Permo-Triassic Deposits: from shallow water to base of slope

Conference on the Geology of Oman, Muscat, Oman, Field Guidebook A0

Nearly Complete Genome Sequence of a Novel Phlebovirus-Like Virus Detected in a Human Plasma Sample by High-Throughput Sequencing.

Here, we report a novel phlebovirus-like virus sequence detected in a plasma sample from a febrile adult patient collected in the United Republic of Tanzania in 2014. A nearly complete RNA sequence was generated by high-throughput sequencing on a HiSeq 2500 instrument and further confirmed after repeating the analysis, starting from the initial sample

In search of dying radio sources in the local universe

Up till now very few dying sources were known, presumably because the dying phase is short at centimeter wavelengths. We therefore have tried to improve the statistics on sources that have ceased to be active, or are intermittently active. The latter sources would partly consist of a fossil radio plasma left over from an earlier phase of activity, plus a recently restarted core and radio jets. Improving the statistics of dying sources will give us a better handle on the evolution of radio sources, in particular the frequency and time scales of radio activity. We have used the WENSS and NVSS surveys, in order to find sources with steep spectral indices, associated with nearby elliptical galaxies. In the cross correlation we presently used only unresolved sources, with flux densities at 1.4 GHz larger than 10 mJy. The eleven candidates thus obtained were observed with the VLA in various configurations, in order to confirm the steepness of the spectra, and to check whether active structures like flat-spectrum cores and jets are present, perhaps at low levels. We estimated the duration of the active and relic phases by modelling the integrated radio spectra using the standard models of spectral evolution. We have found six dying sources and three restarted sources, while the remaining two candidates remain unresolved also with the new VLA data and may be Compact Steep Spectrum sources, with an unusually steep spectrum. The typical age of the active phase, as derived by spectral fits, is in the range 10^7 - 10^8 years. For our sample of dying sources, the age of the relic phase is on average shorter by an order of magnitude than the active phase.Comment: 21 pages, 17 figures, accepted by A&A. For a version with high quality figures, see http://erg.ca.astro.it/preprints/dying2007

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.

The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus

A Multiplexed Urinary Biomarker Panel Has Potential for Alzheimer’s Disease Diagnosis Using Targeted Proteomics and Machine Learning

As disease-modifying therapies are now available for Alzheimer’s disease (AD), accessible, accurate and affordable biomarkers to support diagnosis are urgently needed. We sought to develop a mass spectrometry-based urine test as a high-throughput screening tool for diagnosing AD. We collected urine from a discovery cohort (n = 11) of well-characterised individuals with AD (n = 6) and their asymptomatic, CSF biomarker-negative study partners (n = 5) and used untargeted proteomics for biomarker discovery. Protein biomarkers identified were taken forward to develop a high-throughput, multiplexed and targeted proteomic assay which was tested on an independent cohort (n = 21). The panel of proteins identified are known to be involved in AD pathogenesis. In comparing AD and controls, a panel of proteins including MIEN1, TNFB, VCAM1, REG1B and ABCA7 had a classification accuracy of 86%. These proteins have been previously implicated in AD pathogenesis. This suggests that urine-targeted mass spectrometry has potential utility as a diagnostic screening tool in AD