Identification of the expressome by machine learning on omics data.

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes

Composition and spatial distribution of cephalopods in two North-western Mediterranean areas

The faunistic composition and the spatial distribution of the cephalopod fauna were studied and compared in two areas of the north-western Mediterranean: the Catalan Sea (Spanish coast) and the northern Tyrrhenian Sea (Italian coast). In all, 46 species were collected in the Catalan Sea and 36 in the northern Tyrrhenian Sea. The bathymetric distribution of common species does not differ notably between the two areas. In both, cephalopodabundance is greatest between 50 and 200 m deep. To compare the seasonal changes in bathymetric distribution, four representative species were selected. O. vulgaris is more abundant in both areas between 0 and 50 min autumn; E. cirrhosa and I. coindetii between 50 and 200 m. Both the last species and S. elegans are more abundant in spring in the Catalan Sea and in autumn in the northern Tyrrhenian Sea. The results of cluster analysisshow the presence, in both areas, of three clear associations: one group consists of shallow hauls, another of hauls made over the continental shelf and the third of deeper hauls

The importance of cephalopods to trawl fisheries in the western Mediterranean

The aim of the study was to define the commercial importance of cephalopods caught by trawlers from five Italian and Spanish Mediterranean ports. From summer 1995 to spring 1996, samples of the catches of trawlers were taken on board. The type of fishing activity was recorded and data were collected from at least three commercial hauls for each port, season and bathymetric stratum (350 m). The species composition and yield of the retained and discarded portions of the catch were noted for each port. From these data the commercial importance of each species was evaluated. Cephalopods were commercially important particularly in the shallower bathymetric stratum

Isospin splitting of the nucleon mean field

The isospin splitting of the nucleon mean field is derived from the Brueckner theory extended to asymmetric nuclear matter. The Argonne V18 has been adopted as bare interaction in combination with a microscopic three body force. The isospin splitting of the effective mass is determined from the Brueckner-Hartree-Fock self-energy: It is linear acording to the Lane ansatz and such that $m^*_n > m^*_p$ for neutron-rich matter. The symmetry potential is also determined and a comparison is made with the predictions of the Dirac-Brueckner approach and the phenomenological interactions. The theoretical predictions are also compared with the empirical parametrizations of neutron and proton optical-model potentials based on the experimental nucleon-nucleus scattering and the phenomenological ones adopted in transport-model simulations of heavy-ion collisions. The direct contribution of the rearrangement term due to three-body forces to the single particle potential and symmetry potential is discussed.Comment: 8 pages, 10 figure

Analysis of demersal assemblages off the Tuscany and Latium coasts (north-western Mediterranean)

A four-year time series (1994-1997) of groundfish trawl surveys performed within the European Union Project "MEDITS" (Mediterranean International Trawl Surveys), was analysed to identify and describe the fish assemblages along the continental shelf and slope of Tuscany and Latium (Italy), in the north-western Mediterranean. Cluster analysis was used to group samples with similar species composition in terms of abundance, biomass and frequency of occurrence. Results allowed the identification of four to five broad assemblages along the depth gradient: a strictly coastal group (< 50 m depth), two groups in the upper and lower part of the continental shelf (essentially 50-200 m), an epibathyal group (200450 m) and a group derived from hauls made at depths greater than 450 in. Each assemblage corresponded to a faunistic association with relatively homogeneous and persistent species composition, biomass and density indices

Temperature dependence of single-particle properties in nuclear matter

The single-nucleon potential in hot nuclear matter is investigated in the framework of the Brueckner theory by adopting the realistic Argonne V18 or Nijmegen 93 two-body nucleon-nucleon interaction supplemented by a microscopic three-body force. The rearrangement contribution to the single-particle potential induced by the ground state correlations is calculated in terms of the hole-line expansion of the mass operator and provides a significant repulsive contribution in the low-momentum region around and below the Fermi surface. Increasing temperature leads to a reduction of the effect, while increasing density makes it become stronger. The three-body force suppresses somewhat the ground state correlations due to its strong short-range repulsion, increasing with density. Inclusion of the three-body force contribution results in a quite different temperature dependence of the single-particle potential at high enough densities as compared to that adopting the pure two-body force. The effects of three-body force and ground state correlations on the nucleon effective mass are also discussed.Comment: 14 pages, 5 figure

“Once upon a Time in the Mediterranean”. Long Term Trends of Mediterranean Fisheries Resources Based on Fishers’ Traditional Ecological Knowledge

We investigate long-term changes in the Mediterranean marine resources driving the trawl fisheries by analysing fishers’ perceptions (Traditional Ecological Knowledge, TEK) throughout the Mediterranean Sea for the last 80 years. To this end, we conducted an extended set of interviews with old experienced fishers that enabled us to classify species (or taxa) as 'decreasing' or 'increasing' both in terms of abundance, as well as average size in the catch. The aspect that most clearly emerged in all the investigated areas over time was the notable increase of fishing capacity indicators, such as engine power and fishing depth range. Atlantic mackerel, poor cod, scorpionfishes, striped seabream, and John Dory demonstrated a decreasing trend in the fishers' perceived abundance, while Mediterranean parrotfish, common pandora, cuttlefish, blue and red shrimp, and mullets gave indications of an increasing temporal trend. Although, as a rule, trawler captains did not report any cataclysmic changes (e.g. extinctions), when they were invited to estimate total overall catches, a clear decreasing pattern emerged; this being a notable finding taking into account the steep escalation of fishing efficiency during the past century. The overall deteriorating status of stocks in most Mediterranean regions calls for responsible management and design of rebuilding plans. This should include historical information accounting for past exploitation patterns that could help defining a baseline of fish abundance prior to heavy industrial fisheries exploitation.JRC.G.3-Maritime affair

New Baryons in the Delta eta and Delta omega Channels

The decays of excited nonstrange baryons into the final states Delta eta and Delta omega are examined in a relativized quark pair creation model. The wavefunctions and parameters of the model are fixed by previous calculations of N pi and N pi pi, etc., decays through various quasi-two body channels including N eta and N omega. Our results show that the combination of thresholds just below the region of interest and the isospin selectivity of these channels should allow the discovery of several new baryons in such experiments.Comment: 10 pages, RevTe

OWL-POLAR : semantic policies for agent reasoning

The original publication is available at www.springerlink.comPostprin