A preliminary census of the macrofungi of Mt Wellington, Tasmania- the sequestrate species

This is the fourth and final contribution in a series of papers providing a preliminary documentation of the macrofungi of Mt Wellington, Tasmania. The earlier papers dealt with the gilled Basidiomycota, the non-gilled Basidiomycota and the Ascomycota, respectively, excluding the sequestrate species. The present paper completes the series by dealing with the sequestrate species, of which seven Ascomycota, 76 Basidiomycota, three Glomeromycota and one Zygomycota were found. Seven new genera and 25 new species to be formally described elsewhere, are recorded

DAMA/LIBRA results and perspectives

The DAMA/LIBRA experiment, running at the Gran Sasso National Laboratory of the I.N.F.N. in Italy, has a sensitive mass of about 250 kg highly radiopure NaI(Tl). It is mainly devoted to the investigation of Dark Matter (DM) particles in the Galactic halo by exploiting the model independent DM annual modulation signature. The present DAMA/LIBRA experiment and the former DAMA/NaI one (the first generation experiment having an exposed mass of about 100 kg) have released so far results corresponding to a total exposure of 1.17 ton yr over 13 annual cycles. They provide a model independent evidence of the presence of DM particles in the galactic halo at 8.9 sigma C.L.. A short summary of the obtained results is presented and future perspectives of the experiment mentioned.Comment: 12 pages, Proceed. of the 15th Bled Workshop "What Comes Beyond Standard Models" (December 2012), Vol. 13, No.

FOBI: An ontology to represent food intake data and associate it with metabolomic data

Nutrition research can be conducted by using two complementary approaches: 1) traditional self-reporting methods or 2) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these two very different types of data often hinder their analysis and integration. To manage this challenge, we have developed a novel ontology that describes food and their associated metabolite entities in a hierarchical way. This ontology uses a formal naming system, category definitions, properties and relations between both types of data. The ontology presented is called FOBI (Food-Biomarker Ontology) and it is composed of two interconnected sub-ontologies. One is a 'Food Ontology' consisting of raw foods and multi-component foods while the second is a 'Biomarker Ontology' containing food intake biomarkers classified by their chemical classes. These two sub-ontologies are conceptually independent but interconnected by different properties. This allows data and information regarding foods and food biomarkers to be visualized in a bidirectional way, going from metabolomics to nutritional data or vice versa. Potential applications of this ontology include the annotation of foods and biomarkers using a well-defined and consistent nomenclature, the standardized reporting of metabolomics workflows (e.g. metabolite identification, experimental design), or the application of different enrichment analysis approaches to analyze nutrimetabolomic data. Availability: FOBI is freely available in both OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) formats at the project's Github repository (https://github.com/pcastellanoescuder/FoodBiomarkerOntology) and FOBI visualization tool is available in https://polcastellano.shinyapps.io/FOBI_Visualization_Tool/

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

Metabolomics and proteomics, like other omics domains, usually face a data mining challenge in providing an understandable output to advance in biomarker discovery and precision medicine. Often, statistical analysis is one of the most difficult challenges and it is critical in the subsequent biological interpretation of the results. Because of this, combined with the computational programming skills needed for this type of analysis, several bioinformatic tools aimed at simplifying metabolomics and proteomics data analysis have emerged. However, sometimes the analysis is still limited to a few hidebound statistical methods and to data sets with limited flexibility. POMAShiny is a web-based tool that provides a structured, flexible and user-friendly workflow for the visualization, exploration and statistical analysis of metabolomics and proteomics data. This tool integrates several statistical methods, some of them widely used in other types of omics, and it is based on the POMA R/Bioconductor package, which increases the reproducibility and flexibility of analyses outside the web environment. POMAShiny and POMA are both freely available at https://github.com/nutrimetabolomics/POMAShiny and https://github.com/nutrimetabolomics/POMA, respectively

Dark Matter investigation by DAMA at Gran Sasso

Experimental observations and theoretical arguments at Galaxy and larger scales have suggested that a large fraction of the Universe is composed by Dark Matter particles. This has motivated the DAMA experimental efforts to investigate the presence of such particles in the galactic halo by exploiting a model independent signature and very highly radiopure set-ups deep underground. Few introductory arguments are summarized before presenting a review of the present model independent positive results obtained by the DAMA/NaI and DAMA/LIBRA set-ups at the Gran Sasso National Laboratory of the INFN. Implications and model dependent comparisons with other different kinds of results will be shortly addressed. Some arguments put forward in literature will be confuted.Comment: review article, 71 pages, 25 figures, 8 tables; v2: minor modifications. In publication on the International Journal of Modern Physics

Final model independent result of DAMA/LIBRA-phase1

The results obtained with the total exposure of 1.04 ton x yr collected by DAMA/LIBRA-phase1 deep underground at the Gran Sasso National Laboratory (LNGS) of the I.N.F.N. during 7 annual cycles (i.e. adding a further 0.17 ton x yr exposure) are presented. The DAMA/LIBRA-phase1 data give evidence for the presence of Dark Matter (DM) particles in the galactic halo, on the basis of the exploited model independent DM annual modulation signature by using highly radio-pure NaI(Tl) target, at 7.5 sigma C.L.. Including also the first generation DAMA/NaI experiment (cumulative exposure 1.33 ton x yr, corresponding to 14 annual cycles), the C.L. is 9.3 sigma and the modulation amplitude of the single-hit events in the (2-6) keV energy interval is: (0.0112 \pm 0.0012) cpd/kg/keV; the measured phase is (144 \pm 7) days and the measured period is (0.998 \pm 0.002) yr, values well in agreement with those expected for DM particles. No systematic or side reaction able to mimic the exploited DM signature has been found or suggested by anyone over more than a decade.Comment: 20 pages, 13 figures, 6 tables; in publication on Eur. Phys. J.

Model independent result on possible diurnal effect in DAMA/LIBRA-phase1

The results obtained in the search for possible diurnal effect in the single-hit low energy data collected by DAMA/LIBRA-phase1 (total exposure: 1.04 ton x yr) deep underground at the Gran Sasso National Laboratory (LNGS) of the I.N.F.N. are presented. At the present level of sensitivity the presence of any significant diurnal variation and of diurnal time structures in the data can be excluded for both the cases of solar and sidereal time. In particular, the diurnal modulation amplitude expected, because of the Earth diurnal motion, on the basis of the DAMA Dark Matter annual modulation results is below the present sensitivity.Comment: 14 pages, 5 figures, 2 tables; in publication on Eur. Phys. J.

Interdependent binary choices under social influence: phase diagram for homogeneous unbiased populations

Coupled Ising models are studied in a discrete choice theory framework, where they can be understood to represent interdependent choice making processes for homogeneous populations under social influence. Two different coupling schemes are considered. The nonlocal or group interdependence model is used to study two interrelated groups making the same binary choice. The local or individual interdependence model represents a single group where agents make two binary choices which depend on each other. For both models, phase diagrams, and their implications in socioeconomic contexts, are described and compared in the absence of private deterministic utilities (zero opinion fields).Comment: 17 pages, 3 figures. This is the pre-peer reviewed version of the following article: Ana Fern\'andez del R\'io, Elka Korutcheva and Javier de la Rubia, Interdependent binary choices under social influence, Wiley's Complexity, 2012; which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/cplx.21397/abstrac

Exosome analysis in tumor-draining pulmonary vein identifies NSCLC patients with higher risk of relapse after curative surgery

Since tumor-draining pulmonary vein blood (PV) is enriched in tumor-secreted products, we hypothesized that it would also be enriched in tumor-derived exosomes, which would be important in the metastasis process. We characterized exosomes from PV of 61 resected non-small cell lung cancer (NSCLC) patients to evaluate its potential as relapse biomarkers. Exosomes were characterized using transmission electron microscopy, western blot and nanoparticle tracking analysis and we examined time to relapse (TTR) and overall survival (OS). Differences between PV and peripheral vein were found. PV was enriched in smaller exosomes than the paired peripheral vein (p = 0.01). Moreover, PV exosome size mode was able to identify relapsed patients (Area under the curve [AUC] = 0.781; 95%CI: 0.6641-0.8978), in whom exosome size was smaller (<112 nm; p < 0.001). The combination of PV exosome size and N (lymph node involvement) showed an AUC of 0.89 (95%CI: 0.80-0.97). Moreover, smaller PV exosome size was associated with shorter TTR (28.3 months vs. not reached, p < 0.001) and OS (43.9 months vs. not reached, p = 0.009). Multivariate analyses identified PV exosome size and stage as independent prognostic markers for TTR and OS. PV exosome size is a promising relapse biomarker after surgery that can add valuable information to clinical variables

Reversal of Hartmann's procedure through the stomal side: A new even more minimal invasive technique

Background: Several minimal invasive, mainly laparoscopic-assisted, techniques for reversal of Hartmann's procedure (HP) have been published. The purpose of this pilot study was to assess a minimal invasive procedure through the stomal site that may compare favorably with open or laparoscopic-assisted procedures in terms of operative time, hospital stay and postoperative complications. Methods: HP reversal through the stomal side was attempted in 13 consecutive patients. Lysis of intra-abdominal adhesions was done manually through an incision at the formal stoma side, without direct vision between thumb and index finger. The rectal stump was identified intra-abdominally using a transanal rigid club. A manually controlled stapled end-to-end colorectal anastomosis was created. Results: Mean duration of operation was 81 min (range 58-109 min); mean hospital stay was 4.2 days (range 2-7 days). In two patients the procedure was converted because of strong adhesions in the lower pelvic cavity around the rectal stump that could not be lysed manually safely. No complications occurred in the patients in whom reversal was completely done through the stomal site. Conclusions: In our opinion, restoration of intestinal continuity through the stomal side after HP is a feasible operation, without need for additional incisions. In the hands of a specialist gastrointestinal surgeon this technique can be attempted in all patients, as conversion to a laparoscopic-assisted or an open procedure can be performed when necessary