SecStAnT: Secondary Structure Analysis Tool for data selection, statistics and models building

Abstract Motivation: Atomistic or coarse grained (CG) potentials derived from statistical distributions of internal variables have recently become popular due to the need of simplified interactions for reaching larger scales in simulations or more efficient conformational space sampling. However, the process of parameterization of accurate and predictive statistics-based force fields requires a huge amount of work and is prone to the introduction of bias and errors. Results: This article introduces SecStAnT, a software for the creation and analysis of protein structural datasets with user-defined primary/secondary structure composition, with a particular focus on the CG representation. In addition, the possibility of managing different resolutions and the primary/secondary structure selectivity allow addressing the mapping-backmapping of atomistic to CG representation and study the secondary to primary structure relations. Sample datasets and distributions are reported, including interpretation of structural features. Availability and implementation: SecStAnT is available free of charge at secstant.sourceforge.net/. Source code is freely available on request, implemented in Java and supported on Linux, MS Windows and OSX. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Alien flora in Calabria (Southern Italy): an updated checklist

An updated checklist of the Calabrian alien vascular flora is presented. By way of field, bibliographic, and herbarium research, we recorded 382 alien taxa (representing almost 14% of all regional flora), of which 371 are angiosperms, nine gymnosperms, and two ferns. In relation to the state of spread, the majority of alien species are casual (207 taxa; 54%), followed by naturalized (127; 33%) and invasive (48; 13%), these last include four on the list of Union Concern, sensu Regulation (EU) no. 1143/2014. The most represented families are Asteraceae (39 taxa) and Poaceae (39). Among genera, Amaranthus (nine taxa), Prunus, Euphorbia, and Oxalis (seven taxa) make up those with the greatest number of taxa. A total of 21 taxa were reported for the first time, three of them are new to the European flora (Camptosema rubicundum, Musa xparadisiaca and, only for continental Europe, Ipomoea hederacea), two to the Italian peninsula (Pelargonium graveolens, Schinus terebinthifolia) and 16 to the Calabrian flora (Aeonium arboreum, Asparagus asparagoides, Aspidistra elatior, Bidens sulphurea, Catalpa bignonioides, Citrus xaurantium, Crassula ovata, Cucurbita ficifolia, Dimorphotheca ecklonis, Graptopetalum paraguayense subsp. paraguayense, Kalanchoe laxiflora, Nicotiana tabacum, Phytolacca dioica, Portulaca umbraticola, Talinum paniculatum, Tecomaria capensis). In terms of residence status, there are 291 neophytes (76%), 73 archaeophytes (19%), and 18 regional aliens (5%); neophytes are the most represented group (45 out of 48) among invasive taxa. Concerning life forms, the two most abundant groups are therophytes (30.1%, 115 taxa) and phanerophytes (29.6%, 113 taxa). Regarding habitats, 72% of alien taxa occur in artificial (199 taxa, 52%) and agricultural habitats (75 taxa, 20%). The majority of alien taxa are native to the Americas (159; 41.6%), numerous aliens also originated in Asia (76; 19.9%) and Africa (56; 14.7%). The majority of taxa were introduced for ornamental purposes (55%). Over the past decade, alien taxa in the flora in Calabria have increased from 190 to the current 382 taxa. While this trend could be linked to some extent to increasing awareness of the problem of alien species and the increasing intensity of research over recent decades, it is also most probably due to new introductions resulting from the globalization that relentlessly affects the whole planet.info:eu-repo/semantics/publishedVersio

Una collaborazione tra museo, enti di ricerca e scuola: l'epigrafia digitale e l'alternanza scuola lavoro

This paper presents a rich collaborative exchange between diverse institutions and professions engaged in research, conservation and education, brought together in the context of the Italian school-work exchange programme and with the aim of digitising, studying, and giving access to the epigraphic collection of the Museo Civico Castello Ursino of the city of Catania. The Museum is home to an important set of ancient inscribed texts on stone, with its origins in two local 18th-century antiquarian collections. A number of inscriptions were already on display following older criteria of museum exhibition; but most of the collection is held in storage. Therefore, one of the objectives of the collaboration is to make the rich epigraphic collection of the museum that is not on display accessible to the general public and academic researchers alike. The initial work of the three-year project concerned the digitisation of the catalogue records, as well as the graphic and photographic documentation of the inscriptions; during the second year, an exhibition was mounted in the Castello Ursino to present a selection of inscriptions from Catania. These inscriptions were the focus of an initial round of conservation work and were added to the digital catalogue together with supporting documentation. The inscriptions are encoded in accordance with international standards and controlled vocabularies (in EpiDoc TEI-XML, using Pleiades for geographical locations, and the controlled vocabularies of the EAGLE project for epigraphic types, materials and supports), with the aim of facilitating the creation of Linked Open Data. The exhibition includes two videos and a digital multimedia terminal to enable access to a wider range of materials as well as 3D imaging. The third year will be devoted to finalising both digitisation and documentation, and to more extensive result dissemination via the World Wide Web

<em>Salvia ceratophylloides</em> Ard. (Lamiaceae): A Rare Endemic Species of Calabria (Southern Italy)

Salvia ceratophylloides Ard. is a very precious narrow endemism of Southern Italy. It grows in the suburban surroundings of Reggio Calabria, on coastal strip hilly ridges between 250 and 450 m a.s.l. At the beginning of 1900, it was present in several localities, as evidenced by literature, where it was already very rare. Afterward, despite the research carried out by various botanists, the species was no longer found, due to its disappearing in the places mentioned in literature resulting from the intense environmental transformations suffered by the territory. Therefore, the species since 1997 was included in the “Red Book of the flora of Italy” among the extinct species. The successive research carried out in 2008 made it possible to ascertain new localities at about 10 km of distance from those reported in the literature. The actual population consists of about 1000 individuals, and according to IUNC criteria, the conservation status is critically endangered (CR). The threats to survival and spread of the species are different, but above all, it is the habitat destruction due to urbanization to threaten this species

An Innovative, Open, Interoperable Citizen Engagement Cloud Platform for Smart Government and Users' Interaction

This paper introduces an open, interoperable, and cloud-computing-based citizen engagement platform for the management of administrative processes of public administrations, which also increases the engagement of citizens. The citizen engagement platform is the outcome of a 3-year Italian national project called PRISMA (Interoperable cloud platforms for smart government). The aim of the project is to constitute a new model of digital ecosystem that can support and enable new methods of interaction among public administrations, citizens, companies, and other stakeholders surrounding cities. The platform has been defined by the media as a flexible (enable the addition of any kind of application or service) and open (enable access to open services) Italian "cloud" that allows public administrations to access to a vast knowledge base represented as linked open data to be reused by a stakeholder community with the aim of developing new applications ("Cloud Apps") tailored to the specific needs of citizens. The platform has been used by Catania and Syracuse municipalities, two of the main cities of southern Italy, located in the Sicilian region. The fully adoption of the platform is rapidly spreading around the whole region (local developers have already used available application programming interfaces (APIs) to create additional services for citizens and administrations) to such an extent that other provinces of Sicily and Italy in general expressed their interest for its usage. The platform is available online and, as mentioned above, is open source and provides APIs for full exploitation.Comment: 23 pages, 7 figures, journal pape

Relevant but neglected habitat types by the Directive 92/43 EEC in southern Italy

The 92/43/EEC Habitats Directive is the main European Union legal tool concerning nature conservation. The habitat types listed in Annex I to the Directive are phytosociology-based. It is widely acknowledged that phytosociological analysis is a crucial approach for habitats characterization and for monitoring their conservation status. Based on bibliographic investigations and new field survey campaigns, a list of habitat types neglected by the Habitats Directive is here presented and described for southern Italy. In this paper, 8 new habitat types and 13 subtypes are proposed. For each of these proposed new habitat types, a wide range of information, including ecology, chorology, species composition, syntaxonomy, threats, and conservation status, is here provided. To supply more detailed phytogeographical and coenological information about the proposed new habitat types, distribution maps based on 10 x 10 km reference grids and phytosociological tables including unpublished releves were carried out

Modulation of surface bio-functionality by using gold nanostructures on protein repellent surfaces

The integration of gold nanoparticles (Au NPs) or nanostructures with special optical properties on solid surfaces has become a major research topic in the field of nanobiotechnology in particular for the development of new generation of multifunctional bioanalytical platforms. This has led to considerable research efforts for developing quick and direct nanofabrication methods capable of producing well-ordered 2D nanostructured arrays with tunable morphological, chemical and optical properties. In this paper, we propose a simple and fast nanofabrication method enabling the creation of Au NPs patterns on a non-adhesive and cell repellent plasma-deposited poly(ethyleneoxide) (PEO-like) coating. The immobilization of Au NPs on PEO-like coatings does not require any prior chemical modifications and is achieved by a straightforward and stable self-assembly technique. By varying the size and the concentration of the Au NPs it is possible to control the Au NPs density and spatial distribution on the PEO-like coated surface with direct effects on the bio-functionality of the surface. These nanostructured surfaces have been tested for protein bio-recognition analysis and as a cell culture platform. The developed nanostructured platform has many potential applications in the field of protein-nanoparticle and cell-nanoparticle interaction studies, nanotoxicology and bioengineering.JRC.I.4-Nanobioscience

Prioritizing management actions for invasive non-native plants through expert-based knowledge and species distribution models

Given the high number of non-native plants that are being introduced worldwide and the time required to process formal pest risk analyses, a framework for the prioritization of management actions is urgently required. We therefore propose a framework for a replicable and standardized prioritization for management actions (eradication, control and monitoring) of invasive non-native plants, combining expert knowledge, current and future climatic suitability estimated by species distribution models (SDMs), clustering and ordination techniques. Based on expert consultation and using Italy as case study, invasive non-native plant species were selected and three categories of management actions were identified: eradication, control and containment, and monitoring. Finally, two further classes of priorities were proposed for each of the management actions: “high” and “low” priority. Overall, SDMs highlighted a high and very high suitability for Continental and Mediterranean bioregions for most invasive plants. Cluster analysis revealed three distinct clusters with varying levels of suitability for the Italian bioregions. Cluster 1 exhibited a higher suitability across all Italian bioregions, whereas non-native plants grouped in Cluster 2 predominantly featured high suitability in Mediterranean areas. Finally, Cluster 3 showed the lowest suitability values. Two ordination analysis highlighted the variability in bioclimatic suitability for each non-native plant within each cluster, as well as their current distribution pattern. Lastly, a third ordination, integrating bioclimatic suitability and spatial patterns, has allowed the differentiation of management actions for each non-native plant at both national and bioregional scales. Specifically, seven non-native plants were earmarked for eradication action, six for monitoring action, while the remaining species were deemed suitable for control and containment. Our results and the methodology proposed meet the demand for replicable new early warning tools; that is to predict the location of new outbreaks, to establish priorities for eradication, control and containment, and to monitor invasive non-native species

New national and regional Annex I Habitat records: from #45 to #59

New Italian data on the distribution of Annex I Habitats are reported in this contribution. Specifically, 8 new occurrences in Natura 2000 sites are presented and 27 new cells are added in the EEA 10 km × 10 km reference grid. The new data refer to the Italian administrative regions of Apulia, Campania, Calabria, Lazio, Tuscany, Umbria, Sardinia, and Sicily