1,720,969 research outputs found
Mining sponge phenomena in RNA expression data
No full textIn the last few years, the interactions among competing endogenous RNAs (ceRNAs) have been recognized as a key post-transcriptional regulatory mechanism in cell differentiation, tissue development, and disease. Notably, such sponge phenomena substracting active microRNAs from their silencing targets have been recognized as having a potential oncosuppressive, or oncogenic, role in several cancer types. Hence, the ability to predict sponges from the analysis of large expression data sets (e.g. from international cancer projects) has become an important data mining task in bioinformatics. We present a technique designed to mine sponge phenomena whose presence or absence may discriminate between healthy and unhealthy populations of samples in tumoral or normal expression data sets, thus providing lists of candidates potentially relevant in the pathology. With this aim, we search for pairs of elements acting as ceRNA for a given miRNA, namely, we aim at discovering miRNA-RNA pairs involved in phenomena which are clearly present in one population and almost absent in the other one. The results on tumoral expression data, concerning five different cancer types, confirmed the effectiveness of the approach in mining interesting knowledge. Indeed, 32 out of 33 miRNAs and 22 out of 25 protein-coding genes identified as top scoring in our analysis are corroborated by having been similarly associated with cancer processes in independent studies. In fact, the subset of miRNAs selected by the sponge analysis results in a significant enrichment of annotation for the KEGG32 pathway "microRNAs in cancer"when tested with the commonly used bioinformatic resource DAVID. Moreover, often the cancer datasets where our sponge analysis identified a miRNA as top scoring match the one reported already in the pertaining literature
Vegetation to Crambe hispanica L. in Apulia Region
No full textA phytosociological study of the cenosis to Crambe hispanica L. in Apulia Region is presented. In this Region, the taxon is reported in a critically endangered (CR) status. Two different areas were investigated: the Gargano, in the north of Apulia, and the south-eastern of Murge, in the central part of the Region. On the Gargano the vegetation to C. hispanica prefers the borders of abandoned olive-groves, where it exploits the action of the mitigating effect of the overlooking Varano Lake and the humidity of northern cold winds loaded of rain. Whereas, on the Murge, in the territory of Martina Franca (province of Taranto), where a new and important population of C. hispanica L. was signaled, the taxon locates itself to the borders of cultivated environments (arable lands), where the conditions of greater summer aridity are compensated by the shadowing of few isolated oak trees and, mainly, from reserves of water that accumulate at the bottom of the small "dry stonewalls" (muretti a secco) and/or of the irregular calcareous heaps, resulting from "stone removing work" (spietramento). The vegetation context in which these communities evolved are, in Gargano area, primarily, the scrub vegetation (macchia) referable to Cyclamino repandi-Paliuretum spinae-christi (Biondi 1999), while, in the area of Murge, they reenter in the Quercus troiana Webb subsp. trojana woods areal. The vegetation riliefs and the peculiar environmental features have allowed to ascribe C. hispanica cenosis to a new association of Hordeion leporini: Crambetum hispanicae ass. nova hoc loco. Some strategic devices for in situ maintenance of the taxon and related ecosystems are suggested. © Società Italiana di Fitosociologia
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
New distribution data and relationship with Directive 92/43/EEC on apulian critical taxa growing in Province of Bari
No full textIn this work the authors report news on 20 species growing in Province of Bari. Anthemis hydruntina H. Groves, Ophioglossum lusitanicum L. and Sternbergia colchiciflora Waldst. & Kit., threatened species for Italy and Apulia Region, are reported for the second or third time at regional level, and the first time to Province of Bari; Aegilops biuncialis Vis. and A. uniaristata Vis., reported in the Regional and National Red List, have been found in new stations. Gagea granatellii Parl., Berteroa obliqua (Sm.) DC. subsp. obliqua, Jonopsidium albiflorum Durieu, other 3 species of the Red List, were observed in new stations and provided updates on presence/absence for older works. For Allium garganicum Brullo, Pavone, Salmeri & Terrasi, Cheilanthes acrostica (Balb.) Tod., Geropogon glaber L., Heliotropium supinum L., Orchis laxiflora Lam., Peganum harmala L., Verbena supina L., that are extremely rare taxa at regional or national level and poorly/no documented, important distributional data were provided. New stations of Inula spiraeifolia L., Phlomis fruticosa L. and Scorzonera hirsuta L. were documented. During field surveys two adventitious species of particular interest were also found: Centranthus macrosiphon Boiss. and Convolvulus sabatius Viv. subsp. sabatius. The relationships between these species and the 92/43/EEC Directive show that 13 out of 20 taxa are part of 7 different habitats, while for the other 7 species, insufficient data about plant communities or low numerical consistency of the populations, do not allow the identification of habitat. The data allow the updating of the Natura 2000 Data Forms
The GPR System: an Architecture for Integrating Active And Deductive Rules on Complex Database Objects
No full textThis paper illustrates a prototype system, called GPRS, supporting the Generalized Production Rules database language (GPR for short). The language GPR integrates, in a unified framework, active rules, which allow the specification of event driven computations on data, and deductive rules, which can be used to derive intentional relations in the style of logic programming. The prototype realizes the operational semantics of GPR, implementing both active and deductive behaviors. The rule-evaluation engine of the system is unique. The data model of reference is object based and the system is implemented on top of an object oriented DBMS. Thus, the GPRS prototype represents a concrete proposal of an advanced DBMS for complex objects that supports both active and deductive styles in rule programming
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