The Open Navigation Surface Project

Many hydrographic and oceanographic agencies have moved or are moving towards gridded bathymetric products. However, there is no accepted format to allow these grids to be exchanged while maintaining data and metadata integrity. This paper describes the Open Navigation Surface (ONS) Project, which aims to fill this gap. The ONS Project is an open-source software project designed to provide a freely available, portable source-code library to encapsulate gridded bathymetric surfaces with associated uncertainty values. The data file format is called a Bathymetric Attributed Grid (BAG). The BAG is developed and maintained by the ONS Working Group (ONSWG), and the source code is available via the ONS websit

Heterozygosity at Gm Loci Associated with Humoral Immunity to Osteosarcoma

Familial clustering of osteosarcoma suggests the involvement of genetic factors (1, 2), and the demonstration of a high incidence of osteosarcoma-specific antibodies (3, 4), as well as tumor-specific cell-mediated immunity (5) in patients and their relatives, indicates the involvement of immunological factors in the pathogenesis of this disease. Certain Gm allotypes (genetic markers of IgG) have been shown to be associated with a high relative risk of some forms of cancer. For instance, in Caucasians an unusual Gm haplotype--Gm 1,3;5,13,14--has been found to be associated with neuroblastoma (6), and an increased frequency of Gm (2) has been reported in patients with malignant melanoma (7, 8). A recent report has shown an association of the Gm 1,2; 13,15,16,21 phenotype with lung cancer and primary hepatoma in the Japanese (9). To our knowledge, however, the possible role of Gm allotypes in predisposition to osteosarcoma has not been examined. Immune responsiveness to a variety of antigens in both experimental animals and humans has been shown to be controlled either by major histocompatibility complex (MHC)-linked immune response (Ir) genes or by allotype-linked Ir genes (10-13). In some instances an interactive effect of these two unlinked genetic systems has been observed (12). It is possible that MHC-linked or allotype-linked Ir genes may also influence humoral immunity to tumor antigens. In this report we present evidence for complementary Ir genes controlling immune responses to osteosarcoma-associated antigens (OSAA)

The Open Navigation Surface Project

Many hydrographic and oceanographic agencies have moved or are moving towards gridded bathymetric products. However, there is no accepted format to allow these grids to be exchanged while maintaining data and metadata integrity. This paper describes the Open Navigation Surface (ONS) Project, which aims to fill this gap. The ONS Project is an open-source software project designed to provide a freely available, portable source-code library to encapsulate gridded bathymetric surfaces with associated uncertainty values. The data file format is called a Bathymetric Attributed Grid (BAG). The BAG is developed and maintained by the ONS Working Group (ONSWG), and the source code is available via the ONS website.Muchas agencies hidrogrâficas y oceanogrâficas se han orientado o se estân orientando hacia los productos batimétricos cuadriculados. Sin embargo, no existe un formato aceptado para que estas cuadricuias sean intercambiadas manteniendo la integridad de los datos y los meta datos. Este articulo describe el Proyecto « Superficie de Navegaciôn Abierta » (ONS) cuyo objeto es cubrir este vacio. El proyecto ONS es un proyecto de software de fuente abierta disehado para proveer una biblioteca portâtil de côdigo fuente de libre disponibilidad para encapsular superficies batimétricas cuadriculadas con sus valores de incertidumbre asociados. El formato de archivo de datos es llamado Cuadricula Batimétrica Tributada (BAG). El BAG es desarrollado y mantenido por el Grupo de Trabajo ONS (ONSWG), y el côdigo fuente es disponible a través de sitio web de ONS.De nombreuses agences hydrographiques et océanographiques se sont orientées ou s ’orientent actuellement vers les produits bathymétriques quadrillés. Toutefois, il n'existe pas de format accepté qui permette à ces quadrillages d'être échangés tout en conservant l’intégrité des données et des métadonnées. Le présent article décrit le projet ONS (Open Navigation Surface) qui vise à combler cette lacune. Le projet ONS est un projet de logiciel libre conçu pour fournir une bibliothèque portable de code source à libre disponibilité devant encapsuler des surfaces bathymétriques maillées avec des valeurs d'incertitude associées. Le format du fichier des données est appelé Carroyage bathymétrique attribué (BAG). Le BAG est développé est tenu à jour par le groupe de travail ONS et le code source est disponible sur le site Web ONS

SNPs for Parentage Testing and Traceability in Globally Diverse Breeds of Sheep

DNA-based parentage determination accelerates genetic improvement in sheep by increasing pedigree accuracy. Single nucleotide polymorphism (SNP) markers can be used for determining parentage and to provide unique molecular identifiers for tracing sheep products to their source. However, the utility of a particular ‘‘parentage SNP’’ varies by breed depending on its minor allele frequency (MAF) and its sequence context. Our aims were to identify parentage SNPs with exceptional qualities for use in globally diverse breeds and to develop a subset for use in North American sheep. Starting with genotypes from 2,915 sheep and 74 breed groups provided by the International Sheep Genomics Consortium (ISGC), we analyzed 47,693 autosomal SNPs by multiple criteria and selected 163 with desirable properties for parentage testing. On average, each of the 163 SNPs was highly informative (MAF ≥ 0.3) in 48±5 breed groups. Nearby polymorphisms that could otherwise confound genetic testing were identified by whole genome and Sanger sequencing of 166 sheep from 54 breed groups. A genetic test with 109 of the 163 parentage SNPs was developed for matrix-assisted laser desorption/ionization– time-of-flight mass spectrometry. The scoring rates and accuracies for these 109 SNPs were greater than 99% in a panel of North American sheep. In a blinded set of 96 families (sire, dam, and non-identical twin lambs), each parent of every lamb was identified without using the other parent’s genotype. In 74 ISGC breed groups, the median estimates for probability of a coincidental match between two animals (PI), and the fraction of potential adults excluded from parentage (PE) were 1.1×10(−39) and 0.999987, respectively, for the 109 SNPs combined. The availability of a well-characterized set of 163 parentage SNPs facilitates the development of high-throughput genetic technologies for implementing accurate and economical parentage testing and traceability in many of the world’s sheep breeds

Experimental signatures of emergent quantum electrodynamics in Pr2_2Hf2_2O7_7

In a quantum spin liquid, the magnetic moments of the constituent electron spins evade classical long-range order to form an exotic state that is quantum entangled and coherent over macroscopic length scales [1-2]. Such phases offer promising perspectives for device applications in quantum information technologies, and their study can reveal fundamentally novel physics in quantum matter. Quantum spin ice is an appealing proposal of one such state, in which the fundamental ground state properties and excitations are described by an emergent U(1) lattice gauge theory [3-7]. This quantum-coherent regime has quasiparticles that are predicted to behave like magnetic and electric monopoles, along with a gauge boson playing the role of an artificial photon. However, this emergent lattice quantum electrodynamics has proved elusive in experiments. Here we report neutron scattering measurements of the rare-earth pyrochlore magnet Pr$_2$Hf$_2$O$_7$ that provide evidence for a quantum spin ice ground state. We find a quasi-elastic structure factor with pinch points - a signature of a classical spin ice - that are partially suppressed, as expected in the quantum-coherent regime of the lattice field theory at finite temperature. Our result allows an estimate for the speed of light associated with magnetic photon excitations. We also reveal a continuum of inelastic spin excitations, which resemble predictions for the fractionalized, topological excitations of a quantum spin ice. Taken together, these two signatures suggest that the low-energy physics of Pr$_2$Hf$_2$O$_7$ can be described by emergent quantum electrodynamics. If confirmed, the observation of a quantum spin ice ground state would constitute a concrete example of a three-dimensional quantum spin liquid - a topical state of matter which has so far mostly been explored in lower dimensionalities.Comment: 15 pages, 3 figure

Shannon Information Theory and Molecular Biology

The role and the contribution of Shannon Information Theory to the development of Molecular Biology has been the object of stimulating debates during the last thirty years. This seems to be connected with some semantic charms associated with the use of the word \u201cinformation\u201d in the biological context. Furthermore information itself, if viewed in a broader perspective, is far from being completely defined in a fashion that overcomes the technical level at which the classical Information Theory has been conceived. This review aims at building on the acknowledged contribution of Shannon Information Theory to Molecular Biology, so as to discover if it is only a technical tool to analyze DNA and proteinic sequences, or if it can rise, at least in perspective, to a higher role that exerts an influence on the construction of a suitable model for handling the genetic information in Molecular Biology

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin