The RIPE NCC internet measurement data repository

This paper describes datasets that will shortly be made available to the research community through an Internet measurement data repository operated by the RIPE NCC. The datasets include measurements collected by RIPE NCC projects, packet trace sets recovered from the defunct NLANR website and datasets collected and currently hosted by other research institutions. This work aims to raise awareness of these datasets amongst researchers and to promote discussion about possible changes to the data collection processes to ensure that the measurements are relevant and useful to the community

Efficient depletion of host DNA contamination in malaria clinical sequencing.

The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches Plasmodium falciparum DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci

Epidemiology of alcohol-related emergency hospital admissions in children and adolescents: an e-cohort analysis in Wales in 2006-2011

Funding: This work was supported by funds from the Economic and Social Research Council, the Medical Research Council and Alcohol Research UK to the ELAStiC Project (ES/L015471/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data Availability: The data used in this study are available in the SAIL databank at Swansea University, Swansea, UK. All proposals to use SAIL data are subject to review by an independent Information Governance Review Panel (IGRP). Before any data can be accessed, approval must be given by the IGRP. The IGRP gives careful consideration to each project to ensure proper and appropriate use of SAIL data. When access has been granted, it is gained through a privacy-protecting safe haven and remote access system referred to as the SAIL Gateway. SAIL has established an application process to be followed by anyone who would like to access data via SAIL https://www.saildatabank.com/application-process.Peer reviewedPublisher PD

Understanding cooperation through fitness interdependence

Some acts of human cooperation are not easily explained by traditional models of kinship or reciprocity. Fitness interdependence may provide a unifying conceptual framework, in which cooperation arises from the mutual dependence for survival or reproduction, as occurs among mates, risk-pooling partnerships and brothers-in-arms

Photometry of Variable Stars from Dome A, Antarctica

Dome A on the Antarctic plateau is likely one of the best observing sites on Earth thanks to the excellent atmospheric conditions present at the site during the long polar winter night. We present high-cadence time-series aperture photometry of 10,000 stars with i<14.5 mag located in a 23 square-degree region centered on the south celestial pole. The photometry was obtained with one of the CSTAR telescopes during 128 days of the 2008 Antarctic winter. We used this photometric data set to derive site statistics for Dome A and to search for variable stars. Thanks to the nearly-uninterrupted synoptic coverage, we find 6 times as many variables as previous surveys with similar magnitude limits. We detected 157 variable stars, of which 55% are unclassified, 27% are likely binaries and 17% are likely pulsating stars. The latter category includes delta Scuti, gamma Doradus and RR Lyrae variables. One variable may be a transiting exoplanet.Comment: Accepted for publication in the Astronomical Journal. PDF version with high-resolution figures available at http://faculty.physics.tamu.edu/lmacri/papers/wang11.pd

Oxygen isotope dendrochronology of Llwyn Celyn; One of the oldest houses in Wales

We report the application of oxygen isotope dendrochronology to date a high-status and remarkably unaltered late medieval hall house on the eastern border of South Wales. The oak timbers have either short and complacent ring series, or very strong growth disturbance, and none were suitable for ring-width dendrochronology. By using stable oxygen isotopes from the latewood cellulose, rather than ring widths, it was possible to cross-match and date all 14 timber samples and to provide felling dates related to several phases of building. The hall and solar cross-wing were constructed shortly after 1420CE, which is remarkably early. The house was upgraded using timbers felled in the winter of 1695/6CE by ceiling over of the hall and inserting a chimney. A separate small domestic building was added at the same time and the addition of the kitchen is likely to be contemporaneous. A substantial beast house was added a few years before the house was refurbished, emphasising the importance of cattle as the main source of wealth. A small barn with timbers felled in spring 1843 CE was added later. Llwyn Celyn is one of the most important domestic buildings in Wales, but without the new approach none of the phases of its evolution could have been dated precisely. Oxygen isotope dendrochronology has enormous potential for dating timbers that have small numbers of rings and/or show severe growth disturbance and it works well in regions where tree growth is not strongly constrained by climate. The research was generously supported by the Leverhulme Trust, Natural Environment Research Council, Landmark Trust and the UK National Lottery Heritage Fund

Challenges in mathematical cognition: a collaboratively-derived research agenda

This paper reports on a collaborative exercise designed to generate a coherent agenda for research on mathematical cognition. Following an established method, the exercise brought together 16 mathematical cognition researchers from across the fields of mathematics education, psychology and neuroscience. These participants engaged in a process in which they generated an initial list of research questions with the potential to significantly advance understanding of mathematical cognition, winnowed this list to a smaller set of priority questions, and refined the eventual questions to meet criteria related to clarity, specificity and practicability. The resulting list comprises 26 questions divided into six broad topic areas: elucidating the nature of mathematical thinking, mapping predictors and processes of competence development, charting developmental trajectories and their interactions, fostering conceptual understanding and procedural skill, designing effective interventions, and developing valid and reliable measures. In presenting these questions in this paper, we intend to support greater coherence in both investigation and reporting, to build a stronger base of information for consideration by policymakers, and to encourage researchers to take a consilient approach to addressing important challenges in mathematical cognition

Measuring D_A and H at z=0.35 from the SDSS DR7 LRGs using baryon acoustic oscillations

We present measurements of the angular diameter distance D_A(z) and the Hubble parameter H(z) at z=0.35 using the anisotropy of the baryon acoustic oscillation (BAO) signal measured in the galaxy clustering distribution of the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) Luminous Red Galaxies (LRG) sample. Our work is the first to apply density-field reconstruction to an anisotropic analysis of the acoustic peak. Reconstruction partially removes the effects of non-linear evolution and redshift-space distortions in order to sharpen the acoustic signal. We present the theoretical framework behind the anisotropic BAO signal and give a detailed account of the fitting model we use to extract this signal from the data. Our method focuses only on the acoustic peak anisotropy, rather than the more model-dependent anisotropic information from the broadband power. We test the robustness of our analysis methods on 160 LasDamas DR7 mock catalogues and find that our models are unbiased at the ~0.2% level in measuring the BAO anisotropy. After reconstruction we measure D_A(z=0.35)=1050+/-38 Mpc and H(z=0.35)=84.4+/-7.0 km/s/Mpc assuming a sound horizon of r_s=152.76 Mpc. Note that these measurements are correlated with a correlation coefficient of 0.58. This represents a factor of 1.4 improvement in the error on D_A relative to the pre-reconstruction case; a factor of 1.2 improvement is seen for H.Comment: 30 pages, 21 figures, accepted by MNRAS, updated to version accepted by journa

Neutrino Interferometry In Curved Spacetime

Gravitational lensing introduces the possibility of multiple (macroscopic) paths from an astrophysical neutrino source to a detector. Such a multiplicity of paths can allow for quantum mechanical interference to take place that is qualitatively different to neutrino oscillations in flat space. After an illustrative example clarifying some under-appreciated subtleties of the phase calculation, we derive the form of the quantum mechanical phase for a neutrino mass eigenstate propagating non-radially through a Schwarzschild metric. We subsequently determine the form of the interference pattern seen at a detector. We show that the neutrino signal from a supernova could exhibit the interference effects we discuss were it lensed by an object in a suitable mass range. We finally conclude, however, that -- given current neutrino detector technology -- the probability of such lensing occurring for a (neutrino-detectable) supernova is tiny in the immediate future.Comment: 25 pages, 1 .eps figure. Updated version -- with simplified notation -- accepted for publication in Phys.Rev.D. Extra author adde