Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27–29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database

Peptide transporter 2 (PEPT2) expression in brain protects against 5-aminolevulinic acid neurotoxicity

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65903/1/j.1471-4159.2007.04905.x.pd

Magnetic moments of the low-lying JP= 1/2−J^P=\,1/2^-, 3/2−3/2^- Λ\Lambda resonances within the framework of the chiral quark model

The magnetic moments of the low-lying spin-parity $J^P=$ $1/2^-$, $3/2^-$ $\Lambda$ resonances, like, for example, $\Lambda(1405)$ $1/2^-$, $\Lambda(1520)$ $3/2^-$, as well as their transition magnetic moments, are calculated using the chiral quark model. The results found are compared with those obtained from the nonrelativistic quark model and those of unitary chiral theories, where some of these states are generated through the dynamics of two hadron coupled channels and their unitarization

Dynamically generated resonances

In this talk I report on recent work related to the dynamical generation of baryonic resonances, some made up from pseudoscalar meson-baryon, others from vector meson-baryon and a third type from two meson-one baryon systems. We can establish a correspondence with known baryonic resonances, reinforcing conclusions previously drawn and bringing new light on the nature of some baryonic resonances of higher mass.Comment: Talk given at the Workshop on physics of the excited nucleon-NSTAR 2009, Beijing, april 200

The pd --> ^3He eta pi0 reaction at T_p = 1450 MeV

The cross section for the pd --> ^3He eta pi0 reaction has been measured at a beam energy of 1450 MeV using the WASA detector at the CELSIUS storage ring and detecting one ^3He and four photons from the decays of the two photons. The data indicate that the production mechanism involves the formation of the Delta(1232) isobar. Although the beam energy does not allow the full peak of this resonance to be seen, the invariant masses of all three pairs of final state particles are well reproduced by a phase space Monte Carlo simulation weighted with the p-wave factor of the square of the pi^0 momentum in the ^3Hepi^0 system.Comment: 10 pages, 5 figure

Quantum Histories and Quantum Gravity

This paper reviews the histories approach to quantum mechanics. This discussion is then applied to theories of quantum gravity. It is argued that some of the quantum histories must approximate (in a suitable sense) to classical histories, if the correct classical regime is to be recovered. This observation has significance for the formulation of new theories (such as quantum gravity theories) as it puts a constraint on the kinematics, if the quantum/classical correspondence principle is to be preserved. Consequences for quantum gravity, particularly for Lorentz symmetry and the idea of "emergent geometry", are discussed.Comment: 35 pages (29 pages main body), two figure

P-wave excited baryons from pion- and photo-induced hyperon production

We report evidence for $N(1710)P_{11}$, $N(1875)P_{11}$, $N(1900)P_{13}$, $\Delta(1600)P_{33}$, $\Delta(1910)P_{31}$, and $\Delta(1920)P_{33}$, and find indications that $N(1900)P_{13}$ might have a companion state at 1970\,MeV. The controversial $\Delta(1750)P_{31}$ is not seen. The evidence is derived from a study of data on pion- and photo-induced hyperon production, but other data are included as well. Most of the resonances reported here were found in the Karlsruhe-Helsinki (KH84) and the Carnegie-Mellon (CM) analyses but were challenged recently by the Data Analysis Center at GWU. Our analysis is constrained by the energy independent $\pi N$ scattering amplitudes from either KH84 or GWU. The two $\pi N$ amplitudes from KH84 or GWU, respectively, lead to slightly different $\pi N$ branching ratios of contributing resonances but the debated resonances are required in both series of fits.Comment: 22 pages, 28 figures. Some additional sets of data are adde

Common Variants at 10 Genomic Loci Influence Hemoglobin A(1C) Levels via Glycemic and Nonglycemic Pathways

OBJECTIVE Glycated hemoglobin (HbA1c), used to monitor and diagnose diabetes, is influenced by average glycemia over a 2- to 3-month period. Genetic factors affecting expression, turnover, and abnormal glycation of hemoglobin could also be associated with increased levels of HbA1c. We aimed to identify such genetic factors and investigate the extent to which they influence diabetes classification based on HbA1c levels. RESEARCH DESIGN AND METHODS We studied associations with HbA1c in up to 46,368 nondiabetic adults of European descent from 23 genome-wide association studies (GWAS) and 8 cohorts with de novo genotyped single nucleotide polymorphisms (SNPs). We combined studies using inverse-variance meta-analysis and tested mediation by glycemia using conditional analyses. We estimated the global effect of HbA1c loci using a multilocus risk score, and used net reclassification to estimate genetic effects on diabetes screening. RESULTS Ten loci reached genome-wide significant association with HbA1c, including six new loci near FN3K (lead SNP/P value, rs1046896/P = 1.6 × 10−26), HFE (rs1800562/P = 2.6 × 10−20), TMPRSS6 (rs855791/P = 2.7 × 10−14), ANK1 (rs4737009/P = 6.1 × 10−12), SPTA1 (rs2779116/P = 2.8 × 10−9) and ATP11A/TUBGCP3 (rs7998202/P = 5.2 × 10−9), and four known HbA1c loci: HK1 (rs16926246/P = 3.1 × 10−54), MTNR1B (rs1387153/P = 4.0 × 10−11), GCK (rs1799884/P = 1.5 × 10−20) and G6PC2/ABCB11 (rs552976/P = 8.2 × 10−18). We show that associations with HbA1c are partly a function of hyperglycemia associated with 3 of the 10 loci (GCK, G6PC2 and MTNR1B). The seven nonglycemic loci accounted for a 0.19 (% HbA1c) difference between the extreme 10% tails of the risk score, and would reclassify ∼2% of a general white population screened for diabetes with HbA1c. CONCLUSIONS GWAS identified 10 genetic loci reproducibly associated with HbA1c. Six are novel and seven map to loci where rarer variants cause hereditary anemias and iron storage disorders. Common variants at these loci likely influence HbA1c levels via erythrocyte biology, and confer a small but detectable reclassification of diabetes diagnosis by HbA1c

Hadron Production in Ultra-relativistic Nuclear Collisions: Quarkyonic Matter and a Triple Point in the Phase Diagram of QCD

We argue that features of hadron production in relativistic nuclear collisions, mainly at CERN-SPS energies, may be explained by the existence of three forms of matter: Hadronic Matter, Quarkyonic Matter, and a Quark-Gluon Plasma. We suggest that these meet at a triple point in the QCD phase diagram. Some of the features explained, both qualitatively and semi-quantitatively, include the curve for the decoupling of chemical equilibrium, along with the non-monotonic behavior of strange particle multiplicity ratios at center of mass energies near 10 GeV. If the transition(s) between the three phases are merely crossover(s), the triple point is only approximate.Comment: 28 pages, 9 figures; submitted to Nucl. Phys. A; v2 to eliminate obsolete figs. inadvertently attached at the end of the paper; v3: final version accepted for publicatio

Mutations that permit residual CFTR function delay acquisition of multiple respiratory pathogens in CF patients

<p>Abstract</p> <p>Background</p> <p>Lung infection by various organisms is a characteristic feature of cystic fibrosis (CF). <it>CFTR </it>genotype effects acquisition of <it>Pseudomonas aeruginosa (Pa)</it>, however the effect on acquisition of other infectious organisms that frequently precede <it>Pa </it>is relatively unknown. Understanding the role of CFTR in the acquisition of organisms first detected in patients may help guide symptomatic and molecular-based treatment for CF.</p> <p>Methods</p> <p>Lung infection, defined as a single positive respiratory tract culture, was assessed for 13 organisms in 1,381 individuals with CF. Subjects were divided by predicted CFTR function: 'Residual': carrying at least one partial function <it>CFTR </it>mutation (class IV or V) and 'Minimal' those who do not carry a partial function mutation. Kaplan-Meier estimates were created to assess <it>CFTR </it>effect on age of acquisition for each organism. Cox proportional hazard models were performed to control for possible cofactors. A separate Cox regression was used to determine whether defining infection with <it>Pa</it>, mucoid <it>Pa </it>or <it>Aspergillus (Asp) </it>using alternative criteria affected the results. The influence of severity of lung disease at the time of acquisition was evaluated using stratified Cox regression methods by lung disease categories.</p> <p>Results</p> <p>Subjects with 'Minimal' CFTR function had a higher hazard than patients with 'Residual' function for acquisition of 9 of 13 organisms studied (HR ranging from 1.7 to 3.78 based on the organism studied). Subjects with minimal CFTR function acquired infection at a younger age than those with residual function for 12 of 13 organisms (p-values ranging: < 0.001 to 0.017). Minimal CFTR function also associated with younger age of infection when 3 alternative definitions of infection with <it>Pa</it>, mucoid <it>Pa </it>or <it>Asp </it>were employed. Risk of infection is correlated with CFTR function for 8 of 9 organisms in patients with good lung function (>90%ile) but only 1 of 9 organisms in those with poorer lung function (<50%ile).</p> <p>Conclusions</p> <p>Residual CFTR function correlates with later onset of respiratory tract infection by a wide spectrum of organisms frequently cultured from CF patients. The protective effect conferred by residual CFTR function is diminished in CF patients with more advanced lung disease.</p