Performance and automation of ancient DNA capture with RNA hyRAD probes

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analys- ing ancient DNA (aDNA) extracts, which are often dominated by exogenous environ- mental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic re- striction of fresh DNA extracts to produce RNA probes that cover only a fraction ofthe genome and can serve as baits for capturing homologous fragments from aDNA li- braries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing ex- tremely low endogenous content (20%¿30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensi- tive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypo- methylated regions, which improved data quality by reducing post-mortem DNA dam- age and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture process- ing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.This project received funding from: the University Paul Sabatier IDEX Chaire d’Excellence (OURASI); the CNRS Programme de Recherche Conjoint (PRC); the CNRS International Research Project (IRP AMADEUS); the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 797449; the Russian Foundation for Basic Research, project No. 19-59-15001 “Horses and their importance in the life of the ancient population of Altai and adjacent territories: interdisciplinary research and reconstruction”; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 681605)

The dynamics of Saturn's main aurorae

Saturn's main aurorae are thought to be generated by plasma flow shears associated with a gradient in angular plasma velocity in the outer magnetosphere. Dungey cycle convection across the polar cap, in combination with rotational flow, may maximize (minimize) this flow shear at dawn (dusk) under strong solar wind driving. Using imagery from Cassini's Ultraviolet Imaging Spectrograph, we surprisingly find no related asymmetry in auroral power but demonstrate that the previously observed “dawn arc” is a signature of quasiperiodic auroral plasma injections commencing near dawn, which seem to be transient signatures of magnetotail reconnection and not part of the static main aurorae. We conclude that direct Dungey cycle driving in Saturn's magnetosphere is small compared to internal driving under usual conditions. Saturn's large‐scale auroral dynamics hence seem predominantly controlled by internal plasma loading, with plasma release in the magnetotail being triggered both internally through planetary period oscillation effects and externally through solar wind compressions

Identifying Key Factors Associated with Aggression on Acute Inpatient Psychiatric Wards

Aggressive behaviour is a critical issue for modern acute psychiatric services, not just because of the adverse impact it has on patients and staff, but also because it puts a financial strain on service providers. The aim of this study was to assess the relationship of patient violence to other variables: patient characteristics, features of the service and physical environment, patient routines, staff factors, the use of containment methods, and other patient behaviours. A multivariate cross sectional design was utilised. Data were collected for a six month period on 136 acute psychiatric wards in 26 NHS Trusts in England. Multilevel modelling was conducted to ascertain those factors most strongly associated with verbal aggression, aggression toward objects, and physical aggression against others. High levels of aggression were associated with a high proportion of patients formally detained under mental health legislation, high patient turnover, alcohol use by patients, ward doors being locked, and higher staffing numbers (especially qualified nurses). The findings suggest that the imposition of restrictions on patients exacerbates the problem of violence, and that alcohol management strategies may be a productive intervention. Insufficient evidence is available to draw conclusions about the nature of the link between staffing numbers and violence

A window into fungal endophytism in Salicornia europaea: deciphering fungal characteristics as plant growth promoting agents

Aim Plant-endophytic associations exist only when equilibrium is maintained between both partners. This study analyses the properties of endophytic fungi inhabiting a halophyte growing in high soil salinity and tests whether these fungi are beneficial or detrimental when non-host plants are inoculated. Method Fungi were isolated from Salicornia europaea collected from two sites differing in salinization history (anthropogenic and naturally saline) and analyzed for plant growth promoting abilities and non-host plant interactions. Results Most isolated fungi belonged to Ascomycota (96%) including dematiaceous fungi and commonly known plant pathogens and saprobes. The strains were metabolically active for siderophores, polyamines and indole-3-acetic acid (mainly Aureobasidium sp.) with very low activity for phosphatases. Many showed proteolytic, lipolytic, chitinolytic, cellulolytic and amylolytic activities but low pectolytic activity. Different activities between similar fungal species found in both sites were particularly seen for Epiccocum sp., Arthrinium sp. and Trichoderma sp. Inoculating the non-host Lolium perenne with selected fungi increased plant growth, mainly in the symbiont (Epichloë)-free variety. Arthrinium gamsii CR1-9 and Stereum gausapatum ISK3-11 were most effective for plant growth promotion. Conclusions This research suggests that host lifestyle and soil characteristics have a strong effect on endophytic fungi, and environmental stress could disturb the plant-fungi relations. In favourable conditions, these fungi may be effective in facilitating crop production in non-cultivable saline lands

The origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture

ICAR: endoscopic skull‐base surgery

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Conceptualizing and measuring strategy implementation – a multi-dimensional view

Through quantitative methodological approaches for studying the strategic management and planning process, analysis of data from 208 senior managers involved in strategy processes within ten UK industrial sectors provides evidence on the measurement properties of a multi-dimensional instrument that assesses ten dimensions of strategy implementation. Using exploratory factor analysis, results indicate the sub-constructs (the ten dimensions) are uni-dimensional factors with acceptable reliability and validity; whilst using three additional measures, and correlation and hierarchical regression analysis, the nomological validity for the multi-dimensional strategy implementation construct was established. Relative importance of ten strategy implementation dimensions (activities) for practicing managers is highlighted, with the mutually and combinative effects drawing conclusion that senior management involvement leads the way among the ten key identified activities vital for successful strategy implementation