Nautical Chart Adequacy Evaluation Using Publicly-Available Data

The International Hydrographic Office (IHO) C-55 publication communicates the need to improve the collection, quality and availability of hydrographic data world-wide, while also monitoring and rectifying possible deficiencies and shortcomings that are presented on the chart. This task of evaluating the adequacy of nautical chart products poses a challenge to many national hydrographic offices. This stems from the dearth of readily available spatial information: namely, the lack of reliable and accessible vessel traffic data, and little means to assess the changing nature of both near-shore bathymetry and shoreline in a simple and reliable manner. In this paper, we present the potential use of automatic-identification system (AIS) data, satellite-derived bathymetry (SDB), and airborne-lidar bathymetry (ALB) to provide an operational procedure for evaluating the adequacy and completeness of information of NOAA charts. Preliminary results from three U.S. study sites are presented in this paper: Nantucket Sound, MA; Barnegat Bay Inlet, NJ; and Barataria Bay, LA. Based on the publically-available datasets it was possible to identify changes in the charts and develop a reconnaissance procedure to monitor these changes on a yearly basis

Chart Adequacy: Workshop and GEBCO Training

In July, 2015 the first NOAA Chart Adequacy Workshop was held in Silver Spring, Maryland, USA. Following a three-day workshop (14th to 16th July, 2015), four Nippon Foundation GEBCO students stayed at NOAA for an additional 10-day training at Office of Coast Survey’s Marine Chart Division. The key objective of the NOAA Chart Adequacy Workshop was to demonstrate techniques to evaluate the suitability of nautical chart products using chart quality information and publicly-available information. The attendees were cartographers, hydrographers and potential chart producers from hydrographic offices and government agencies around the world. The nations of the participants in the workshop included: Indonesia, Israel, Japan, Kenya, Malaysia, Philippines, South Korea, Sri Lanka, United Kingdom, United States and Venezuela. Through instructor presentations and GIS laboratory exercises (provided by Dr. Shachak Pe’eri and Lt Anthony Klemm), the participants generated the key layers that are involved in the NOAA procedure. A vessel traffic layer was generated by classification of navigational routes using Automatic Identification Systems (AIS) information. A bathymetric difference layer was generated by identifying areas that showed significant bathymetric changes identified by comparing Satellite-Derived Bathymetry (SDB) or other surveys of opportunity, with the existing chart. A hydrographic characteristics layer was generated by classification of chart quality information. Chart data (including the smooth sheet sounding sets) for the procedure were provided in a vector format with the appropriate metadata according to IHO S-57. Raster Navigational Charts were also used as a background and as a reference for the Bathymetric Difference layer

Mechanisms for Controlling HIV-1 Infection: A Gene Therapy Approach

Current anti-retroviral treatment (ART) for HIV-1 is highly effectively at controlling the infection. However, during early infection the virus establishes a latent reservoir, which is not impacted by ART. Any treatment interruption rapidly results in virus rebound from the latent reservoir to pre-therapy levels and thus ART does not constitute an HIV-1 cure. Alternate treatments are currently being explored in the form of gene therapy, following the success of the Berlin patient who has had undetectable virus since 2007. This review will describe the contrasting cure approaches that are currently the focus of multiple studies to control HIV, then focus in on functional cure gene therapy strategies; specifically, epigenetic silencing of HIV-1 by various methods, including RNA-directed transcriptional gene silencing. The various delivery strategies for targeting cells of the latent reservoir will be reviewed and finally, the clinical status and current challenges for ex vivo versus in vivo gene therapy delivery approaches will be discussed

Hydrography from Fisheries Surveys: Filling coverage gaps with bathymetry extracted from Simrad EK60 water column data

The collection of available fisheries acoustic data holds significant seafloor mapping potential. We estimate that in the Northeast United States, Simrad EK60 data from the NOAA Fisheries fleet could increase bathymetric coverage by as much as nine percent. This article describes initial automated processes and techniques used to: extract the seafloor from Simrad EK60 water column data collected with NOAA Fisheries vessels, obtain and apply best available information to realize the seafloor relative to chart datum, and verify the outcome with existing qualified bathymetry.La recopilación de los datos acústicos disponibles sobre pesca encierra un importante potencial de cartografía de los fondos marinos. Estimamos que en el Noreste de los Estados Unidos, los datos del Simrad EK60 de la flota pesquera de la NOAA podrían aumentar la cobertura batimétrica hasta un 9%. Este artículo describe los procesos y técnicas automatizados iniciales utilizados para: extraer el fondo marino desde los datos de la columna registrados por el Simrad EK60 recogidos con los barcos de pesca de la NOAA, obtener y aplicar la mejor información disponible para reconocer el fondo marino en relación con el datum de la carta y verificar el resultado con la batimetría cualificada existente.L’ensemble disponible de données acoustiques issues de la pêche représente un potentiel significatif pour la cartographie du fond marin. Nous estimons que dans le nord-est des Etats-Unis, les données Simrad EK60 issues de la flotte de pêche de la NOAA pourraient accroître la couverture bathymétrique jusqu’à neuf pourcent. Le présent article décrit les processus et techniques automatisés initiaux utilisés pour : extraire les données relatives au fond marin à partir des données de la colonne d’eau Simrad EK60 qui sont collectées par les navires de pêche de la NOAA, obtenir et appliquer les meilleures informations disponibles pour réaliser la cartographie du fond marin par rapport au zéro des cartes, et vérifier le résultat avec les données bathymétriques homologuées existantes

Evidence for weathering and volcanism during the PETM from Arctic Ocean and Peri-Tethys osmium isotope records

Sudden global warming during the Paleocene–Eocene Thermal Maximum (PETM, 55.9 Ma) occurred because of the rapid release of several thousand gigatonnes of isotopically light carbon into the oceans and atmosphere; however, the cause of this release is not well understood. Some studies have linked carbon injection to volcanic activity associated with the North Atlantic Igneous Province (NAIP), while others have emphasised carbon cycle feedbacks associated with orbital forcing. This study presents the osmium isotope compositions of mudrocks that were deposited during the PETM at four locations (one from the Arctic Ocean, and three from the Peri-Tethys). The Os-isotope records all exhibit a shift of similar magnitude towards relatively radiogenic values across the PETM. This observation confirms that there was a transient, global increase in the flux of radiogenic Os from the weathering of continental rocks in response to elevated temperatures at that time. The tectonic effects of NAIP volcanic emplacement near the onset of the PETM is recorded by anomalously radiogenic Os-isotope compositions of PETM-age Arctic Ocean samples, which indicate an interval of hydrographic restriction that can be linked tectonic uplift due to hotspot volcanism in the North Atlantic seaway. The Peri-Tethys data also document a transient, higher flux of unradiogenic osmium into the ocean near the beginning of the PETM, most likely from the weathering of young mafic rocks associated with the NAIP. These observations support the hypothesis that volcanism played a major role in triggering the cascade of environmental changes during the PETM, and highlight the influence of paleogeography on the Os isotope characteristics of marine water masses

A threading receptor for polysaccharides

Cellulose, chitin and related polysaccharides are key renewable sources of organic molecules and materials. However, poor solubility tends to hamper their exploitation. Synthetic receptors could aid dissolution provided they are capable of cooperative action, for example by multiple threading on a single polysaccharide molecule. Here we report a synthetic receptor designed to form threaded complexes (polypseudorotaxanes) with these natural polymers. The receptor binds fragments of the polysaccharides in aqueous solution with high affinities (Ka up to 19,000 M−1), and is shown—by nuclear Overhauser effect spectroscopy—to adopt the threading geometry. Evidence from induced circular dichroism and atomic force microscopy implies that the receptor also forms polypseudorotaxanes with cellulose and its polycationic analogue chitosan. The results hold promise for polysaccharide solubilization under mild conditions, as well as for new approaches to the design of biologically active molecules

A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine

Advancements in next-generation sequencing and other -omics technologies are accelerating the detailed molecular characterization of individual patient tumors, and driving the evolution of precision medicine. Cancer is no longer considered a single disease, but rather, a diverse array of diseases wherein each patient has a unique collection of germline variants and somatic mutations. Molecular profiling of patient-derived samples has led to a data explosion that could help us understand the contributions of environment and germline to risk, therapeutic response, and outcome. To maximize the value of these data, an interdisciplinary approach is paramount. The National Cancer Institute (NCI) has initiated multiple projects to characterize tumor samples using multi-omic approaches. These projects harness the expertise of clinicians, biologists, computer scientists, and software engineers to investigate cancer biology and therapeutic response in multidisciplinary teams. Petabytes of cancer genomic, transcriptomic, epigenomic, proteomic, and imaging data have been generated by these projects. To address the data analysis challenges associated with these large datasets, the NCI has sponsored the development of the Genomic Data Commons (GDC) and three Cloud Resources. The GDC ensures data and metadata quality, ingests and harmonizes genomic data, and securely redistributes the data. During its pilot phase, the Cloud Resources tested multiple cloud-based approaches for enhancing data access, collaboration, computational scalability, resource democratization, and reproducibility. These NCI-led efforts are continuously being refined to better support open data practices and precision oncology, and to serve as building blocks of the NCI Cancer Research Data Commons

A Common Variant Associated with Dyslexia Reduces Expression of the KIAA0319 Gene

Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility. The causative variant(s) remains unknown but may modulate gene expression, given that (1) a dyslexia-associated haplotype has been implicated in the reduced expression of KIAA0319, and (2) the strongest association has been found for the region spanning exon 1 of KIAA0319. Here, we test the hypothesis that variant(s) responsible for reduced KIAA0319 expression resides on the risk haplotype close to the gene's transcription start site. We identified seven single-nucleotide polymorphisms on the risk haplotype immediately upstream of KIAA0319 and determined that three of these are strongly associated with multiple reading-related traits. Using luciferase-expressing constructs containing the KIAA0319 upstream region, we characterized the minimal promoter and additional putative transcriptional regulator regions. This revealed that the minor allele of rs9461045, which shows the strongest association with dyslexia in our sample (max p-value = 0.0001), confers reduced luciferase expression in both neuronal and non-neuronal cell lines. Additionally, we found that the presence of this rs9461045 dyslexia-associated allele creates a nuclear protein-binding site, likely for the transcriptional silencer OCT-1. Knocking down OCT-1 expression in the neuronal cell line SHSY5Y using an siRNA restores KIAA0319 expression from the risk haplotype to nearly that seen from the non-risk haplotype. Our study thus pinpoints a common variant as altering the function of a dyslexia candidate gene and provides an illustrative example of the strategic approach needed to dissect the molecular basis of complex genetic traits