The Late Prehistoric of the East Fork of the Trinity River

Over the last 42 years, the authors have studied in detail the sites and archeological remains ascribed to the Late Prehistoric period of the East Fork of the Trinity River and its tributaries. This includes 20 major sites and a larger number of smaller campsites that occur within a 75 km by 15 km north-south corridor from Collin County in the north to northwestern Kaufman County in the south. As part of this study, we have accessed and examined all known extant collections from previous investigations with a combined artifact assemblage of nearly 32,000 specimens. In addition, we obtained access to the unpublished field notes and maps from many previous researchers and combined them with our own field and laboratory observations. The results of this study confirms the conclusion of both Bruseth and Martin and Prikryl that the \textit{Wylie Focus}, as originally proposed by Stephenson, is an outdated concept. A new chronological sequence consisting of a Woodland period followed by two Late Prehistoric period phases is proposed. In detailing the proposed new sequences, extensive information on each major site, site features such as the distinctive rim-and-pit structures, burials, hearths and caches, and the diagnostic artifacts that characterize each cultural phase are provided. We also detail how the Late Prehistoric of the East Fork is a unique culture, similar but yet distinctly different from the surrounding sites including Bird Point Island (41FT201) and Adams Ranch (41NV177) in Freestone and Navarro counties

Ceramic Types from Late Prehistoric Sites along the East Fork of the Trinity River

Ceramics are one of the key diagnostic artifacts that define the Late Prehistoric culture of the peoples that lived along the East Fork of the Trinity and its tributaries. We are completing a 42 year re evaluation of the Late Prehistoric period of the area and have st udied nearly 32,000 artifacts, of which over 10,200 are ceramic sherds. From this study, 20 distinct ceramic types have been recognized. Plain ware, both shell tempered and sandy paste/grog tempered, are the predominant ceramic types present, comprising ov er 90 percent of the total ceramic assemblage. While there is little direct evidence for indigenous manufacture, the abundance of these types suggests they were produced locally. Lesser quantities of decorated ware of distinct Caddo ceramic types from the Red River and East Texas suggest they are likely the product of exchange. There is also a small amount of Puebloan material indicative of a longer distance exchange

Single electron charging of impurity sites visualized by scanning gate experiments on a quantum point contact

A quantum point contact (QPC) patterned on a two-dimensional electron gas is investigated with a scanning gate setup operated at a temperature of 300 mK. The conductance of the point contact is recorded while the local potential is modified by scanning the tip. Single electron charging of impurities induced by the local potential is observed as a stepwise conductance change of the constriction. By selectively changing the state of some of these impurities, it is possible to observe changes in transmission resonances of the QPC. The location of such impurities is determined, and their density is estimated to be below 50 per \mu m^2, corresponding to less than 1 % of the doping concentration

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease

Copyright: © 2013 Eyre 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 creditedClostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2–8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients’ first and last samples was 60 (29.5–118.5) [0–561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00–1.28) and within-host diversity was 0.28 SNVs/called genome (0.05–0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.Peer reviewe

A Bayesian semi-parametric model for thermal proteome profiling.

Funder: Wellcome TrustThe thermal stability of proteins can be altered when they interact with small molecules, other biomolecules or are subject to post-translation modifications. Thus monitoring the thermal stability of proteins under various cellular perturbations can provide insights into protein function, as well as potentially determine drug targets and off-targets. Thermal proteome profiling is a highly multiplexed mass-spectrommetry method for monitoring the melting behaviour of thousands of proteins in a single experiment. In essence, thermal proteome profiling assumes that proteins denature upon heating and hence become insoluble. Thus, by tracking the relative solubility of proteins at sequentially increasing temperatures, one can report on the thermal stability of a protein. Standard thermodynamics predicts a sigmoidal relationship between temperature and relative solubility and this is the basis of current robust statistical procedures. However, current methods do not model deviations from this behaviour and they do not quantify uncertainty in the melting profiles. To overcome these challenges, we propose the application of Bayesian functional data analysis tools which allow complex temperature-solubility behaviours. Our methods have improved sensitivity over the state-of-the art, identify new drug-protein associations and have less restrictive assumptions than current approaches. Our methods allows for comprehensive analysis of proteins that deviate from the predicted sigmoid behaviour and we uncover potentially biphasic phenomena with a series of published datasets

Electron-beam propagation in a two-dimensional electron gas

A quantum mechanical model based on a Green's function approach has been used to calculate the transmission probability of electrons traversing a two-dimensional electron gas injected and detected via mode-selective quantum point contacts. Two-dimensional scattering potentials, back-scattering, and temperature effects were included in order to compare the calculated results with experimentally observed interference patterns. The results yield detailed information about the distribution, size, and the energetic height of the scattering potentials.Comment: 7 pages, 6 figure

Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution

Clostridioides difficile is a common cause of nosocomial diarrhoea. Toxins TcdA and TcdB are considered to be the main virulence factors and are encoded by the PaLoc region, while the binary toxin encoded in the CdtLoc region also contributes to pathogenicity. Variant toxinotypes reflect the genetic diversity of a key toxin-encoding 19 kb genetic element (the PaLoc). Here, we present analysis of a comprehensive collection of all known major C. difficile toxinotypes to address the evolutionary relationships of the toxin gene variants, the mechanisms underlying the origin and development of variability in toxin genes and the PaLoc, and the relationship between structure and function in TcdB variants. The structure of both toxin genes is modular, composed of interspersed blocks of sequences corresponding to functional domains and having different evolutionary histories, as shown by the distribution of mutations along the toxin genes and by incongruences of domain phylogenies compared to overall C. difficile cluster organization. In TcdB protein, four mutation patterns could be differentiated, which correlated very well with the type of TcdB cytopathic effect (CPE) on cultured cells. Mapping these mutations to the three-dimensional structure of the TcdB showed that the majority of the variation occurs in surface residues and that point mutation at residue 449 in alpha helix 16 differentiated strains with different types of CPE. In contrast to the PaLoc, phylogenetic trees of the CdtLoc were more consistent with the core genome phylogenies, but there were clues that CdtLoc can also be exchanged between strains

rRNA sequencing in molecular microbiological diagnosis of bacterial infections in the autopsy setting

Diagnosing the aetiology of infectious diseases at autopsy, such as pneumonia, meningitis, sepsis or SUDI, is complicated due to issues including post mortem contamination, difficulty culturing fastidious organisms and subjective interpretation of polymicrobial cultures. Death of organisms may also occur post mortem, especially if antibiotics were given to the patient, but residual DNA from non-viable organisms, amenable to molecular detection, may remain. The 16S rRNA gene is present in all bacteria with conserved and hyper-variable regions along its length, allowing amplification and sequencing of all bacterial 16S sequences present in a sample. 16S sequencing offers potential advantages over culture-based diagnostics and is increasingly used in clinical practice. It has been used to identify bacteria in formalin fixed paraffin embedded (FFPE) surgical pathology specimens but its use has not been reported in autopsy diagnosis. This talk will summarise a study aimed to assess the utility of 16S sequencing as an adjunctive microbiological test in the autopsy. Our preliminary work has used post mortem lung tissue samples from children dying with pneumonia as part of the Pneumonia Etiology Research for Child Health (PERCH) project. The technique has identified known pathogens in some cases and provided additional diagnostic information in others. The presentation will discuss the technical aspects of 16S sequencing from FFPE and autopsy material, and the issues surrounding its application to diagnosis in comparison with standard culture based diagnostics on surgical/autopsy material