Real time- and control software for the new orbit measurement system for the CERN SPS

The 240 channel SPS Orbit acquisition system is implemented on a PowerPC under the LynxOS operating system, making use of multi threaded real-time capabilities. The acquired data is transferred efficiently by DMA via the PCI bus into the main memory. System configuration aspects were implemented in a Broker architecture, where individual threads communicate with an Oracle database and the acquisition systems. This Broker hides the implementation details of the front-end systems. A versatile configuration client is provided in Java, to provide both local graphical user interfaces and remote WWW access using a dedicated gateway to the SL equipment layer. The timing diagnostics of the acquisition system are provided in a LabView application integrating oscilloscope control and channel multiplex control. This paper describes in detail the technical solutions implemented and reports on the arguments, which have led to particular choices

The status of GNSS data processing systems to estimate integrated water vapour for use in numerical weather prediction models

Modern Numerical Weather Prediction (NWP) models make use of the GNSS-derived Zenith Total Delay (ZTD) or Integrated Water Vapour (IWV) estimates to enhance the quality of their forecasts. Usually, the ZTD is assimilated into the NWP models on 3- hourly to 6-hourly intervals but with the advancement of NWP models towards higher update rates e.g. 1-hourly cycling in the Rapid Update Cycle (RUC) NWP, it has become of high interest to estimate ZTD on sub-hourly intervals. In turn, this imposes requirements related to the timeliness and accuracy of the ZTD estimates and has lead to a development of various strategies to process GNSS observations to obtain ZTD with different latencies and accuracies. Using present GNSS products and tools, ZTD can be estimated in real-time (RT), near real-time (NRT) and post-processing (PP) modes. The aim of this study is to provide an overview and accuracy assessment of various RT, NRT, and PP IWV estimation systems and comparing their achieved accuracy with the user requirements for GNSS meteorology. The NRT systems are based on Bernese GPS Software 5.0 and use a double-differencing strategy whereas the PP system is based on the Bernese GNSS Software 5.2 using the precise point positioning (PPP) strategy. The RT systems are based on the BKG Ntrip Client 2.7 and the PPPWizard both using PPP. The PPP-Wizard allows integer ambiguity resolution at a single station and therefore the effect of fixing integer ambiguities on ZTD estimates will also be presented

Solvent-driven aqueous separations for hypersaline brine concentration and resource recovery

Solvent-driven separation processes can extract water and high-value minerals from high salinity or contaminated brines, simultaneously reducing the environmental impact of brine disposal and enabling resource recovery. The efficient dewatering of hypersaline brines is essential for the sustainable minimal and zero liquid discharge processing of industrial wastewaters. Fractional crystallization can selectively extract ions from contaminated waste streams, allowing critical materials to be recycled, including transition and lanthanide metals required for renewable energy generation and storage. Mass transfer in solvent-driven water extraction occurs across a liquid–liquid interface, eliminating the scaling and fouling of membrane and heat exchanger surfaces and limiting the need for extensive pretreatment. Solvent-driven fractional crystallization can leverage sequential treatment and control of process conditions to rapidly recover salts without requiring evaporation of water. Despite promising applications, the principles and potential of solvent-driven aqueous separations remain poorly understood. This critical review explores the opportunities presented by solvent-based aqueous separations from the molecular to process scale, evaluating the chemistry of solvation and system design in the broader context of desalination, resource recovery, water softening, and mineral production

OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

<p>Abstract</p> <p>Background</p> <p>Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required.</p> <p>Results</p> <p>Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes <url>http://ibi.imim.es/osirisform.html</url>. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, <url>http://ibi.imim.es/OSIRISv1.2.html</url>) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented.</p> <p>Conclusion</p> <p>OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.</p

Deficiency of the clock gene Bmal1 affects neural progenitor cell migration

We demonstrate the impact of a disrupted molecular clock in Bmal1-deficient (Bmal1−/−) mice on migration of neural progenitor cells (NPCs). Proliferation of NPCs in rostral migratory stream (RMS) was reduced in Bmal1−/− mice, consistent with our earlier studies on adult neurogenesis in hippocampus. However, a significantly higher number of NPCs from Bmal1−/− mice reached the olfactory bulb as compared to wild-type littermates (Bmal1+/+ mice), indicating a higher migration velocity in Bmal1−/− mice. In isolated NPCs from Bmal1−/− mice, not only migration velocity and expression pattern of genes involved in detoxification of reactive oxygen species were affected, but also RNA oxidation of catalase was increased and catalase protein levels were decreased. Bmal1+/+ migration phenotype could be restored by treatment with catalase, while treatment of NPCs from Bmal1+/+ mice with hydrogen peroxide mimicked Bmal1−/− migration phenotype. Thus, we conclude that Bmal1 deficiency affects NPC migration as a consequence of dysregulated detoxification of reactive oxygen species