Silchester: changing visions of a Roman town. Integrating geophysics and archaeology - the results of the Silchester Mapping Project 2005-10

Silchester (Calleva Atrebatum) is a Roman town in Hampshire, in central southern Britain. Unlike many the site was abandoned in the post-Roman period leaving it as a largely green-field site now. The Amphitheatre, Town Wall and some Outer Defences all remain visible for the visitor to see. The town has been highly influential in the development of Romano-British archaeology due to the large-scale excavation by the Society of Antiquaries in 1890-1908 developed an overall plan of the site. This volume draws together for the first time all the fieldwork known to have taken place from the earliest located trenches in the 1720s up until the modern campaigns of Michael Fulford (1974-present). The cut-off date is 2013. It integrates this work with a new geophysical survey of the interior and vicinity to provide a new overarching narrative for the town. The volume starts with a historiography of work on the city from earliest antiquarian investigations through to recent campaigns; and this sense of historiography and changing interpretations of the site permeates the later discussion, showing how new discoveries have transformed understandings. The core of the volume contains the empirical data. Work has taken place digitising all the past excavation plans, and combining this with other datasets including: two major fieldwalking campaigns, the aerial photographic plots, landscape analysis from earlier maps from the Ordnance Survey and earlier sources, LiDAR, other mapping data, and finally with 217 ha of new geophysical prospection in and around the town. An atlas has been created which shows these data in a variety of formats, together with a detailed text outlining all the past interventions within each sheet, and providing a summary of the discoveries together with references to their later reinterpretation where relevant. The final sections provide essays in interpretation, with thematic reviews of: the defences and linear earthworks; the development of the oppidum; the interpretation of Roman military metalwork; an interpretation of the evidence for the mortuary landscape of the town; discussions of urban infrastructure, trade, industry and pubic entertainment. Finally a narrative overview is provided seeing how the town’s remains have been interpreted within an historical setting. There are methodological innovations differentiating the signal strength of features in the fluxgate gradiometry data to map ‘hotspots’ representing possible cremations pyre areas, middens, and industrial activities to develop our understanding of the mortuary landscape and also that of shops and workshops within the towns; these techniques could readily be applied to other large-scale surveys of Roman cities which have already been undertaken. The work provides the first overall synthesis of the city since Boon (1974). The new work includes a significantly revised impression of the development and chronology of the earthworks surrounding the town; mapping of all the Later Iron Age finds and evidence for the development of the street grid from both excavation data and geophysics; it has discovered several new cemetery areas including a series of large Later Iron Age or early Roman burial enclosures. Features are found which may represent elusive evidence for large-scale tanning operations near the town; and there are traces on the gravel terrace edge of a series of parallel lines which may be indicative of a circus, though ground-truthing is required to test that. The overall urban assessment and synthesis enables Silchester to be seen alongside the other recent comprehensive reviews of major cities in south-east Britain, such as Verulamium (Niblett and Thompson 2005) and Colchester (Radford et al. 2013)

Excavation and survey at the Giant’s Grave, Slochd Measach, Nereabolls, a Neolithic chambered cairn on the Isle of Islay, Argyll & Bute

The ‘Giant’s Grave’, formally known as Slochd Measach, Nereabolls, (SM3927) is located on the Isle of Islay in western Scotland and is one of seven confirmed Clyde Cairns on the island. We describe the standing remains and excavations between 2015-18 intended to address the origin, architecture and use of this monument. We found that the cairn was most likely constructed between 3516-336 cal BC in one continuous effort. It was modified and reused on at least four occasions during the Early and Late Bronze Age, and extensively robbed during the Iron Age. This post-Neolithic activity left a small collection of ceramic vessels may have been used for funerary purposes of votive offerings. We compare the architecture of the Giant’s Grave with that of other cairns on Islay and in the wider region

The DiskMass Survey. II. Error Budget

We present a performance analysis of the DiskMass Survey. The survey uses collisionless tracers in the form of disk stars to measure the surface-density of spiral disks, to provide an absolute calibration of the stellar mass-to-light ratio, and to yield robust estimates of the dark-matter halo density profile in the inner regions of galaxies. We find a disk inclination range of 25-35 degrees is optimal for our measurements, consistent with our survey design to select nearly face-on galaxies. Uncertainties in disk scale-heights are significant, but can be estimated from radial scale-lengths to 25% now, and more precisely in the future. We detail the spectroscopic analysis used to derive line-of-sight velocity dispersions, precise at low surface-brightness, and accurate in the presence of composite stellar populations. Our methods take full advantage of large-grasp integral-field spectroscopy and an extensive library of observed stars. We show that the baryon-to-total mass fraction (F_b) is not a well-defined observational quantity because it is coupled to the halo mass model. This remains true even when the disk mass is known and spatially-extended rotation curves are available. In contrast, the fraction of the rotation speed supplied by the disk at 2.2 scale lengths (disk maximality) is a robust observational indicator of the baryonic disk contribution to the potential. We construct the error-budget for the key quantities: dynamical disk mass surface-density, disk stellar mass-to-light ratio, and disk maximality (V_disk / V_circular). Random and systematic errors in these quantities for individual galaxies will be ~25%, while survey precision for sample quartiles are reduced to 10%, largely devoid of systematic errors outside of distance uncertainties.Comment: To appear in ApJ; 88 pages, 4 tables, 18 figures. High-resolution version available at http://www.astro.wisc.edu/~mab/publications/DMS_II_preprint.pd

The WiggleZ Dark Energy Survey: the selection function and z=0.6 galaxy power spectrum

We report one of the most accurate measurements of the three-dimensional large-scale galaxy power spectrum achieved to date, using 56,159 redshifts of bright emission-line galaxies at effective redshift z=0.6 from the WiggleZ Dark Energy Survey at the Anglo-Australian Telescope. We describe in detail how we construct the survey selection function allowing for the varying target completeness and redshift completeness. We measure the total power with an accuracy of approximately 5% in wavenumber bands of dk=0.01 h/Mpc. A model power spectrum including non-linear corrections, combined with a linear galaxy bias factor and a simple model for redshift-space distortions, provides a good fit to our data for scales k < 0.4 h/Mpc. The large-scale shape of the power spectrum is consistent with the best-fitting matter and baryon densities determined by observations of the Cosmic Microwave Background radiation. By splitting the power spectrum measurement as a function of tangential and radial wavenumbers we delineate the characteristic imprint of peculiar velocities. We use these to determine the growth rate of structure as a function of redshift in the range 0.4 < z < 0.8, including a data point at z=0.78 with an accuracy of 20%. Our growth rate measurements are a close match to the self-consistent prediction of the LCDM model. The WiggleZ Survey data will allow a wide range of investigations into the cosmological model, cosmic expansion and growth history, topology of cosmic structure, and Gaussianity of the initial conditions. Our calculation of the survey selection function will be released at a future date via our website wigglez.swin.edu.au.Comment: 21 pages, 22 figures, accepted for publication in MNRA

Knowledge gaps in our perceptual model of Great Britain’s hydrology

There is a no lack of significant open questions in the field of hydrology. How will hydrological connectivity between freshwater bodies be altered by future human alterations to the hydrological cycle? Where does water go when it rains? Or what is the future space-time variability of flood and drought events? However, the answers to these questions will vary with location due to the specific and often poorly understood local boundary conditions and system properties that control the functional behaviour of a catchment or any other hydrologic control volume. We suggest that an open, shared and evolving perceptual model of a region’s hydrology is critical to tailor our science questions, as it would be for any other study domain from the plot to the continental scale. In this opinion piece, we begin to discuss the elements of and point out some knowledge gaps in the perceptual model of the terrestrial water cycle of Great Britain. We discuss six major knowledge gaps and propose four key ways to reduce them. While the specific knowledge gaps in our perceptual model do not necessarily transfer to other places, we believe that the development of such perceptual models should be at the core of the debate for all hydrologic communities, and we encourage others to have a similar debate for their hydrologic domain

A spitting image: molecular diagnostics applied to saliva enhance detection of Streptococcus pneumoniae and pneumococcal serotype carriage

BackgroundDespite strong historical records on the accuracy of saliva testing, oral fluids are considered poorly suited for pneumococcal carriage detection. We evaluated an approach for carriage surveillance and vaccine studies that increases the sensitivity and specificity of pneumococcus and pneumococcal serotype detection in saliva samples.MethodsQuantitative PCR (qPCR)-based methods were applied to detect pneumococcus and pneumococcal serotypes in 971 saliva samples collected from 653 toddlers and 318 adults. Results were compared with culture-based and qPCR-based detection in nasopharyngeal samples collected from children and in nasopharyngeal and oropharyngeal samples collected from adults. Optimal Cq cut-offs for positivity in qPCRs were determined via receiver operating characteristic curve analysis and accuracy of different approaches was assessed using a composite reference for pneumococcal and for serotype carriage based on isolation of live pneumococcus from the person or positivity of saliva samples determined with qPCR. To evaluate the inter-laboratory reproducibility of the method, 229 culture-enriched samples were tested independently in the second center.ResultsIn total, 51.5% of saliva samples from children and 31.8% of saliva samples from adults were positive for pneumococcus. Detection of pneumococcus by qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to diagnostic culture of nasopharyngeal samples in children (Cohen’s κ: 0.69–0.79 vs. 0.61–0.73) and in adults (κ: 0.84–0.95 vs. 0.04–0.33) and culture of oropharyngeal samples in adults (κ: 0.84–0.95 vs. −0.12–0.19). Similarly, detection of serotypes with qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to nasopharyngeal culture in children (κ: 0.73–0.82 vs. 0.61–0.73) and adults (κ: 0.90–0.96 vs. 0.00–0.30) and oropharyngeal culture in adults (κ: 0.90–0.96 vs. −0.13 to 0.30). However, results of qPCRs targeting serotype 4, 5, and 17F and serogroups 9, 12, and 35 were excluded due to assays’ lack of specificity. We observed excellent quantitative agreement for qPCR-based detection of pneumococcus between laboratories. After exclusion of serotype/serogroup-specific assays with insufficient specificity, moderate agreement (κ 0.68, 95% CI 0.58–0.77) was observed.ConclusionMolecular testing of culture-enriched saliva samples improves the sensitivity of overall surveillance of pneumococcal carriage in children and adults, but limitations of qPCR-based approaches for pneumococcal serotypes carriage detection should be considered

Impact of age on pneumococcal colonization of the nasopharynx and oral cavity: an ecological perspective

Pneumococcal carriage studies have suggested that pneumococcal colonization in adults is largely limited to the oral cavity and oropharynx. In this study, we used total abundance-based β-diversity (dissimilarity) and β-diversity components to characterize age-related differences in pneumococcal serotype composition of respiratory samples. quantitative PCR (qPCR) was applied to detect pneumococcal serotypes in nasopharyngeal samples collected from 946 toddlers and 602 adults, saliva samples collected from a subset of 653 toddlers, and saliva and oropharyngeal samples collected from a subset of 318 adults. Bacterial culture rates from nasopharyngeal samples were used to characterize age-related differences in rates of colonizing bacteria. Dissimilarity in pneumococcal serotype composition was low among saliva and nasopharyngeal samples from children. In contrast, respiratory samples from adults exhibited high serotype dissimilarity, which predominantly consisted of abundance gradients and was associated with reduced nasopharyngeal colonization. Age-related serotype dissimilarity was high among nasopharyngeal samples and relatively low for saliva samples. Reduced nasopharyngeal colonization by pneumococcal serotypes coincided with significantly reduced Moraxella catarrhalis and Haemophilus influenzae and increased Staphylococcus aureus nasopharyngeal colonization rates among adults. Findings from this study suggest that within-host environmental conditions, utilized in the upper airways by pneumococcus and other bacteria, undergo age-related changes. It may result in a host-driven ecological succession of bacterial species colonizing the nasopharynx and lead to competitive exclusion of pneumococcus from the nasopharynx but not from the oral habitat. This explains the poor performance of nasopharyngeal samples for pneumococcal carriage among adults and indicates that in adults saliva more accurately represents the epidemiology of pneumococcal carriage than nasopharyngeal samples

A spitting image: molecular diagnostics applied to saliva enhance detection of Streptococcus pneumoniae and pneumococcal serotype carriage

BACKGROUND: Despite strong historical records on the accuracy of saliva testing, oral fluids are considered poorly suited for pneumococcal carriage detection. We evaluated an approach for carriage surveillance and vaccine studies that increases the sensitivity and specificity of pneumococcus and pneumococcal serotype detection in saliva samples. METHODS: Quantitative PCR (qPCR)-based methods were applied to detect pneumococcus and pneumococcal serotypes in 971 saliva samples collected from 653 toddlers and 318 adults. Results were compared with culture-based and qPCR-based detection in nasopharyngeal samples collected from children and in nasopharyngeal and oropharyngeal samples collected from adults. Optimal C q cut-offs for positivity in qPCRs were determined via receiver operating characteristic curve analysis and accuracy of different approaches was assessed using a composite reference for pneumococcal and for serotype carriage based on isolation of live pneumococcus from the person or positivity of saliva samples determined with qPCR. To evaluate the inter-laboratory reproducibility of the method, 229 culture-enriched samples were tested independently in the second center. RESULTS: In total, 51.5% of saliva samples from children and 31.8% of saliva samples from adults were positive for pneumococcus. Detection of pneumococcus by qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to diagnostic culture of nasopharyngeal samples in children (Cohen's κ: 0.69-0.79 vs. 0.61-0.73) and in adults (κ: 0.84-0.95 vs. 0.04-0.33) and culture of oropharyngeal samples in adults (κ: 0.84-0.95 vs. -0.12-0.19). Similarly, detection of serotypes with qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to nasopharyngeal culture in children (κ: 0.73-0.82 vs. 0.61-0.73) and adults (κ: 0.90-0.96 vs. 0.00-0.30) and oropharyngeal culture in adults (κ: 0.90-0.96 vs. -0.13 to 0.30). However, results of qPCRs targeting serotype 4, 5, and 17F and serogroups 9, 12, and 35 were excluded due to assays' lack of specificity. We observed excellent quantitative agreement for qPCR-based detection of pneumococcus between laboratories. After exclusion of serotype/serogroup-specific assays with insufficient specificity, moderate agreement (κ 0.68, 95% CI 0.58-0.77) was observed. CONCLUSION: Molecular testing of culture-enriched saliva samples improves the sensitivity of overall surveillance of pneumococcal carriage in children and adults, but limitations of qPCR-based approaches for pneumococcal serotypes carriage detection should be considered

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P &lt; 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men