Neutron activation analysis of archeological artifacts using the ISIS pulsed neutron source

Archeological artifacts can be analyzed after neutron irradiation at the pulsed ISIS neutron and muon source, UK, using a newly installed high purity germanium gamma ray spectrometer to perform neutron activation analysis. In this work, the details of the measurement methods and data analysis are presented. In particular, it is explained how Monte Carlo calculations are necessary to evaluate the detection efficiency, taking into account self-shielding effects. The results for two certified bronze standards are presented. The good agreement between expected and measured compositions is promising for the use of this technique for archeological artifacts where the elemental concentration is often unknown. As an example, the analysis of a Chinese sword from the first or second century BC is presented

The Hand of Cercopithecoides williamsi (Mammalia, Primates): Earliest Evidence for Thumb Reduction among Colobine Monkeys

Thumb reduction is among the most important features distinguishing the African and Asian colobines from each other and from other Old World monkeys. In this study we demonstrate that the partial skeleton KNM-ER 4420 from Koobi Fora, Kenya, dated to 1.9 Ma and assigned to the Plio-Pleistocene colobine species Cercopithecoides williamsi, shows marked reduction of its first metacarpal relative to the medial metacarpals. Thus, KNM-ER 4420 is the first documented occurrence of cercopithecid pollical reduction in the fossil record. In the size of its first metacarpal relative to the medial metacarpals, C. williamsi is similar to extant African colobines, but different from cercopithecines, extant Asian colobines and the Late Miocene colobines Microcolobus and Mesopithecus. This feature clearly links the genus Cercopithecoides with the extant African colobine clade and makes it the first definitive African colobine in the fossil record. The postcranial adaptations to terrestriality in Cercopithecoides are most likely secondary, while ancestral colobinans (and colobines) were arboreal. Finally, the absence of any evidence for pollical reduction in Mesopithecus implies either independent thumb reduction in African and Asian colobines or multiple colobine dispersal events out of Africa. Based on the available evidence, we consider the first scenario more likely

Herbivore-induced shifts in carbon and nitrogen allocation in red oak seedlings

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65993/1/j.1469-8137.2008.02420.x.pd

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo.Peer reviewe

Evolution of the modern baboon (Papio hamadryas): A reassessment of the African Plio-Pleistocene record

Baboons ( Papio hamadryas) are among the most successful extant primates, with a minimum of six distinctive forms throughout Sub-Saharan Africa. However, their presence in the fossil record is unclear. Three early fossil taxa are generally recognized, all from South Africa: Papio izodi , Papio robinsoni and Papio angusticeps. Because of their derived appearance, P. angusticeps and P. robinsoni have sometimes been considered subspecies of P. hamadryas and have been used as biochronological markers for the Plio- Pleistocene hominin sites where they are found. We reexamined fossil Papio forms from across Africa with an emphasis on their distinguishing features and distribution. We fi nd that P. robinsoni and P. angusticeps are distinct from each other in several cranial features, but overlap extensively in dental size. Contrary to previous assessments, no diagnostic cranio- mandibular material suggests these two forms co-occur, and dental variation at each site is comparable to that within P. h. ursinus , suggesting that only one form is present in each case. P izodi, however, may co-occur with P. robinsoni, or another Papio form, at Sterkfontein Member 4. P izodi appears more primitive than P. robinsoni and P. angusticeps . P. robinsoni is slightly distinct from P. hamadryas subspecies in its combination of features while P. angusticeps might be included within one of the modern P. hamadryas varieties (i.e., P. h. angusticeps ). No de fi nitive Papio fossils are currently documented in eastern Africa until the Middle Pleistocene, pointing to southern Africa as the geographic place of origin for the genus. These results have implications for Plio-Pleistocene biochronology and baboon evolution

In-Plane Anisotropy and Temperature Dependence of Oxygen Phonon Modes in YBa₂Cu₃O₆.₉₅

Inelastic pulsed neutron scattering measurements on YBa2Cu3O6.95 single crystals indicate that the sample has a distinct a-b plane anisotropy in the oxygen vibrations. The Cu-O bond-stretching-type phonons, which are suspected to interact strongly with charge, are simultaneously observed along the a and b directions due to a 7-meV splitting arising from the orthorhombicity, even though the sample is twinned. The bond-stretching LO branch with the polarization along a (perpendicular to the chain) loses intensity beyond the middle of the zone, indicating branch splitting as seen in doped nickelates, with the second branch being located at 10 meV below. The mode along b has a continuous dispersion. These modes show temperature dependence, which parallels that of superconductive order parameter, suggesting significant involvement of phonons in the superconductivity of this compound

Transmitted Drug Resistance in the CFAR Network of Integrated Clinical Systems Cohort: Prevalence and Effects on Pre-Therapy CD4 and Viral Load

Human immunodeficiency virus type 1 (HIV-1) genomes often carry one or more mutations associated with drug resistance upon transmission into a therapy-naïve individual. We assessed the prevalence and clinical significance of transmitted drug resistance (TDR) in chronically-infected therapy-naïve patients enrolled in a multi-center cohort in North America. Pre-therapy clinical significance was quantified by plasma viral load (pVL) and CD4+ cell count (CD4) at baseline. Naïve bulk sequences of HIV-1 protease and reverse transcriptase (RT) were screened for resistance mutations as defined by the World Health Organization surveillance list. The overall prevalence of TDR was 14.2%. We used a Bayesian network to identify co-transmission of TDR mutations in clusters associated with specific drugs or drug classes. Aggregate effects of mutations by drug class were estimated by fitting linear models of pVL and CD4 on weighted sums over TDR mutations according to the Stanford HIV Database algorithm. Transmitted resistance to both classes of reverse transcriptase inhibitors was significantly associated with lower CD4, but had opposing effects on pVL. In contrast, position-specific analyses of TDR mutations revealed substantial effects on CD4 and pVL at several residue positions that were being masked in the aggregate analyses, and significant interaction effects as well. Residue positions in RT with predominant effects on CD4 or pVL (D67 and M184) were re-evaluated in causal models using an inverse probability-weighting scheme to address the problem of confounding by other mutations and demographic or risk factors. We found that causal effect estimates of mutations M184V/I ( pVL) and D67N/G ( and pVL) were compensated by K103N/S and K219Q/E/N/R. As TDR becomes an increasing dilemma in this modern era of highly-active antiretroviral therapy, these results have immediate significance for the clinical management of HIV-1 infections and our understanding of the ongoing adaptation of HIV-1 to human populations