular parts of landscape constituting most-visited core areas, effectively narrowing the calculation of habitat use. Finally, the dead-reckoned data showed badgers spent more time near to field margins and hedges than simple GPS data would suggest. Conclusion: Significant differences emerge when analyses of habitat use and movements are compared between calculations made using just GPS data or GPS-enabled dead-reckoned data. In particular, use of dead-reckoned data showed that animals moved 2.2 times farther, had better-defined use of the habitat (revealing clear core areas), and made more use of certain habitats (field margins, hedges). Use of dead-reckoning to provide detailed accounts of animal movement and highlight the minutiae of interactions with the environment should be considered an important technique in the ecologist's toolkit.

Application of HRGS for forensic characterization of uranium oxides, pure uranium metals and uranium alloys.

A nondestructive iterative method for uranium-bearing material characterization with HRGS developed earlier in Burdeinyi et al. (2020) is applied to determine matrix densities, uranium mass fraction and uranium isotope masses of uranium ore, UO2 and U3O8 powders, fuel elements in the form of UO2 microspheres, uranium metal and uranium alloys. It is shown that U3O8 powders with uranium mass fraction of about 84% can be distinguished from the powders of UO2 with uranium mass fraction of about 87%; uranium products in the form of liquid or loose powder with matrix density of 0.5-2.0g/cm3 can be distinguished from uranium products in the form of compacted fuel elements with matrix density of 6.0-10.0g/cm3 and from pure metal uranium and uranium alloys with matrix density of 14.0-19.0g/cm3. In fuel microspheres based on UO2 the uranium mass fraction 88.02% measured by HRGS is consistent, within the measurement uncertainties, with the results of isotope dilution mass spectrometry 87.76±0.64% and also is confirmed by X-ray diffraction technique. The uranium mass fraction of the uranium ore estimated as 0.08% by HRGS is consistent, within the measurement uncertainties, with the value 0.09±0.01% determined with WDXRF. Densities of two different uranium metal samples, estimated as 18.42g/cm3 and 19.33g/cm3 by HRGS are consistent with values 18.24±0.55g/cm3 and 18.86±0.59g/cm3, respectively, obtained by the gas pycnometry technique.

Estimating the case fatality ratio for COVID-19 using a time-shifted distribution analysis.

Estimating the case fatality ratio (CFR) for COVID-19 is an important aspect of public health. However, calculating CFR accurately is problematic early in a novel disease outbreak, due to uncertainties regarding the time course of disease and difficulties in diagnosis and reporting of cases. In this work, we present a simple method for calculating the CFR using only public case and death data over time by exploiting the correspondence between the time distributions of cases and deaths. The time-shifted distribution (TSD) analysis generates two parameters of interest: the delay time between reporting of cases and deaths and the CFR. These parameters converge reliably over time once the exponential growth phase has finished. Analysis is performed for early COVID-19 outbreaks in many countries, and we discuss corrections to CFR values using excess-death and seroprevalence data to estimate the infection fatality ratio (IFR). While CFR values range from 0.2% to 20% in different countries, estimates for IFR are mostly around 0.5-0.8% for countries that experienced moderate outbreaks and 1-3% for severe outbreaks. The simplicity and transparency of TSD analysis enhance its usefulness in characterizing a new disease as well as the state of the health and reporting systems.

The role of the 2D-to-3D transition in x-ray diffraction analysis of crystallite size.

The diffraction behaviour of stacked layers of graphene and hexagonal boron nitride are studied computationally by direct calculation of the diffraction pattern using the Debye scattering equation. Analysis of the position and profile of the diffraction peaks show that while single-layer graphene is unambiguously a 2D material, ordered stacks of three or more layers diffract as bulk material. Following the Scherrer equation, we correlate the known crystallite size with the diffraction peak parameters and observe strong affine relationships which exist separately for single-layer, bi-layer and three or more layer (bulk) structures. We determine a series of expressions to calculate the crystallite size which do not suffer the well-known size-dependence or rely on assumptions about the shape. We present a detailed workflow showing how these expressions can be applied to experimental data.

Heavy metal (PTE) ecotoxicology, data review: Traditional vs. a compositional approach.

Potentially Toxic Elements (PTEs) otherwise known as heavy metals are ubiquitous in soils and can have a range of negative health and environmental impacts. In terrestrial systems understanding how PTEs move in the environment is made challenging by the complex interactions within soil and the wider environment and the compositional nature of PTEs. PTEs are compositional because data of individual PTEs within in a sample are ratios which may be under a sum constraint, where individual components sum up to a whole. In this study three different scenarios were considered, one using the centred log ratio transformation (clr) a compositional transformation, the more "traditional" log10 transformation (log10) and untransformed data acting as a comparison (unt) were applied to four different datasets. Three were the Liver, Muscle and Kidney tissue of Eurasian Badgers (Meles meles) and the fourth was soil and data were extracted from a regional geospatial survey. Cluster analysis demonstrated that the clr and log10 transformation were able to resolve compositional trends at the point of the individual sample, whilst unt could not and did not meet the preconditions for the next phase of analysis. At the level of compositional trends between PTEs complex heatmaps demonstrated that clr was able to isolate PTE relationships and highlight commonalities between different datasets, whilst log10 could not. In the final phase, principal component analysis (PCA) of the clr transformation showed similarities between the signals in the soft tissues and the disparities they had with soil, whilst the log10 transformation was unable to achieve this. Overall, the clr transformation was shown to perform more consistently under a variety of analytical scenarios and the compositional approach will provide more realistic interpretations about PTEs in both soil and animal soft tissue than the log10 or unt conditions.

Potentially toxic element accumulation in badgers (Meles meles): a compositional approach.

Potentially Toxic Elements (PTEs) in Badgers (Meles meles), otherwise known as heavy metals, are unique amongst environmental pollutants occurring, both naturally and anthropogenically. PTEs have a broad range of negative health and environmental effects, therefore identifying their sources and pathways through the environment is imperative for public health policy. This is difficult in terrestrial systems due to the compositional nature of soil geochemistry. In this study, a compositional statistical approach was used to identify how PTEs accumulate in a terrestrial carnivorous mammal, Eurasian Badgers (Meles meles). Compositional principal component analysis (PCA) was used on geochemical data from the Tellus survey, the soil baseline and badger tissue data to map geo-spatial patterns of PTEs and show accumulative trends measured in time. Mapping PCs identified distinct regions of PTE presence in soil and PTE accumulation in badger tissues in Northern Ireland. PTEs were most elevated in liver, kidney and then muscle tissues. Liver and kidney showed the most distinct geo-spatial patterns of accumulation and muscle was the most depleted. PC1 and 2 for each type were modelled using generalised additive mixed models (GAMM) to identify trends through time. PC1 for the liver and muscle were associated with rainfall and ∂N15 in the liver, showing a link to diet and a bioaccumulation pathway, whilst PC2 for both tissues was associated with mean temperature, showing a link to seasonal activity and a bioaccessibility pathway. However, in kidney tissue these trends are reversed and PC1 was associated with bioaccessibility and PC2 with bioaccumulation. Combined these techniques can elucidate both geo-spatial trends in PTEs and the mechanisms by which they move in environment and in future may be an effective tool for assessing PTE bioavailability in environmental health surveys.

Emergence of a non-sporulating secondary phenotype in Clostridium (Clostridioides) difficile ribotype 078 isolated from humans and animals.

Clostridium (Clostridioides) difficile is a Gram positive, spore forming anaerobic bacterium that is a leading cause of antibiotic associated diarrhoea in the developed world. C. difficile is a genetically diverse species that can be divided into 8 phylogenetically distinct clades with clade 5 found to be genetically distant from all others. Isolates with the PCR ribotype 078 belong to clade 5, and are often associated with C. difficile infection in both humans and animals. Colonisation of animals and humans by ribotype 078 raises questions about possible zoonotic transmission, and also the diversity of reservoirs for ribotype 078 strains within the environment. One of the key factors which enables C. difficile to be a successful, highly transmissible pathogen is its ability to produce oxygen resistant spores capable of surviving harsh conditions. Here we describe the existence of a non-sporulating variant of C. difficile ribotype 078 harbouring mutations leading to premature stop codons within the master regulator, Spo0A. As sporulation is imperative to the successful transmission of C. difficile this study was undertaken to investigate phenotypic characteristics of this asporogenous phenotype with regards to growth rate, antibiotic susceptibility, toxin production and biofilm formation.

Geochronology of an Apollo 16 Clast Provides Evidence for a Basin-Forming Impact 4.3 Billion Years Ago.

We examined lithic breccias from the Apollo sample collection in order to identify ferroan anorthosite samples suitable for geochronology, and better define the age relationships between rocks of the lunar highlands. Clast 3A is a previously unstudied noritic anorthosite from Apollo 16 lithic breccia 60016 with textural evidence of slow subsolidus recrystallization. We estimate a cooling rate of ~10 °C/Myr and calculate a pyroxene solvus temperature of 1,100-1,000 °C. Pyroxene exsolution lamellae (1-3 µm) indicate that the last stage of cooling was rapid at ~0.2 °C/year, typical of rates observed in thick ejecta blankets. We calculate concordant ages from the 147Sm-143Nd, 146Sm-142Nd, Rb-Sr, and Ar-Ar isotopic systems of 4,302 ± 28, 4,296 + 39/-53, 4,275 ± 38, and 4,311 ± 31 Ma, respectively, with a weighted average of 4,304 ± 12 Ma. The closure temperature of the Sm-Nd system is ~855 ± 14 °C, whereas the closure temperature of the Ar-Ar system is 275 ± 25 °C. Cooling from 855 to 275 °C at 10 °C/Myr should result in an age difference between the two isotopic systems of ~60 Myr. The concordant Sm-Nd, Rb-Sr, and Ar-Ar ages imply that they record the time the rock was excavated by a large impact from the midcrust. The ages clearly predate various late accretion scenarios in which an uptick in impacts at 3.8 Ga is preceded by a period of relative quiescence between 4.4 and ~4.1 Ga, and instead are consistent with decreasing accretion rates following the formation of the Moon.

Graphitization of Glassy Carbon after Compression at Room Temperature.

Glassy carbon is a technologically important material with isotropic properties that is nongraphitizing up to ∼3000 °C and displays complete or "superelastic" recovery from large compression. The pressure limit of these properties is not yet known. Here we use experiments and modeling to show permanent densification, and preferred orientation occurs in glassy carbon loaded to 45 GPa and above, where 45 GPa represents the limit to the superelastic and nongraphitizing properties of the material. The changes are explained by a transformation from its sp^{2} rich starting structure to a sp^{3} rich phase that reverts to fully sp^{2} bonded oriented graphite during pressure release.

Plutonium segregation in glassy aerodynamic fallout from a nuclear weapon test.

This study combines electron microscopy equipped with energy dispersive spectroscopy to probe major element composition and autoradiography to map plutonium in order to examine the spatial relationships between plutonium and fallout composition in aerodynamic glassy fallout from a nuclear weapon test. A sample set of 48 individual fallout specimens were interrogated to reveal that the significant chemical heterogeneity of this sample set could be described compositionally with a relatively small number of compositional endmembers. Furthermore, high concentrations of plutonium were never associated with several endmember compositions and concentrated with the so-called mafic glass endmember. This result suggests that it is the physical characteristics of the compositional endmembers and not the chemical characteristics of the individual component elements that govern the un-burnt plutonium distribution with respect to major element composition in fallout.

Functional Genomics Tools for Haemonchus contortus and Lessons From Other Helminths.

The availability of genome and transcriptome data for parasitic nematodes, including Haemonchus contortus, has highlighted the need to develop functional genomics tools. Comparative genomic analysis, particularly using data from the free-living nematode Caenorhabditis elegans, can help predict gene function. Reliable approaches to study function directly in parasitic nematodes are currently lacking. However, gene knockdown by RNA interference (RNAi) is being successfully used in schistosome and planarian species to define gene functions. Lessons from these systems may be applied to improve RNAi in H. contortus. Previous studies in H. contortus and related nematodes demonstrated reliable RNAi-mediated silencing of some genes, but not others. Current data suggest that susceptibility to RNAi in these nematodes is limited to genes expressed in sites accessible to the environment, such as the gut, amphids and excretory cell. Therefore, RNAi is functional in H. contortus, but improvements are needed to develop this system as a functional genomics platform. Here, we summarize RNAi studies on H. contortus and discuss the optimization of RNA delivery and improvements to culture methods to enhance larval development, protein turnover and the induction of phenotypic effects in vitro. The transgenic delivery of RNA or dominant-negative gene constructs and the recently developed CRISPR/Cas genome-editing technique are considered as potential alternative approaches for gene knockout. This is a key time to devote greater effort in progressing from genome to function, to improve our understanding of the biology of Haemonchus and identify novel targets for parasite control.

Reaction paths of phosphine dissociation on silicon (001).

Using density functional theory and guided by extensive scanning tunneling microscopy (STM) image data, we formulate a detailed mechanism for the dissociation of phosphine (PH3) molecules on the Si(001) surface at room temperature. We distinguish between a main sequence of dissociation that involves PH2+H, PH+2H, and P+3H as observable intermediates, and a secondary sequence that gives rise to PH+H, P+2H, and isolated phosphorus adatoms. The latter sequence arises because PH2 fragments are surprisingly mobile on Si(001) and can diffuse away from the third hydrogen atom that makes up the PH3 stoichiometry. Our calculated activation energies describe the competition between diffusion and dissociation pathways and hence provide a comprehensive model for the numerous adsorbate species observed in STM experiments.

Step by step: reconstruction of terrestrial animal movement paths by dead-reckoning.

BACKGROUND: Research on wild animal ecology is increasingly employing GPS telemetry in order to determine animal movement. However, GPS systems record position intermittently, providing no information on latent position or track tortuosity. High frequency GPS have high power requirements, which necessitates large batteries (often effectively precluding their use on small animals) or reduced deployment duration. Dead-reckoning is an alternative approach which has the potential to 'fill in the gaps' between less resolute forms of telemetry without incurring the power costs. However, although this method has been used in aquatic environments, no explicit demonstration of terrestrial dead-reckoning has been presented. RESULTS: We perform a simple validation experiment to assess the rate of error accumulation in terrestrial dead-reckoning. In addition, examples of successful implementation of dead-reckoning are given using data from the domestic dog Canus lupus, horse Equus ferus, cow Bos taurus and wild badger Meles meles. CONCLUSIONS: This study documents how terrestrial dead-reckoning can be undertaken, describing derivation of heading from tri-axial accelerometer and tri-axial magnetometer data, correction for hard and soft iron distortions on the magnetometer output, and presenting a novel correction procedure to marry dead-reckoned paths to ground-truthed positions. This study is the first explicit demonstration of terrestrial dead-reckoning, which provides a workable method of deriving the paths of animals on a step-by-step scale. The wider implications of this method for the understanding of animal movement ecology are discussed.

Reaction pathways for pyridine adsorption on silicon (0 0 1).

Density functional theory is used to describe the reactions of chemisorption of pyridine on the silicon (0 0 1) surface. Adsorption energies of six relevant structures, and the activation energies between them are reported. We consider in detail the dative to tight-bridge transition for which conflicting results have been reported in the literature, and provide a description of the formation of inter-row chains observed in high-coverage experiments. We demonstrate that the choice of DFT functional has a considerable effect on the relative energetics and of the four DFT functionals considered, we find that the range-separated hybrid ωB97X-D functional with empirical dispersion provides the most consistent description of the experiment data.

Density and structural effects in the radiation tolerance of TiO2 polymorphs.

The radiation response of TiO2 has been studied using molecular dynamics. The simulations are motivated by experimental observations that the three low-pressure polymorphs, rutile, brookite and anatase, exhibit vastly different tolerances to amorphization under ion-beam irradiation. To understand the role of structure we perform large numbers of simulations using the small thermal spike method. We quantify to high statistical accuracy the number of defects created as a function of temperature and structure type, and reproduce all the main trends observed experimentally. To evaluate a hypothesis that volumetric strain relative to the amorphous phase is an important driving force for defect recovery, we perform spike simulations in which the crystalline density is varied over a wide range. Remarkably, the large differences between the polymorphs disappear once the density difference is taken into account. This finding demonstrates that density is an important factor which controls radiation tolerance in TiO2.