The Cube-Connected-Cycles: A Versatile Network for Parallel Computation

Coordinated Science Laboratory was formerly known as Control Systems LaboratoryJoint Services Electronics Program / N00014-79-C-0424National Science Foundation / NSF MCS-78-1364

In vivo staining with alizarin for ageing studies on chondrichthyan fishes

Age determination for stock assessments and conservation of cartilaginous fishes is mainly obtained by counting the annual growth bands in vertebrae. Recent studies show numerous inconsistencies and the need for systematic validation. We assessed the effectiveness of the fluorochrome alizarin red S, a common skeleton vital marker used as a time stamp for teleost fishes, on chondrichthyan. Twenty-five captive small-spotted catsharks (Scyliorhinus canicula) were marked by alizarin red S intraperitoneal injections. The fluorochrome produced a wide fluorescent mark on sectioned vertebral centra of all injected fish. Alizarin red S did not have a deleterious effect on growth during three months monitoring. The marks obtained remained stable in vivo for more than four years after injections and were resistant to fading during the observation under the microscope excitation light. Our results suggest that alizarin red S is an effective tool for long time vital marking of chondrichthyans

Hemodynamic and antifibrotic effects of a selective liver nitric oxide donor V-PYRRO/NO in bile duct ligated rats.

AIM: To assess whether a liver specific nitric oxide (NO) donor (V-PYRRO/NO) would prevent the development of portal hypertension and liver fibrosis in rats with bile duct ligation (BDL). METHODS: Treatment (placebo or V-PYRRO/NO 0.53 micromol/kg per hour) was administered i.v. to rats 2 d before BDL (D-2) and maintained until the day of hemodynamic measurement (D26). Intra-hepatic NO level was estimated by measuring liver cGMP level. Effects of V-PYRRO/NO on liver fibrosis and lipid peroxidation were also assessed. RESULTS: Compared to placebo treatment, V-PYRRO/NO improved splanchnic hemodynamics in BDL rats: portal pressure was significantly reduced by 27% (P<0.0001) and collateral circulation development was almost completely blocked (splenorenal shunt blood flow by 74%, P=0.007). Moreover, V-PYRRO/NO significantly prevented liver fibrosis development in BDL rats (by 30% in hepatic hydroxyproline content and 31% in the area of fibrosis, P<0.0001 respectively), this effect being probably due to a decrease in lipid peroxidation by 44% in the hepatic malondialdehyde level (P=0.007). Interestingly, we observed a significant and expected increase in liver cGMP, without any systemic hemodynamic effects (mean arterial pressure, vascular systemic resistance and cardiac output) in both sham-operated and BDL rats treated with V-PYRRO/NO. This result is in accordance with studies on V-PYRRO/NO metabolism showing a specific release of NO in the liver. CONCLUSION: Continuous administrations of V-PYRRO/NO in BDL rats improved liver fibrosis and splanchnic hemodynamics without any noxious systemic hemo-dynamic effects

Certified Computer Algebra on top of an Interactive Theorem Prover

Contains fulltext : 35027.pdf (publisher's version ) (Open Access

Transiting exoplanets from the CoRoT space mission VIII. CoRoT-7b: the first Super-Earth with measured radius

We report the discovery of very shallow (DF/F = 3.4 10-4), periodic dips in the light curve of an active V = 11.7 G9V star observed by the CoRoT satellite, which we interpret as due to the presence of a transiting companion. We describe the 3-colour CoRoT data and complementary ground-based observations that support the planetary nature of the companion. Methods. We use CoRoT color information, good angular resolution ground-based photometric observations in- and out- of transit, adaptive optics imaging, near-infrared spectroscopy and preliminary results from Radial Velocity measurements, to test the diluted eclipsing binary scenarios. The parameters of the host star are derived from optical spectra, which were then combined with the CoRoT light curve to derive parameters of the companion. We examine carefully all conceivable cases of false positives, and all tests performed support the planetary hypothesis. Blends with separation larger than 0.40 arcsec or triple systems are almost excluded with a 8 10-4 risk left. We conclude that, as far as we have been exhaustive, we have discovered a planetary companion, named CoRoT-7b, for which we derive a period of 0.853 59 +/- 3 10-5 day and a radius of Rp = 1.68 +/- 0.09 REarth. Analysis of preliminary radial velocity data yields an upper limit of 21 MEarth for the companion mass, supporting the finding. CoRoT-7b is very likely the first Super-Earth with a measured radius.Comment: Accepted in Astronomy and Astrophysics; typos and language corrections; version sent to the printer w few upgrade

Programmable active memories in real-time tasks: implementing data-driven triggers for LHC experiments

The future Large Hadron Collider (LHC), to be built at CERN, presents among other technological challenges a formidable problem of real-time data analysis. At a primary event rate of 40 MHz, a multi-stage trigger system has to analyze data to decide which is the fraction of events that should be preserved on permanent storage for further analysis. We report on implementations of local algorithms for feature extraction as part of triggering, using the detectors of the proposed ATLAS experiment as a model. The algorithms were implemented for a decision frequency of 100 kHz, on different data-driven programmable devices based on structures of field- programmable gate arrays and memories. The implementations were demonstrated at full speed with emulated input, and were also integrated into a prototype detector running in a test beam at CERN, in June 1994

One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR

Some fungi with pleomorphic life-cycles still bear two names despite more than 20 years of molecular phylogenetics that have shown how to merge the two systems of classification, the asexual “Deuteromycota” and the sexual “Eumycota”. Mycologists have begun to flout nomenclatorial regulations and use just one name for one fungus. The International Code of Botanical Nomenclature (ICBN) must change to accommodate current practice or become irrelevant. The fundamental difference in the size of fungi and plants had a role in the origin of dual nomenclature and continues to hinder the development of an ICBN that fully accommodates microscopic fungi. A nomenclatorial crisis also looms due to environmental sequencing, which suggests that most fungi will have to be named without a physical specimen. Mycology may need to break from the ICBN and create a MycoCode to account for fungi known only from environmental nucleic acid sequence (i.e. ENAS fungi)

Detection of BRCA1, BRCA2, and ATM Alterations in Matched Tumor Tissue and Circulating Tumor DNA in Patients with Prostate Cancer Screened in PROfound.

PURPOSE: Not all patients with metastatic castration-resistant prostate cancer (mCRPC) have sufficient tumor tissue available for multigene molecular testing. Furthermore, samples may fail because of difficulties within the testing procedure. Optimization of screening techniques may reduce failure rates; however, a need remains for additional testing methods to detect cancers with alterations in homologous recombination repair genes. We evaluated the utility of plasma-derived circulating tumor DNA (ctDNA) in identifying deleterious BRCA1, BRCA2 (BRCA), and ATM alterations in screened patients with mCRPC from the phase III PROfound study. EXPERIMENTAL DESIGN: Tumor tissue samples were sequenced prospectively at Foundation Medicine, Inc. (FMI) using an investigational next-generation sequencing (NGS) assay based on FoundationOne®Liquid to inform trial eligibility. Matched ctDNA samples were retrospectively sequenced at FMI, using an investigational assay based on FoundationOne®Liquid CDx. RESULTS: 81% (503/619) of ctDNA samples yielded an NGS result, of which 491 had a tumor tissue result. BRCA and ATM status in tissue compared with ctDNA showed 81% positive percentage agreement and 92% negative percentage agreement, using tissue as reference. At variant-subtype level, using tissue as reference, concordance was high for nonsense (93%), splice (87%), and frameshift (86%) alterations but lower for large rearrangements (63%) and homozygous deletions (27%), with low ctDNA fraction being a limiting factor. CONCLUSIONS: We demonstrate that ctDNA can greatly complement tissue testing in identifying patients with mCRPC and BRCA or ATM alterations who are potentially suitable for receiving targeted PARP inhibitor treatments, particularly patients with no or insufficient tissue for genomic analyses

Maïdo observatory: a new high-altitude station facility at Reunion Island (21° S, 55° E) for long-term atmospheric remote sensing and in situ measurements

Since the nineties, atmospheric measurement systems have been deployed at Reunion Island, mainly for monitoring the atmospheric composition in the framework of NDSC/NDACC (Network for the Detection of <i>Stratospheric</i> Change/Network for the Detection of Atmospheric Composition Change). The location of Reunion Island presents a great interest because there are very few multi-instrumented stations in the tropics and particularly in the southern hemisphere. In 2012, a new observatory was commissioned in Maïdo at 2200 m above sea level: it hosts various instruments for atmospheric measurements, including lidar systems, spectro-radiometers and in situ gas and aerosol measurements. <br><br> This new high-altitude Maïdo station provides an opportunity:<br> 1. to improve the performance of the optical instruments above the marine boundary layer, and to open new perspectives on upper troposphere and lower stratosphere studies;<br> 2. to develop in situ measurements of the atmospheric composition for climate change surveys, in a reference site in the tropical/subtropical region of the southern hemisphere;<br> 3. to offer trans-national access to host experiments or measurement campaigns for focused process studies