Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus

Dental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of physical, chemical, and molecular means. Recently, studies have attempted to reconstruct diet from archaeological dental calculus using archaeogenetic techniques. While dental calculus may provide a relatively stable environment for DNA preservation, the detection of plants and animals possibly consumed by an individual through DNA analysis is primarily hindered by microbial richness and incomplete reference databases. Moreover, high genomic similarity within eukaryotic groups - such as mammals - can obfuscate precise taxonomic identification. In the current study we demonstrate the challenges associated with accurate taxonomic identification and authentication of dietary taxa in ancient DNA data using both synthetic and ancient dental calculus datasets. We highlight common errors and sources of contamination across ancient DNA datasets, provide recommendations for dietary DNA validation, and call for caution in the interpretation of diet from dental calculus and other archaeological microbiome substrates.J.A.F.Y. was partially funded by the European Research Council (ERC) under the European Union's Horizon 2020 research innovation programme (ERC-2015-StG 678901-FoodTransforms to Philipp W. Stockhammer, Ludwig Maximilian University Munich, Germany). Z.F. was supported by the Werner Siemens Stiftung through Dr. Christina Warinner. This research was supported in part through computational resources provided by the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History (J.A.F.Y).Ye

Theoretical Overview: The New Mesons

After commenting on the state of contemporary hadronic physics and spectroscopy, I highlight four areas where the action is: searching for the relevant degrees of freedom, mesons with beauty and charm, chiral symmetry and the D_{sJ} levels, and X(3872) and the lost tribes of charmonium.Comment: 10 pages, uses jpconf.cls; talk at First Meeting of the APS Topical Group on Hadronic Physic

Measuring the Spectra of High Energy Neutrinos with a Kilometer-Scale Neutrino Telescope

We investigate the potential of a future kilometer-scale neutrino telescope such as the proposed IceCube detector in the South Pole, to measure and disentangle the yet unknown components of the cosmic neutrino flux, the prompt atmospheric neutrinos coming from the decay of charmed particles and the extra-galactic neutrinos, in the 10 TeV to 1 EeV energy range. Assuming a power law type spectra, $d\phi_\nu/dE_\nu \sim \alpha E_\nu^\beta$, we quantify the discriminating power of the IceCube detector and discuss how well we can determine magnitude ($\alpha$) as well as slope ($\beta$) of these two components of the high energy neutrino spectrum, taking into account the background coming from the conventional atmospheric neutrinos.Comment: 21 pages, 7 figure

Theoretical study of lepton events in the atmospheric neutrino experiments at SuperK

Super-Kamiokande has reported the results for the lepton events in the atmospheric neutrino experiment. These results have been presented for a 22.5kT water fiducial mass on an exposure of 1489 days, and the events are divided into sub-GeV, multi-GeV and PC events. We present a study of nuclear medium effects in the sub-GeV energy region of atmospheric neutrino events for the quasielastic scattering, incoherent and coherent pion production processes, as they give the most dominant contribution to the lepton events in this energy region. We have used the atmospheric neutrino flux given by Honda et al. These calculations have been done in the local density approximation. We take into account the effect of Pauli blocking, Fermi motion, Coulomb effect, renormalization of weak transition strengths in the nuclear medium in the case of the quasielastic reactions. The inelastic reactions leading to production of leptons along with pions is calculated in a $\Delta$- dominance model by taking into account the renormalization of $\Delta$ properties in the nuclear medium and the final state interaction effects of the outgoing pions with the residual nucleus. We present the results for the lepton events obtained in our model with and without nuclear medium effects, and compare them with the Monte Carlo predictions used in the simulation and the experimentally observed events reported by the Super-Kamiokande collaboration.Comment: 23 pages, 13 figure

Assessing Communities of Practice in health policy : A conceptual framework as a first step towards empirical research

Peer reviewe

Can lepton flavor violating interactions explain the atmospheric neutrino problem?

We investigate whether flavor changing neutrino interactions (FCNIs) can be sufficiently large to provide a viable solution to the atmospheric neutrino problem. Effective operators induced by heavy boson exchange that allow for flavor changing neutrino scattering off quarks or electrons are related by an $SU(2)_L$ rotation to operators that induce anomalous tau decays. Since $SU(2)_L$ violation is small for New Physics at or above the weak scale, one can use the upper bounds on lepton flavor violating tau decays or on lepton universality violation to put severe, model-independent bounds on the relevant non-standard neutrino interactions. Also $Z$-induced flavor changing neutral currents, due to heavy singlet neutrinos, are too small to be relevant for the atmospheric neutrino anomaly. We conclude that the FCNI solution to the atmospheric neutrino problem is ruled out.Comment: 16 pages, no figures, Late

Adiposity has differing associations with incident coronary heart disease and mortality in the Scottish population: cross-sectional surveys with follow-up

Objective: Investigation of the association of excess adiposity with three different outcomes: all-cause mortality, coronary heart disease (CHD) mortality and incident CHD. Design: Cross-sectional surveys linked to hospital admissions and death records. Subjects: 19 329 adults (aged 18–86 years) from a representative sample of the Scottish population. Measurements: Gender-stratified Cox proportional hazards models were used to estimate hazard ratios (HRs) for all-cause mortality, CHD mortality and incident CHD. Separate models incorporating the anthropometric measurements body mass index (BMI), waist circumference (WC) or waist–hip ratio (WHR) were created adjusted for age, year of survey, smoking status and alcohol consumption. Results: For both genders, BMI-defined obesity (greater than or equal to30 kg m−2) was not associated with either an increased risk of all-cause mortality or CHD mortality. However, there was an increased risk of incident CHD among the obese men (hazard ratio (HR)=1.78; 95% confidence interval=1.37–2.31) and obese women (HR=1.93; 95% confidence interval=1.44–2.59). There was a similar pattern for WC with regard to the three outcomes; for incident CHD, the HR=1.70 (1.35–2.14) for men and 1.71 (1.28–2.29) for women in the highest WC category (men greater than or equal to102 cm, women greater than or equal to88 cm), synonymous with abdominal obesity. For men, the highest category of WHR (greater than or equal to1.0) was associated with an increased risk of all-cause mortality (1.29; 1.04–1.60) and incident CHD (1.55; 1.19–2.01). Among women with a high WHR (greater than or equal to0.85) there was an increased risk of all outcomes: all-cause mortality (1.56; 1.26–1.94), CHD mortality (2.49; 1.36–4.56) and incident CHD (1.76; 1.31–2.38). Conclusions: In this study excess adiposity was associated with an increased risk of incident CHD but not necessarily death. One possibility is that modern medical intervention has contributed to improved survival of first CHD events. The future health burden of increased obesity levels may manifest as an increase in the prevalence of individuals living with CHD and its consequences

The efficacy of whole human genome capture on ancient dental calculus and dentin

Objectives: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. Results: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to fourfold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples

A Study of Cosmic Ray Composition in the Knee Region using Multiple Muon Events in the Soudan 2 Detector

Deep underground muon events recorded by the Soudan 2 detector, located at a depth of 2100 meters of water equivalent, have been used to infer the nuclear composition of cosmic rays in the "knee" region of the cosmic ray energy spectrum. The observed muon multiplicity distribution favors a composition model with a substantial proton content in the energy region 800,000 - 13,000,000 GeV/nucleus.Comment: 38 pages including 11 figures, Latex, submitted to Physical Review

Natural Neutrino Mass Matrix

Naturalness of the neutrino mass hierarchy and mixing is studied. First we select among 12 neutrino mixing patterns a few patterns, which could form the natural neutrino mass matrix. Further we show that if the Dirac neutrino mass matrix is taken as the natural one in the quark sector, then only two mixing patterns without the large mixing lead to the natural right-handed Majorana mass matrix. The rest of the chosen patterns with three degenerate mass solution lead to the unnatural right-handed Majorana mass matrix in the see-saw mechanism. Notice however, that for the chosen two natural patterns there could be a huge mass hierarchy such as ${\cal O}(10^{4\sim 6})$ in order to reproduce the inverse mass hierarchy of the light neutrinos.Comment: 31 pages, LaTex file, no figures, arguments made more clear, main conclusions unchanged, version accepted for publication in PRD Reort-no: Lund-Mph-97/14 Revise