Reconstructing Christian lifeways: a bioarchaeological study of medieval inhabitants from Portmahomack, Scotland and Norton Priory, England.

This thesis investigates lifeways of medieval Christian communities from Portmahomack, Northeast Scotland and Norton Priory, Northwest England, to ascertain the extent to which skeletal indicators of diet, disease or trauma reflect religious or social influences. Osteology and palaeopathology methods on human adult and sub-adult skeletons from Portmahomack (6th to 17th century) and Norton Priory (12th to 16th century) was undertaken to provide evidence relating to the four key themes proposed in this study: ‘biological or familial affinity’, ‘the living environment’, ‘trauma and conflict’, and ‘diet and nutrition-related stresses’. Stable carbon and nitrogen isotope analysis of bone collagen from adult humans from Portmahomack (including and a sub-sample of sub-adults) and Norton Priory were measured for dietary reconstructions. Faunal bone collagen was also analysed from Portmahomack and Norton Priory (plus a selection of fish bones from Chester Cathedral) to provide isotopic baselines to reconstruct human diets. The results suggest past lifeways of Christian communities from Portmahomack and Norton Priory can indeed be successfully reconstructed through bioarchaeology. The evidence from this study has found that skeletal traits, alongside burial evidence, can elucidate familial affinities, especially from Norton Priory, and that differences in cultural and religious practices are reflected within the living environment of ecclesiastic and lay groups. Evidence of violence, reflecting interpersonal conflict and vulnerability was found from both Portmahomack and Norton Priory, which was inconsistent with the role of ecclesiastic and lay communities that were expected to follow strict Christian doctrines. Stable isotope data revealed a diachronic change in diet at Portmahomack; no fish were consumed during the monastic period, whereas significant amounts were consumed by layfolk in the later periods, suggesting Christian dietary practices changed over time. The isotope data from Norton Priory reflected a more homogeneous diet that did not change greatly over time, suggesting conformity to the same fasting practices. Overall, this study has demonstrated that adopting a multidisciplinary bioarchaeological approach, integrating skeletal, chemical, archaeological, and historical evidence, results in a powerful research tool that enables reconstructions of medieval Christian lifeways and interpretations of religious and social influences therein

Integrating isotopes and documentary evidence : dietary patterns in a late medieval and early modern mining community, Sweden

We would like to thank the Archaeological Research Laboratory, Stockholm University, Sweden and the Tandem Laboratory (Ångström Laboratory), Uppsala University, Sweden, for undertaking the analyses of stable nitrogen and carbon isotopes in both human and animal collagen samples. Also, thanks to Elin Ahlin Sundman for providing the δ13C and δ15N values for animal references from Västerås. This research (Bäckström’s PhD employment at Lund University, Sweden) was supported by the Berit Wallenberg Foundation (BWS 2010.0176) and Jakob and Johan Söderberg’s foundation. The ‘Sala project’ (excavations and analyses) has been funded by Riksens Clenodium, Jernkontoret, Birgit and Gad Rausing’s Foundation, SAU’s Research Foundation, the Royal Physiographic Society of Lund, Berit Wallenbergs Foundation, Åke Wibergs Foundation, Lars Hiertas Memory, Helge Ax:son Johnson’s Foundation and The Royal Swedish Academy of Sciences.Peer reviewedPublisher PD

Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.

The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics

Pharmacologic targeting of renal ischemia-reperfusion injury using a normothermic machine perfusion platform.

Normothermic machine perfusion (NMP) is an emerging modality for kidney preservation prior to transplantation. NMP may allow directed pharmacomodulation of renal ischemia-reperfusion injury (IRI) without the need for systemic donor/recipient therapies. Three proven anti-IRI agents not in widespread clinical use, CD47-blocking antibody (αCD47Ab), soluble complement receptor 1 (sCR1), and recombinant thrombomodulin (rTM), were compared in a murine model of kidney IRI. The most effective agent was then utilized in a custom NMP circuit for the treatment of isolated porcine kidneys, ascertaining the impact of the drug on perfusion and IRI-related parameters. αCD47Ab conferred the greatest protection against IRI in mice after 24 hours. αCD47Ab was therefore chosen as the candidate agent for addition to the NMP circuit. CD47 receptor binding was demonstrated by immunofluorescence. Renal perfusion/flow improved with CD47 blockade, with a corresponding reduction in oxidative stress and histologic damage compared to untreated NMP kidneys. Tubular and glomerular functional parameters were not significantly impacted by αCD47Ab treatment during NMP. In a murine renal IRI model, αCD47Ab was confirmed as a superior anti-IRI agent compared to therapies targeting other pathways. NMP enabled effective, direct delivery of this drug to porcine kidneys, although further efficacy needs to be proven in the transplantation setting

Long memory estimation for complex-valued time series

Long memory has been observed for time series across a multitude of fields and the accurate estimation of such dependence, e.g. via the Hurst exponent, is crucial for the modelling and prediction of many dynamic systems of interest. Many physical processes (such as wind data), are more naturally expressed as a complex-valued time series to represent magnitude and phase information (wind speed and direction). With data collection ubiquitously unreliable, irregular sampling or missingness is also commonplace and can cause bias in a range of analysis tasks, including Hurst estimation. This article proposes a new Hurst exponent estimation technique for complex-valued persistent data sampled with potential irregularity. Our approach is justified through establishing attractive theoretical properties of a new complex-valued wavelet lifting transform, also introduced in this paper. We demonstrate the accuracy of the proposed estimation method through simulations across a range of sampling scenarios and complex- and real-valued persistent processes. For wind data, our method highlights that inclusion of the intrinsic correlations between the real and imaginary data, inherent in our complex-valued approach, can produce different persistence estimates than when using real-valued analysis. Such analysis could then support alternative modelling or policy decisions compared with conclusions based on real-valued estimation

The V471A polymorphism in autophagy-related gene ATG7 modifies age at onset specifically in Italian Huntington disease patients

The cause of Huntington disease (HD) is a polyglutamine repeat expansion of more than 36 units in the huntingtin protein, which is inversely correlated with the age at onset of the disease. However, additional genetic factors are believed to modify the course and the age at onset of HD. Recently, we identified the V471A polymorphism in the autophagy-related gene ATG7, a key component of the autophagy pathway that plays an important role in HD pathogenesis, to be associated with the age at onset in a large group of European Huntington disease patients. To confirm this association in a second independent patient cohort, we analysed the ATG7 V471A polymorphism in additional 1,464 European HD patients of the “REGISTRY” cohort from the European Huntington Disease Network (EHDN). In the entire REGISTRY cohort we could not confirm a modifying effect of the ATG7 V471A polymorphism. However, analysing a modifying effect of ATG7 in these REGISTRY patients and in patients of our previous HD cohort according to their ethnic origin, we identified a significant effect of the ATG7 V471A polymorphism on the HD age at onset only in the Italian population (327 patients). In these Italian patients, the polymorphism is associated with a 6-years earlier disease onset and thus seems to have an aggravating effect. We could specify the role of ATG7 as a genetic modifier for HD particularly in the Italian population. This result affirms the modifying influence of the autophagic pathway on the course of HD, but also suggests population-specific modifying mechanisms in HD pathogenesis

Reconstructing the childhood diet of individuals buried with the Pictish monastic community at Portmahomack

NoThis research aims to reconstruct the childhood diets (aged 9–10 years) of the individuals buried during the active years of the Pictish monastic community (hereafter referred to as PMC) from early medieval (7th–11th century) Portmahomack in north-east Scotland, using 13C and 15N isotopes. Dietary reconstructions were achieved by isotope analysis of δ13C and δ15N on the tooth root apex from permanent first molars (M1) of 26 adult male individuals. The results indicate that the individuals in PMC predominantly consumed terrestrial C3 resources during childhood, with a rich terrestrial protein diet and some marine resource consumption. Statistically significant differences were observed between childhood and adulthood diets (the latter derived from previous research), suggesting that when these individuals were children, they consumed more marine protein than in later years as adults. This is true for all individuals, whether or not they spent significant time in Portmahomack during their childhoods. This is the most extensive study of the childhood diet of individuals from the PMC and so makes a significant contribution to augmenting information on diet and lifestyles in Pictish Scotland

Optical and Crystallographic Properties of Inverse Opal Photonic Crystals Grown by Atomic Layer Deposition

ABSTRACTWe report a technique for the formation of infiltrated and inverse opal structures that produces high quality, low porosity conformal material structures. ZnS:Mn and TiO2 were deposited within the void space of an opal lattice by atomic layer deposition. The resulting structures were etched with HF to remove the silica opal template. Infiltrated and inverse opals were characterized by SEM, XRD, and transmission/reflection spectroscopy. The reflectance spectra exhibited features corresponding to strong low and high order photonic band gaps in the (111) direction (γ-L). In addition, deliberate partial infiltrations and multi-layered inverse opals have been formed. The effectiveness of a post-deposition heat treatment for converting TiO2 films to rutile was also studied.</jats:p

The Microbial Community of a Terrestrial Anoxic Inter-Tidal Zone: A Model for Laboratory-Based Studies of Potentially Habitable Ancient Lacustrine Systems on Mars.

Evidence indicates that Gale crater on Mars harboured a fluvio-lacustrine environment that was subjected to physio-chemical variations such as changes in redox conditions and evaporation with salinity changes, over time. Microbial communities from terrestrial environmental analogues sites are important for studying such potential habitability environments on early Mars, especially in laboratory-based simulation experiments. Traditionally, such studies have predominantly focused on microorganisms from extreme terrestrial environments. These are applicable to a range of Martian environments; however, they lack relevance to the lacustrine systems. In this study, we characterise an anoxic inter-tidal zone as a terrestrial analogue for the Gale crater lake system according to its chemical and physical properties, and its microbiological community. The sub-surface inter-tidal environment of the River Dee estuary, United Kingdom (53°21′15.40″ N, 3°10′24.95″ W) was selected and compared with available data from Early Hesperian-time Gale crater, and temperature, redox, and pH were similar. Compared to subsurface ‘groundwater’-type fluids invoked for the Gale subsurface, salinity was higher at the River Dee site, which are more comparable to increases in salinity that likely occurred as the Gale crater lake evolved. Similarities in clay abundance indicated similar access to, specifically, the bio-essential elements Mg, Fe and K. The River Dee microbial community consisted of taxa that were known to have members that could utilise chemolithoautotrophic and chemoorganoheterotrophic metabolism and such a mixed metabolic capability would potentially have been feasible on Mars. Microorganisms isolated from the site were able to grow under environment conditions that, based on mineralogical data, were similar to that of the Gale crater’s aqueous environment at Yellowknife Bay. Thus, the results from this study suggest that the microbial community from an anoxic inter-tidal zone is a plausible terrestrial analogue for studying habitability of fluvio-lacustrine systems on early Mars, using laboratory-based simulation experiments