Radiocarbon dates from the Oxford AMS system: archaeometry datelist 35

This is the 35th list of AMS radiocarbon determinations measured at the Oxford Radiocarbon Accelerator Unit (ORAU). Amongst some of the sites included here are the latest series of determinations from the key sites of Abydos, El Mirón, Ban Chiang, Grotte de Pigeons (Taforalt), Alepotrypa and Oberkassel, as well as others dating to the Palaeolithic, Mesolithic and later periods. Comments on the significance of the results are provided by the submitters of the material

RADIOCARBON AND STABLE ISOTOPE EVIDENCE OF DIETARY CHANGE FROM THE MESOLITHIC TO THE MIDDLE AGES IN THE IRON GATES: NEW RESULTS FROM LEPENSKI VIR

This is the published version, also available here: https://journals.uair.arizona.edu/index.php/radiocarbon/article/view/4269.A previous radiocarbon dating and stable isotope study of directly associated ungulate and human bone samples from Late Mesolithic burials at Schela Cladovei in Romania established that there is a freshwater reservoir effect of approximately 500 yr in the Iron Gates reach of the Danube River valley in southeast Europe. Using the d15N values as an indicator of the percentage of freshwater protein in the human diet, the 14C data for 24 skeletons from the site of Lepenski Vir were corrected for this reservoir effect. The results of the paired 14C and stable isotope measurements provide evidence of substantial dietary change over the period from about 9000 BP to about 300 BP. The data from the Early Mesolithic to the Chalcolithic are consistent with a 2-component dietary system, where the linear plot of isotopic values reflects mixing between the 2 end-members to differing degrees. Typically, the individuals of Mesolithic age have much heavier d15N signals and slightly heavier d13C, while individuals of Early Neolithic and Chalcolithic age have lighter d15N and d13C values. Contrary to our earlier suggestion, there is no evidence of a substantial population that had a transitional diet midway between those that were characteristic of the Mesolithic and Neolithic. However, several individuals with Final Mesolithic 14C ages show d15N and d13C values that are similar to the Neolithic dietary pattern. Provisionally, these are interpreted either as incomers who originated in early farming communities outside the Iron Gates region or as indigenous individuals representing the earliest Neolithic of the Iron Gates. The results from Roman and Medieval age burials show a deviation from the linear function, suggesting the presence of a new major dietary component containing isotopically heavier carbon. This is interpreted as a consequence of the introduction of millet into the human food chain

Methodological approaches to determining the marine radiocarbon reservoir effect

The marine radiocarbon reservoir effect is an offset in 14C age between contemporaneous organisms from the terrestrial environment and organisms that derive their carbon from the marine environment. Quantification of this effect is of crucial importance for correct calibration of the <sup>14</sup>C ages of marine-influenced samples to the calendrical timescale. This is fundamental to the construction of archaeological and palaeoenvironmental chronologies when such samples are employed in <sup>14</sup>C analysis. Quantitative measurements of temporal variations in regional marine reservoir ages also have the potential to be used as a measure of process changes within Earth surface systems, due to their link with climatic and oceanic changes. The various approaches to quantification of the marine radiocarbon reservoir effect are assessed, focusing particularly on the North Atlantic Ocean. Currently, the global average marine reservoir age of surface waters, R(t), is c. 400 radiocarbon years; however, regional values deviate from this as a function of climate and oceanic circulation systems. These local deviations from R(t) are expressed as +R values. Hence, polar waters exhibit greater reservoir ages (δR = c. +400 to +800 <sup>14</sup>C y) than equatorial waters (δR = c. 0 <sup>14</sup>C y). Observed temporal variations in δR appear to reflect climatic and oceanographic changes. We assess three approaches to quantification of marine reservoir effects using known age samples (from museum collections), tephra isochrones (present onshore/offshore) and paired marine/terrestrial samples (from the same context in, for example, archaeological sites). The strengths and limitations of these approaches are evaluated using examples from the North Atlantic region. It is proposed that, with a suitable protocol, accelerator mass spectrometry (AMS) measurements on paired, short-lived, single entity marine and terrestrial samples from archaeological deposits is the most promising approach to constraining changes over at least the last 5 ky BP

A note on "symmetric" vielbeins in bimetric, massive, perturbative and non perturbative gravities

We consider a manifold endowed with two different vielbeins $E^{A}{}_{\mu}$ and $L^{A}{}_{\mu}$ corresponding to two different metrics $g_{\mu\nu}$ and $f_{\mu\nu}$. Such a situation arises generically in bimetric or massive gravity (including the recently discussed version of de Rham, Gabadadze and Tolley), as well as in perturbative quantum gravity where one vielbein parametrizes the background space-time and the other the dynamical degrees of freedom. We determine the conditions under which the relation $g^{\mu\nu} E^{A}{}_{\mu} L^{B}{}_{\nu} = g^{\mu\nu} E^{B}{}_{\mu} L^{A}{}_{\nu}$ can be imposed (or the "Deser-van Nieuwenhuizen" gauge chosen). We clarify and correct various statements which have been made about this issue.Comment: 20 pages. Section 7, prop. 6 and 7. added. Some results made more precis

From density-matrix renormalization group to matrix product states

In this paper we give an introduction to the numerical density matrix renormalization group (DMRG) algorithm, from the perspective of the more general matrix product state (MPS) formulation. We cover in detail the differences between the original DMRG formulation and the MPS approach, demonstrating the additional flexibility that arises from constructing both the wavefunction and the Hamiltonian in MPS form. We also show how to make use of global symmetries, for both the Abelian and non-Abelian cases.Comment: Numerous small changes and clarifications, added a figur

Geometric De-noising of Protein-Protein Interaction Networks

Understanding complex networks of protein-protein interactions (PPIs) is one of the foremost challenges of the post-genomic era. Due to the recent advances in experimental bio-technology, including yeast-2-hybrid (Y2H), tandem affinity purification (TAP) and other high-throughput methods for protein-protein interaction (PPI) detection, huge amounts of PPI network data are becoming available. Of major concern, however, are the levels of noise and incompleteness. For example, for Y2H screens, it is thought that the false positive rate could be as high as 64%, and the false negative rate may range from 43% to 71%. TAP experiments are believed to have comparable levels of noise

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Mathematical modelling of polyamine metabolism in bloodstream-form trypanosoma brucei: An application to drug target identification

© 2013 Gu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedThis article has been made available through the Brunel Open Access Publishing Fund.We present the first computational kinetic model of polyamine metabolism in bloodstream-form Trypanosoma brucei, the causative agent of human African trypanosomiasis. We systematically extracted the polyamine pathway from the complete metabolic network while still maintaining the predictive capability of the pathway. The kinetic model is constructed on the basis of information gleaned from the experimental biology literature and defined as a set of ordinary differential equations. We applied Michaelis-Menten kinetics featuring regulatory factors to describe enzymatic activities that are well defined. Uncharacterised enzyme kinetics were approximated and justified with available physiological properties of the system. Optimisation-based dynamic simulations were performed to train the model with experimental data and inconsistent predictions prompted an iterative procedure of model refinement. Good agreement between simulation results and measured data reported in various experimental conditions shows that the model has good applicability in spite of there being gaps in the required data. With this kinetic model, the relative importance of the individual pathway enzymes was assessed. We observed that, at low-to-moderate levels of inhibition, enzymes catalysing reactions of de novo AdoMet (MAT) and ornithine production (OrnPt) have more efficient inhibitory effect on total trypanothione content in comparison to other enzymes in the pathway. In our model, prozyme and TSHSyn (the production catalyst of total trypanothione) were also found to exhibit potent control on total trypanothione content but only when they were strongly inhibited. Different chemotherapeutic strategies against T. brucei were investigated using this model and interruption of polyamine synthesis via joint inhibition of MAT or OrnPt together with other polyamine enzymes was identified as an optimal therapeutic strategy.The work was carried out under a PhD programme partly funded by Prof. Ray Welland, School of Computing Science, University of Glasgo

Agent based modelling helps in understanding the rules by which fibroblasts support keratinocyte colony formation

Background: Autologous keratincoytes are routinely expanded using irradiated mouse fibroblasts and bovine serum for clinical use. With growing concerns about the safety of these xenobiotic materials, it is desirable to culture keratinocytes in media without animal derived products. An improved understanding of epithelial/mesenchymal interactions could assist in this. Methodology/Principal Findings: A keratincyte/fibroblast o-culture model was developed by extending an agent-based keratinocyte colony formation model to include the response of keratinocytes to both fibroblasts and serum. The model was validated by comparison of the in virtuo and in vitro multicellular behaviour of keratinocytes and fibroblasts in single and co-culture in Greens medium. To test the robustness of the model, several properties of the fibroblasts were changed to investigate their influence on the multicellular morphogenesis of keratinocyes and fibroblasts. The model was then used to generate hypotheses to explore the interactions of both proliferative and growth arrested fibroblasts with keratinocytes. The key predictions arising from the model which were confirmed by in vitro experiments were that 1) the ratio of fibroblasts to keratinocytes would critically influence keratinocyte colony expansion, 2) this ratio needed to be optimum at the beginning of the co-culture, 3) proliferative fibroblasts would be more effective than irradiated cells in expanding keratinocytes and 4) in the presence of an adequate number of fibroblasts, keratinocyte expansion would be independent of serum. Conclusions: A closely associated computational and biological approach is a powerful tool for understanding complex biological systems such as the interactions between keratinocytes and fibroblasts. The key outcome of this study is the finding that the early addition of a critical ratio of proliferative fibroblasts can give rapid keratinocyte expansion without the use of irradiated mouse fibroblasts and bovine serum