Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts

BACKGROUND: This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a finite mixture of multivariate Gaussian densities. However, given we had more technical replicates from the same tissue for each quantitative measurement, we also employed a finite mixture of linear mixed models, with tissue-specific random effects. RESULTS: A panel of human tissues was analysed through quantitative real-time PCR methods, to quantify the relative amount of mRNA encoding different IGF-1 alternative splicing variants. After an appropriate, preliminary, equalization of the quantitative data, we provided an estimate of the distribution of the observed concentrations for the different IGF-1 mRNA splice variants in the cohort of tissues by employing suitable kernel density estimators. We observed that the analysed IGF-1 mRNA splice variants were characterized by multimodal distributions, which could be interpreted as describing the presence of several sub-population, i.e. potential tissue clusters. In this context, a formal clustering approach based on a finite mixture model (FMM) with Gaussian components is proposed. Due to the presence of potential dependence between the technical replicates (originated by repeated quantitative measurements of the same mRNA splice isoform in the same tissue) we have also employed the finite mixture of linear mixed models (FMLMM), which allowed to take into account this kind of within-tissue dependence. CONCLUSIONS: The FMM and the FMLMM provided a convenient yet formal setting for a model-based clustering of the human tissues in sub-populations, characterized by homogeneous values of concentrations of the mRNAs for one or multiple IGF-1 alternative splicing isoforms. The proposed approaches can be applied to any cohort of tissues expressing several alternatively spliced mRNAs generated by the same gene, and can overcome the limitations of clustering methods based on simple comparisons between splice isoform expression levels

Status of Salerno Laboratory (Measurements in Nuclear Emulsion)

A report on the analysis work in the Salerno Emulsion Laboratory is presented. It is related to the search for nu_mu->nu_tau oscillations in CHORUS experiment, the calibrations in the WANF (West Area Neutrino Facility) at Cern and tests and preparation for new experiments.Comment: Proc. The First International Workshop of Nuclear Emulsion Techniques (12-24 June 1998, Nagoya, Japan), 15 pages, 11 figure

Unfreezing of molecular motions in protein-polymer conjugates: a calorimetric study

Protein-polymer conjugates are a promising class of biohybrids. In this work, the dynamics of a set of biodegradable conjugates myoglobin-poly(ethyl ethylene phosphate) (My-PEEP) with variations in the number of attached polymers and their molar mass in the dry-state, have been investigated to understand the role of polymer on protein dynamics. We performed Differential Scanning Calorimetry measurements between 190 and 300 K, observing the large-scale dynamics arising from reorganization of conformational states, i.e. within the 100 s timescale. The application of an annealing time during the cooling scans was used to investigate the non-equilibrium glassy-state of the samples, observing the relaxation enthalpy at different annealing temperatures. This procedure permitted to extensively describe the transition broadness and the system relaxation kinetics in the glassy state. The samples show an experimental behaviour different from the theoretical predictions, suggesting the establishment of interactions among the protein and the polymer chains. The different behaviour of the conjugates and the physical mixture (composed of the protein and the polymer physically mixed) highlighted the importance of the covalent bond in defining the system dynamics

Hemp cakes composition and ruminal degradability as influenced by the cold pressing parameters

The growing consumers interest in the oil has made available several hemp by-products for animal feeding. The main of them are the cakes resulting from mechanical extraction of oil which may contain remarkable levels of protein, but also varying amounts of fibre and fat in relation to both seeds’ composition and extraction process. The aim of this study was to investigate the influence of the pressure and the botanical variety on hemp cakes composition. Seeds from Futura75 and Uso31 cultivars with rather similar composition (respectively, in percent of dry matter, Crude protein, CP, 20.9 vs. 19.9, fat 23.6 vs. 23.3, NDF 48.8 vs. 49.6) were pressed in an experimental mechanical screw press powered by 2.2 kW electric motor and equipped with temperature sensors to control the oil extraction temperature. Each hemp variety was pressed at growing extraction pressures gained by fitting four different nozzle diameters on the screw press (14, 12, 8, 6mm). For each pressure level, the seeds were pressed twice for a total of 16 cake samples which were analysed for chemical composition and in vitro digestibility of DM (IVDMD) and NDF (IVNDFD), determined based on a 48-h incubation in a Daisy II system. A two-way analysis of variance (proc GLM) was performed with variety (n=2), pressure (n=4), and their interaction as factors. Statistical significance was attained only between the extreme values of pressure (14 vs. 6mm) and resulted in an increment of the concentration of NDF, ADF and lignin (p < .05) as an effect of the reduction of the fat content (p < .05). Despite the small differences between the whole seed compositions, the Uso31 and Futura75 cakes diverged for the CP, ADF (p < .05), NDF and lignin (p < .001), whereas no differences were observed for fat. It is self-evident that the pressure worked differently on the two varieties, though no significant interactions pressure*- variety were highlighted. The IVDMD and IVNDFD were affected by both pressure and variety (p < .001) with the higher values observed for pressure at 14mm and the variety Uso31. Overall, the nutritional characteristics of hemp cakes can be strongly influenced by the botanical variety even regardless of the chemical composition whereas they can be significantly modified only by more than doubling the pressure applied to seeds

The geological record of storm events over the last 1000 years in the Salerno Bay (Southern Tyrrhenian Sea): new proxy evidences

International audienceThe shallow marine Late Holocene wedge of the northern Salerno Bay shelf (Southern Tyrrhenian Sea) discloses the presence of four decimetric shelf-tapering sand beds. Their internal features, depicted by cores analysis and their stratigraphic position, revealed by VHR seismic investigations, inferred sandy layers as being the result of flash deposition, storm controlled, thus episodic. Stratigraphic correlations among cores lead to constrain sandy layers deposition to storm events falling in the 11th, 16th, 19th and 20th centuries. A certain attribution of the most recent event bed to the major cloudburst that hit the Salerno region in 1954A.D. and resulted in a disastrous flood of the Bonea stream, was formerly achieved. A tentative link with two sea-storms that occurred in the 1544A.D. and in the 1879A.D. and well documented by historical sources is here proposed to explain the deposition of the two previous event beds. The deposition of these sandy layers must be related to major storm events, since their preservation in the stratigraphic record is not common. Lithostratigraphic and textural differences between flood and sea-storm emplacement emerge from the study of sandy layers in cores and point to a prevalence of sea-storm deposits in the middle shelf compared to flood deposits. Seismic stratigraphic evidence lead us to suppose that the style of episodic flash deposition has been running on for the last 2-3kyr and is probably linked to a climatic trend of the region

Motor imagery training speeds up gait recovery and decreases the risk of falls in patients submitted to total knee arthroplasty

With Motor imagery (MI), movements are mentally rehearsed without overt actions; this procedure has been adopted in motor rehabilitation, primarily in brain-damaged patients. Here we rather tested the clinical potentials of MI in purely&nbsp;orthopaedic patients who, by definition, should maximally benefit of mental exercises because of their intact brain. To this end we studied the recovery of gait after total knee arthroplasty and evaluated whether MI combined with physiotherapy could speed up the recovery of gait and even limit the occurrence of future falls. We studied 48 patients at the beginning and by the end of the post-surgery residential rehabilitation program: half of them completed a specific MI training supported by computerized visual stimulation (experimental group); the other half performed a non-motoric cognitive training (control group). All patients also had standard physiotherapy. By the end of the rehabilitation, the experimental group showed a better recovery of gait and active knee flexion-extension movements, and less pain. The number of falls or near falls after surgery was significantly lower in the experimental group. These results show that MI can improve gait abilities and limit future falls in orthopaedic patients, without collateral risks and with limited costs

Status of the Cylindical-GEM project for the KLOE-2 Inner Tracker

The status of the R&D on the Cylindrical-GEM (CGEM) detector foreseen as Inner Tracker for KLOE-2, the upgrade of the KLOE experiment at the DAFNE phi-factory, will be presented. The R&D includes several activities: i) the construction and complete characterization of the full-size CGEM prototype, equipped with 650 microns pitch 1-D longitudinal strips; ii) the study of the 2-D readout with XV patterned strips and operation in magnetic field (up to 1.5T), performed with small planar prototypes in a dedicated test at the H4-SPS beam facility; iii) the characterization of the single-mask GEM technology for the realization of large-area GEM foils.Comment: 4 pages, 10 figures, Presented at Vienna Conference on Instrumentation (Feb 15-20, 2010, Vienna, Austria). Submitted to the Proceeding