Comparing and contrasting the νμ→ντ\nu_{\mu} \to \nu_{\tau} and νμ→νs\nu_{\mu} \to \nu_s solutions to the atmospheric neutrino problem with SuperKamiokande data

The $\nu_{\mu} \to \nu_{\tau}$ and $\nu_{\mu} \to \nu_s$ solutions to the atmospheric neutrino problem are compared with SuperKamiokande data. The differences between these solutions due to matter effects in the Earth are calculated for the ratio of $\mu$-like to $e$-like events and for up-down flux asymmetries. These quantities are chosen because they are relatively insensitive to theoretical uncertainties in the overall neutrino flux normalisation and detection cross-sections and efficiencies. A $\chi^2$ analysis using these quantities is performed yielding $3\sigma$ ranges which are approximately given by $(0.725 - 1.0, 4 \times 10^{-4} - 2 \times 10^{-2} eV^2)$ and $(0.74 - 1.0, 1 \times 10^{-3} - 2 \times 10^{-2} eV^2)$ for $(\sin^2 2\theta,\Delta m^2)$ for the $\nu_{\mu} \to \nu_{\tau}$ and $\nu_{\mu} \to \nu_s$ solutions, respectively. Values of $\Delta m^2$ smaller than about $2 \times 10^{-3}$ eV$^2$ are disfavoured for the $\nu_{\mu} \to \nu_s$ solution, suggesting that future long baseline experiments should see a positive signal if this scenario is the correct one.Comment: revtex, 22 pages, 12 figure

Atmospheric neutrino oscillations with three neutrinos and a mass hierarchy

A comprehensive formalism for the description of neutrino oscillations in the Earth in a general scheme with three massive neutrinos and the mass hierarchy m_1<<m_2<<m_3 is presented. Using this formalism, which is valid both in vacuum and in a medium, the matter effect on the oscillations of low-energy neutrinos is discussed, pointing out the existence of very long oscillations which are independent of the neutrino masses and the neutrino energy, and are very sensitive to the matter density along the neutrino trajectory. As an example of application of the formulation, a fit of the Kamiokande atmospheric neutrino data with the matter effect taken into account for neutrinos propagating in the Earth is presented. The results of the fit indicate that 4*10^{-3} eV^2 < m_3^2 nu_e, nu_munu_tau, nu_enu_tau) could be large. Hence, long-baseline experiments with reactor (CHOOZ and Palo Verde) and accelerator (K2K, MINOS and ICARUS) neutrinos could observe neutrino oscillations in all channels with a relatively large statistics.Comment: 42 pages, including 7 figure

Contrasting Pediatric and Adult Methicillin-resistant Staphylococcus aureus Isolates

Children may share a reservoir of MRSA strains that have an antimicrobial drug resistance profile distinct from that of adults

Construction and comparison of three reference‐quality genome assemblies for soybean

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Construction and comparison of three reference‐quality genome assemblies for soybean

We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species

Construction and comparison of three reference-quality genome assemblies for soybean.

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G.&nbsp;max. The G.&nbsp;max assemblies provided are for widely used US cultivars: the northern line Williams&nbsp;82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G.&nbsp;soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7&nbsp;single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7&nbsp;snps&nbsp;per&nbsp;kb between these lines and G.&nbsp;soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G.&nbsp;soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G.&nbsp;soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species