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

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

A 1 m3^3 Gas Time Projection Chamber with Optical Readout for Directional Dark Matter Searches: the CYGNO Experiment

The aim of the CYGNO project is the construction and operation of a 1~m$^3$ gas TPC for directional dark matter searches and coherent neutrino scattering measurements, as a prototype toward the 100-1000~m$^3$ (0.15-1.5 tons) CYGNUS network of underground experiments. In such a TPC, electrons produced by dark-matter- or neutrino-induced nuclear recoils will drift toward and will be multiplied by a three-layer GEM structure, and the light produced in the avalanche processes will be readout by a sCMOS camera, providing a 2D image of the event with a resolution of a few hundred micrometers. Photomultipliers will also provide a simultaneous fast readout of the time profile of the light production, giving information about the third coordinate and hence allowing a 3D reconstruction of the event, from which the direction of the nuclear recoil and consequently the direction of the incoming particle can be inferred. Such a detailed reconstruction of the event topology will also allow a pure and efficient signal to background discrimination. These two features are the key to reach and overcome the solar neutrino background that will ultimately limit non-directional dark matter searches.Comment: 5 page, 7 figures, contribution to the Conference Records of 2018 IEEE NSS/MI

In vitro and in vivo evaluation of a new active heat moisture exchanger.

INTRODUCTION: In order to improve the efficiency of heat moisture exchangers (HMEs), new hybrid humidifiers (active HMEs) that add water and heat to HMEs have been developed. In this study we evaluated the efficiency, both in vitro and in vivo, of a new active HME (the Performer; StarMed, Mirandola, Italy) as compared with that of existing HMEs (Hygroster and Hygrobac; Mallinckrodt, Mirandola, Italy). METHODS: We tested the efficiency by measuring the temperature and absolute humidity (AH) in vitro using a test lung ventilated at three levels of minute ventilation (5, 10 and 15 l/min) and at two tidal volumes (0.5 and 1 l), and in vivo in 42 patients with acute lung injury (arterial oxygen tension/fractional inspired oxygen ratio 283 +/- 72 mmHg). We also evaluated the efficiency in vivo after 12 hours. RESULTS: In vitro, passive Performer and Hygrobac had higher airway temperature and AH (29.2 +/- 0.7 degrees C and 29.2 +/- 0.5 degrees C, [P < 0.05]; AH: 28.9 +/- 1.6 mgH2O/l and 28.1 +/- 0.8 mgH2O/l, [P < 0.05]) than did Hygroster (airway temperature: 28.1 +/- 0.3 degrees C [P < 0.05]; AH: 27 +/- 1.2 mgH2O/l [P < 0.05]). Both devices suffered a loss of efficiency at the highest minute ventilation and tidal volume, and at the lowest minute ventilation. Active Performer had higher airway temperature and AH (31.9 +/- 0.3 degrees C and 34.3 +/- 0.6 mgH2O/l; [P < 0.05]) than did Hygrobac and Hygroster, and was not influenced by minute ventilation or tidal volume. In vivo, the efficiency of passive Performer was similar to that of Hygrobac but better than Hygroster, whereas Active Performer was better than both. The active Performer exhibited good efficiency when used for up to 12 hours in vivo. CONCLUSION: This study showed that active Performer may provide adequate conditioning of inspired gases, both as a passive and as an active device

Circulating haematopoietic and endothelial progenitor cells are decreased in COPD

Circulating CD34+ cells are haemopoietic progenitors that may play a role in tissue repair. No data are available on circulating progenitors in chronic obstructive pulmonary disease (COPD). Circulating CD34+ cells were studied in 18 patients with moderate-to-severe COPD (age: mean+/-sd 68+/-8 yrs; forced expiratory volume in one second: 48+/-12% predicted) and 12 controls, at rest and after endurance exercise. Plasma concentrations of haematopoietic growth factors (FMS-like tyrosine kinase 3 (Flt3) ligand, kit ligand), markers of hypoxia (vascular endothelial growth factor (VEGF)) and stimulators of angiogenesis (VEGF, hepatocyte growth factor (HGF)) and markers of systemic inflammation (tumour necrosis factor (TNF)-alpha, interleukin (IL)-6, IL-8) were measured. Compared with the controls, the COPD patients showed a three-fold reduction in CD34+ cell counts (3.3+/-2.5 versus 10.3+/-4.2 cells.microL-1), and a 50% decrease in AC133+ cells. In the COPD patients, progenitor-derived haemopoietic and endothelial cell colonies were reduced by 30-50%. However, four COPD patients showed progenitor counts in the normal range associated with lower TNF-alpha levels. In the entire sample, CD34+ cell counts correlated with exercise capacity and severity of airflow obstruction. After endurance exercise, progenitor counts were unchanged, while plasma Flt3 ligand and VEGF only increased in the COPD patients. Plasma HGF levels were higher in the COPD patients compared with the controls and correlated inversely with the number of progenitor-derived colonies. In conclusion, circulating CD34+ cells and endothelial progenitors were decreased in chronic obstructive pulmonary disease patients and could be correlated with disease severity

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