Spectroscopic Analysis in the Virtual Observatory Environment with SPLAT-VO

SPLAT-VO is a powerful graphical tool for displaying, comparing, modifying and analyzing astronomical spectra, as well as searching and retrieving spectra from services around the world using Virtual Observatory (VO) protocols and services. The development of SPLAT-VO started in 1999, as part of the Starlink StarJava initiative, sometime before that of the VO, so initial support for the VO was necessarily added once VO standards and services became available. Further developments were supported by the Joint Astronomy Centre, Hawaii until 2009. Since end of 2011 development of SPLAT-VO has been continued by the German Astrophysical Virtual Observatory, and the Astronomical Institute of the Academy of Sciences of the Czech Republic. From this time several new features have been added, including support for the latest VO protocols, along with new visualization and spectra storing capabilities. This paper presents the history of SPLAT-VO, it's capabilities, recent additions and future plans, as well as a discussion on the motivations and lessons learned up to now.Comment: 15 pages, 6 figures, accepted for publication in Astronomy & Computin

IVOA Recommendation: Simple Spectral Access Protocol Version 1.1

The Simple Spectral Access (SSA) Protocol (SSAP) defines a uniform interface to remotely discover and access one dimensional spectra. SSA is a member of an integrated family of data access interfaces altogether comprising the Data Access Layer (DAL) of the IVOA. SSA is based on a more general data model capable of describing most tabular spectrophotometric data, including time series and spectral energy distributions (SEDs) as well as 1-D spectra; however the scope of the SSA interface as specified in this document is limited to simple 1-D spectra, including simple aggregations of 1-D spectra. The form of the SSA interface is simple: clients first query the global resource registry to find services of interest and then issue a data discovery query to selected services to determine what relevant data is available from each service; the candidate datasets available are described uniformly in a VOTable format document which is returned in response to the query. Finally, the client may retrieve selected datasets for analysis. Spectrum datasets returned by an SSA spectrum service may be either precomputed, archival datasets, or they may be virtual data which is computed on the fly to respond to a client request. Spectrum datasets may conform to a standard data model defined by SSA, or may be native spectra with custom project-defined content. Spectra may be returned in any of a number of standard data formats. Spectral data is generally stored externally to the VO in a format specific to each spectral data collection; currently there is no standard way to represent astronomical spectra, and virtually every project does it differently. Hence spectra may be actively mediated to the standard SSA-defined data model at access time by the service, so that client analysis programs do not have to be familiar with the idiosyncratic details of each data collection to be accessed

PrankWeb: a web server for ligand binding site prediction and visualization.

PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively

Nanocrystalline diamond protects Zr cladding surface against oxygen and hydrogen uptake : Nuclear fuel durability enhancement

In this work, we demonstrate and describe an effective method of protecting zirconium fuel cladding against oxygen and hydrogen uptake at both accident and working temperatures in water-cooled nuclear reactor environments. Zr alloy samples were coated with nanocrystalline diamond (NCD) layers of different thicknesses, grown in a microwave plasma chemical vapor deposition apparatus. In addition to showing that such an NCD layer prevents the Zr alloy from directly interacting with water, we show that carbon released from the NCD film enters the underlying Zr material and changes its properties, such that uptake of oxygen and hydrogen is significantly decreased. After 100–170 days of exposure to hot water at 360 °C, the oxidation of the NCD-coated Zr plates was typically decreased by 40%. Protective NCD layers may prolong the lifetime of nuclear cladding and consequently enhance nuclear fuel burnup. NCD may also serve as a passive element for nuclear safety. NCD-coated ZIRLO claddings have been selected as a candidate for Accident Tolerant Fuel in commercially operated reactors in 2020

IVOA Recommendation: Observation Data Model Core Components and its Implementation in the Table Access Protocol Version 1.0

This document defines the core components of the Observation data model that are necessary to perform data discovery when querying data centers for observations of interest. It exposes use-cases to be carried out, explains the model and provides guidelines for its implementation as a data access service based on the Table Access Protocol (TAP). It aims at providing a simple model easy to understand and to implement by data providers that wish to publish their data into the Virtual Observatory. This interface integrates data modeling and data access aspects in a single service and is named ObsTAP. It will be referenced as such in the IVOA registries. There will be a separate document to cover the full Observation data model. In this document, the Observation Data Model Core Components (ObsCoreDM) defines the core components of queryable metadata required for global discovery of observational data. It is meant to allow a single query to be posed to TAP services at multiple sites to perform global data discovery without having to understand the details of the services present at each site. It defines a minimal set of basic metadata and thus allows for a reasonable cost of implementation by data providers. The combination of the ObsCoreDM with TAP is referred to as an ObsTAP service. As with most of the VO Data Models, ObsCoreDM makes use of STC, Utypes, Units and UCDs. The ObsCoreDM can be serialized as a VOTable. ObsCoreDM can make reference to more complete data models such as ObsProvDM (the Observation Provenance Data Model, to come), Characterisation DM, Spectrum DM or Simple Spectral Line Data Model (SSLDM).Comment: About the IVOA: http://www.ivoa.net; editors: Doug Tody, Alberto Micol, Daniel Durand, Mireille Louy

Teriflunomide Is an Indirect Human Constitutive Androstane Receptor (CAR) Activator Interacting With Epidermal Growth Factor (EGF) Signaling

The constitutive androstane receptor (CAR) is a nuclear receptor involved mainly in xenobiotic and endobiotic metabolism regulation. CAR is activated directly by its ligands via the ligand binding domain (LBD) or indirectly by inhibition of the epidermal growth factor (EGF) signaling. We found that leflunomide (LEF) and its main metabolite teriflunomide (TER), both used for autoimmune diseases treatment, induce the prototype CAR target gene CYP2B6 in primary human hepatocytes. As TER was discovered to be an EGF receptor antagonist, we sought to determine if TER is an indirect activator of CAR. In primary human hepatocytes and in differentiated HepaRG cells, we found that LEF and TER up-regulate CAR target genes CYP2B6 and CYP3A4 mRNAs and enzymatic activities. TER stimulated CAR+A mutant translocation into the nucleus but neither LEF nor TER activated the CAR LBD, CAR3 variant or pregnane X receptor (PXR) in gene reporter assays. Interestingly, TER significantly up-regulated CAR mRNA expression, a result which could be a consequence of both EGF receptor and ELK-1 transcription factor inhibition by TER or by TER-mediated activation of glucocorticoid receptor (GR), an upstream hormonal regulator of CAR. We can conclude that TER is a novel indirect CAR activator which through EGF inhibition and GR activation controls both detoxification and some intermediary metabolism genes

IVOA Recommendation: Spectrum Data Model 1.1

We present a data model describing the structure of spectrophotometric datasets with spectral and temporal coordinates and associated metadata. This data model may be used to represent spectra, time series data, segments of SED (Spectral Energy Distributions) and other spectral or temporal associations.Comment: http://www.ivoa.ne

Serotonin limits generation of chromaffin cells during adrenal organ development

Adrenal glands are the major organs releasing catecholamines and regulating our stress response. The mechanisms balancing generation of adrenergic chromaffin cells and protecting against neuroblastoma tumors are still enigmatic. Here we revealed that serotonin (5HT) controls the numbers of chromaffin cells by acting upon their immediate progenitor "bridge" cells via 5-hydroxytryptamine receptor 3A (HTR3A), and the aggressive HTR3Ahigh human neuroblastoma cell lines reduce proliferation in response to HTR3A-specific agonists. In embryos (in vivo), the physiological increase of 5HT caused a prolongation of the cell cycle in "bridge" progenitors leading to a smaller chromaffin population and changing the balance of hormones and behavioral patterns in adulthood. These behavioral effects and smaller adrenals were mirrored in the progeny of pregnant female mice subjected to experimental stress, suggesting a maternal-fetal link that controls developmental adaptations. Finally, these results corresponded to a size-distribution of adrenals found in wild rodents with different coping strategies

PDBe-KB: a community-driven resource for structural and functional annotations.

The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession