A Substance Flow Model for Global Phosphorus

A mechanistic model of phosphorus flows through the global food system was developed to address questions about the relative effectiveness of and interactions among potential conservation interventions. Phosphorus is required as a fertilizer for producing food, and there is no substitute. Most phosphorus used in agriculture is mined, and 75% of the world’s reserves are controlled by a single country: Morocco. Thus the world’s food supply is potentially vulnerable to geopolitical conditions. Although known reserves can satisfy current demand for several centuries, it is nevertheless the case that an essential resource is being used unsustainably. Only about 10% of the phosphorus used in agriculture reaches our plates. Losses along the way contribute to water pollution, causing eutrophication. In freshwater bodies this produces toxic drinking water and fish kills. In the coastal marine environment eutrophication causes hypoxic (low oxygen) zones, popularly called “dead zones, in many parts of the world. Thus conservation of phosphorus is of interest both to preserve the resource and to prevent pollution. The conservation interventions considered include: population control; reduction in meat fraction in the diet (MFD); animal manure use efficiency (MUE); agricultural phosphorus use efficiency (PUE); the fraction of food supply that is wasted; the fraction of food waste that is recycled; the fraction of human waste that is recycled. The model shows that the meat fraction in the diet is the most sensitive of these factors, and this factor interacts with PUE and MUE. Furthermore, there is a minimum MFD below which it actually becomes necessary to mine more phosphorus. Another conclusion is that recycling is much less effective than reduction in conserving the resource

MeerKLASS: MeerKAT Large Area Synoptic Survey

We discuss the ground-breaking science that will be possible with a wide area survey, using the MeerKAT telescope, known as MeerKLASS (MeerKAT Large Area Synoptic Survey). The current specifications of MeerKAT make it a great fit for science applications that require large survey speeds but not necessarily high angular resolutions. In particular, for cosmology, a large survey over $\sim 4,000 \, {\rm deg}^2$ for $\sim 4,000$ hours will potentially provide the first ever measurements of the baryon acoustic oscillations using the 21cm intensity mapping technique, with enough accuracy to impose constraints on the nature of dark energy. The combination with multi-wavelength data will give unique additional information, such as exquisite constraints on primordial non-Gaussianity using the multi-tracer technique, as well as a better handle on foregrounds and systematics. Such a wide survey with MeerKAT is also a great match for HI galaxy studies, providing unrivalled statistics in the pre-SKA era for galaxies resolved in the HI emission line beyond local structures at z > 0.01. It will also produce a large continuum galaxy sample down to a depth of about 5\,$\mu$Jy in L-band, which is quite unique over such large areas and will allow studies of the large-scale structure of the Universe out to high redshifts, complementing the galaxy HI survey to form a transformational multi-wavelength approach to study galaxy dynamics and evolution. Finally, the same survey will supply unique information for a range of other science applications, including a large statistical investigation of galaxy clusters as well as produce a rotation measure map across a huge swathe of the sky. The MeerKLASS survey will be a crucial step on the road to using SKA1-MID for cosmological applications and other commensal surveys, as described in the top priority SKA key science projects (abridged).Comment: Larger version of the paper submitted to the Proceedings of Science, "MeerKAT Science: On the Pathway to the SKA", Stellenbosch, 25-27 May 201

Superior T memory stem cell persistence supports long-lived T cell memory

Long-lived memory T cells are able to persist in the host in the absence of antigen; however, the mechanism by which they are maintained is not well understood. Recently, a subset of human T cells, stem cell memory T cells (TSCM cells), was shown to be self-renewing and multipotent, thereby providing a potential reservoir for T cell memory throughout life. However, their in vivo dynamics and homeostasis still remain to be defined due to the lack of suitable animal models. We identified T cells with a TSCM phenotype and stem cell–like properties in nonhuman primates. These cells were the least-differentiated memory subset, were functionally distinct from conventional memory cells, and served as precursors of central memory. Antigen-specific TSCM cells preferentially localized to LNs and were virtually absent from mucosal surfaces. They were generated in the acute phase of viral infection, preferentially survived in comparison with all other memory cells following elimination of antigen, and stably persisted for the long term. Thus, one mechanism for maintenance of long-term T cell memory derives from the unique homeostatic properties of TSCM cells. Vaccination strategies designed to elicit durable cellular immunity should target the generation of TSCM cells

Efficient Transmission and Characterization of Creutzfeldt–Jakob Disease Strains in Bank Voles

Transmission of prions between species is limited by the “species barrier,” which hampers a full characterization of human prion strains in the mouse model. We report that the efficiency of primary transmission of prions from Creutzfeldt–Jakob disease patients to a wild rodent species, the bank vole (Clethrionomys glareolus), is comparable to that reported in transgenic mice carrying human prion protein, in spite of a low prion protein–sequence homology between man and vole. Voles infected with sporadic and genetic Creutzfeldt–Jakob disease isolates show strain-specific patterns of spongiform degeneration and pathological prion protein–deposition, and accumulate protease-resistant prion protein with biochemical properties similar to the human counterpart. Adaptation of genetic Creutzfeldt–Jakob disease isolates to voles shows little or no evidence of a transmission barrier, in contrast to the striking barriers observed during transmission of mouse, hamster, and sheep prions to voles. Our results imply that in voles there is no clear relationship between the degree of homology of the prion protein of the donor and recipient species and susceptibility, consistent with the view that the prion strain gives a major contribution to the species barrier. The vole is therefore a valuable model to study human prion diversity and, being susceptible to a range of animal prions, represents a unique tool for comparing isolates from different species

Analysis of multiple single nucleotide polymorphisms closely positioned in the ovine PRNP gene using linear fluorescent probes and melting curve analysis

<p>Abstract</p> <p>Background</p> <p>Resistance and susceptibility to scrapie has been associated with single nucleotide polymorphisms located within codons 136, 154 and 171 of the ovine prion protein gene (<it>PRNP</it>). Dual-labelled HyBeacon probes were developed to analyse single and clustered polymorphisms within these and neighbouring codons.</p> <p>Methods</p> <p>Extracted DNAs and unpurified blood samples were genotyped with respect to polymorphisms in <it>PRNP </it>codons 136, 141, 154 and 171. PCR amplicons were investigated using a LightTyper instrument, measuring the stability of probe/target hybridisation through peak melting temperatures and determining the sequence of nucleotides at polymorphic sites.</p> <p>Results</p> <p>The performance of HyBeacon assays was evaluated in a validation study comparing genotypes with those obtained using a primer extension assay (Sequenom MassEXTEND) analysed on a MALDI-ToF mass spectrometer. Over 12,000 sheep samples were successfully genotyped, reliably detecting A¹³⁶, V¹³⁶, T¹³⁶, T¹³⁷, L¹⁴¹, F¹⁴¹R¹⁵⁴, H¹⁵⁴, L¹⁶⁸, R¹⁷¹, Q¹⁷¹, H¹⁷¹and K¹⁷¹sequence variants using only 4 HyBeacon probes.</p> <p>Conclusion</p> <p>HyBeacon assays provide an extremely robust and accurate method for the analysis of single and clustered <it>PRNP </it>polymorphisms in a high-throughput format. The flexibility of the diagnostic tests ensures that samples are correctly genotyped even in the presence of additional sequence variations that flank the polymorphisms of interest. Such sequence variations may also be neutralised using universal bases such as 5-nitroindole if required.</p

Galaxy Counts at 24 Microns in the SWIRE Fields

This paper presents galaxy source counts at 24 microns in the six Spitzer Wide-field InfraRed Extragalactic (SWIRE) fields. The source counts are compared to counts in other fields, and to model predictions that have been updated since the launch of Spitzer. This analysis confirms a very steep rise in the Euclidean-normalized differential number counts between 2 mJy and 0.3 mJy. Variations in the counts between fields show the effects of sample variance in the flux range 0.5-10 mJy, up to 100% larger than Poisson errors. Nonetheless, a "shoulder" in the normalized counts persists at around 3 mJy. The peak of the normalized counts at 0.3 mJy is higher and narrower than most models predict. In the ELAIS N1 field, the 24 micron data are combined with Spitzer-IRAC data and five-band optical imaging, and these bandmerged data are fit with photometric redshift templates. Above 1 mJy the counts are dominated by galaxies at z less than 0.3. By 300 microJy, about 25% are between z ~ 0.3-0.8, and a significant fraction are at z ~ 1.3-2. At low redshifts the counts are dominated by spirals, and starbursts rise in number density to outnumber the spirals' contribution to the counts below 1 mJy.Comment: 10 pages, 8 figures, accepted 3 November 2007 for publication in The Astronomical Journal, formatted with emulateapj styl

<i>Gaia</i> Data Release 1. Summary of the astrometric, photometric, and survey properties

Context. At about 1000 days after the launch of Gaia we present the first Gaia data release, Gaia DR1, consisting of astrometry and photometry for over 1 billion sources brighter than magnitude 20.7. Aims. A summary of Gaia DR1 is presented along with illustrations of the scientific quality of the data, followed by a discussion of the limitations due to the preliminary nature of this release. Methods. The raw data collected by Gaia during the first 14 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into an astrometric and photometric catalogue. Results. Gaia DR1 consists of three components: a primary astrometric data set which contains the positions, parallaxes, and mean proper motions for about 2 million of the brightest stars in common with the HIPPARCOS and Tycho-2 catalogues – a realisation of the Tycho-Gaia Astrometric Solution (TGAS) – and a secondary astrometric data set containing the positions for an additional 1.1 billion sources. The second component is the photometric data set, consisting of mean G-band magnitudes for all sources. The G-band light curves and the characteristics of ∼3000 Cepheid and RR-Lyrae stars, observed at high cadence around the south ecliptic pole, form the third component. For the primary astrometric data set the typical uncertainty is about 0.3 mas for the positions and parallaxes, and about 1 mas yr−1 for the proper motions. A systematic component of ∼0.3 mas should be added to the parallax uncertainties. For the subset of ∼94 000 HIPPARCOS stars in the primary data set, the proper motions are much more precise at about 0.06 mas yr−1. For the secondary astrometric data set, the typical uncertainty of the positions is ∼10 mas. The median uncertainties on the mean G-band magnitudes range from the mmag level to ∼0.03 mag over the magnitude range 5 to 20.7. Conclusions. Gaia DR1 is an important milestone ahead of the next Gaia data release, which will feature five-parameter astrometry for all sources. Extensive validation shows that Gaia DR1 represents a major advance in the mapping of the heavens and the availability of basic stellar data that underpin observational astrophysics. Nevertheless, the very preliminary nature of this first Gaia data release does lead to a number of important limitations to the data quality which should be carefully considered before drawing conclusions from the data

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead.

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology

Photometric redshifts in the SWIRE Survey

We present the SWIRE Photometric Redshift Catalogue, 1025119 redshifts of unprecedented reliability and accuracy. Our method is based on fixed galaxy and QSO templates applied to data at 0.36-4.5 mu, and on a set of 4 infrared emission templates fitted to infrared excess data at 3.6-170 mu. The code involves two passes through the data, to try to optimize recognition of AGN dust tori. A few carefully justified priors are used and are the key to supression of outliers. Extinction, A_V, is allowed as a free parameter. We use a set of 5982 spectroscopic redshifts, taken from the literature and from our own spectroscopic surveys, to analyze the performance of our method as a function of the number of photometric bands used in the solution and the reduced chi^2. For 7 photometric bands the rms value of (z_{phot}-z_{spec})/(1+z_{spec}) is 3.5%, and the percentage of catastrophic outliers is ~1%. We discuss the redshift distributions at 3.6 and 24 mu. In individual fields, structure in the redshift distribution corresponds to clusters which can be seen in the spectroscopic redshift distribution. 10% of sources in the SWIRE photometric redshift catalogue have z >2, and 4% have z>3, so this catalogue is a huge resource for high redshift galaxies. A key parameter for understanding the evolutionary status of infrared galaxies is L_{ir}/L_{opt}, which can be interpreted as the specific star-formation rate for starbursts. For dust tori around Type 1 AGN, L_{tor}/L_{opt} is a measure of the torus covering factor and we deduce a mean covering factor of 40%.Comment: 22 pages, 23 figures. Accepted for publication in MNRAS. Revised 28/2/08. Version with figures at full resolution at http://astro.ic.ac.uk/~mrr/swirephotzcat/swirephotz5.pdf.g