PAV ontology: provenance, authoring and versioning

Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as DC Terms and the W3C PROV-O are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. We identify the specific need for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing just enough descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the PROV-O ontology to support broader interoperability. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related approaches, namely Provenance Vocabulary, DC Terms and BIBFRAME. We identify similarities and analyze their differences with PAV, outlining strengths and weaknesses of our proposed model. We specify SKOS mappings that align PAV with DC Terms.Comment: 22 pages (incl 5 tables and 19 figures). Submitted to Journal of Biomedical Semantics 2013-04-26 (#1858276535979415). Revised article submitted 2013-08-30. Second revised article submitted 2013-10-06. Accepted 2013-10-07. Author proofs sent 2013-10-09 and 2013-10-16. Published 2013-11-22. Final version 2013-12-06. http://www.jbiomedsem.com/content/4/1/3

Commentary on: "Pityriasis Rosea Recurrence is Much Higher than Previously Known: A Prospective Study".

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A cerebral bridge from olfactory cognition to spatial navigation

An evolutionary paradox is the variability of the olfactory bulb size, in contrast to the other brain regions, which are sized proportionally to the peripheral function. This variability seems to be the result of selection for the olfactory function. This disagreement may derive from considering smell as a sense linked to odorous discrimination. In many vertebrates and in terrestrial and marine mammals, the sense of smell has evolved into functions related to the eco-localization. So, if the olfactory function involves spatial perception and navigation, this, couldexplain the proportional discrepancy between the olfactory bulb and olfactory cortex. Humans are able to discriminate a spatial position as a function of olfactory cues. Vice versa, in neurodegenerative syndromes the orientation capacity and olfactory perception are impaired. This leads us to think that could be a common cross-modal processing, of phylogenetic origin, which links olfactory perception and spatial orientation. Starting from these theoretical assumptions, we conducted a basic research, on 100 healthy subjects, investigating, through both behavioral and electroencephalographic data, the connection between spatial memory span and olfactory spatial memory span. Subjects were assessed through a three-condition task: normal Corsi Block Test (CBT), ‘Olfactory’ Block Test (OBT) and a ‘Semantic-Olfactory’ Block Test (SOBT). CBT consisted in a test on spatial memory span; OBT consisted in a presentation a spatial sequences of 9 different odorants (i.e., Eucalyptol, Carvone, Eugenol, Isoamyl Acetate, Geraniol, Phenethyl Alcohol, Acetophenone, Cinnamon, Hexanal) instilled on paper square not recognizable by any sign, positioned on a CBT, and showed in a spatial navigation way, and SOBT consisted of a semantic labelled of olfactory spatial navigation. A GLM repeated measure highlighted significant differences during the three conditions. Subjects had different SPANs due to different conditions. The Semantic olfactory memory SPAN was inferior respect Olfactory span and Spatial Span. Furthermore was found a significant positive correlation between the three condition. The 5 subjects with higher SPAN scores, 5 with medium scores and the 5 subjects with lower SPAN scores were recruited to investigate ERP components elicited during the cross-modal task. Subjects had to perform, during a high-density EEG recording, an olfactory task (administered through the device US2017127971 (A1) “? 2017-05-11), an EEG Posner spatial cueing task and a go/no-go olfactory semantic categorization task. The results of this study will be discussed in light of a theoretical connection between these three aspects of cortical functions that seem strongly interconnected

MAC Layer QoS Mechanisms for a Geostationary Satellite Network

An efficient resource management is crucial in supporting multimedia traffic in satellite networks. To this, Dynamic Bandwidth Allocation Capabilities mechanisms can be exploited to deliver the required QoS while optimising the bandwidth utilization. This paper just deals with the design of innovative algorithms for scheduling and sending the resource requests queued on a EuroSkyWay [1,2] satellite terminal to a Traffic Resource Manager (TRM). The effectiveness of the defined mechanisms has been evaluated through computer simulations. Particularly, by considering different mixes of MPEG-2 traffic and HTTP traffic, the Average Waiting Time (AWT) of the requests and their Losses Percentage have been calculated and compared with those ones obtained using algorithms proposed in MAC layer EuroSkyWay specifications

Detecting Recent Dynamics in Large-Scale Landslides via the Digital Image Correlation of Airborne Optic and LiDAR Datasets: Test Sites in South Tyrol (Italy)

Large-scale slow-moving deep-seated landslides are complex and potentially highly damaging phenomena. The detection of their dynamics in terms of displacement rate distribution is therefore a key point to achieve a better understanding of their behavior and support risk management. Due to their large dimensions, ranging from 1.5 to almost 4 km(2), in situ monitoring is generally integrated using satellite and airborne remote sensing techniques. In the framework of the EFRE-FESR SoLoMon project, three test-sites located in the Autonomous Province of Bolzano (Italy) were selected for testing the possibility of retrieving significant slope displacement data from the analysis of multi-temporal airborne optic and light detection and ranging (LiDAR) surveys with digital image correlation (DIC) algorithms such as normalized cross-correlation (NCC) and phase correlation (PC). The test-sites were selected for a number of reasons: they are relevant in terms of hazard and risk; they are representative of different type of slope movements (earth-slides, deep seated gravitational slope Deformation and rockslides), and different rates of displacement (from few cm/years to some m/years); and they have been mapped and monitored with ground-based systems for many years (DIC results can be validated both qualitatively and quantitatively). Specifically, NCC and PC algorithms were applied to high-resolution (5 to 25 cm/px) airborne optic and LiDAR-derived datasets (such as hillshade and slope maps computed from digital terrain models) acquired during the 2019-2021 period. Qualitative and quantitative validation was performed based on periodic GNSS surveys as well as on manual homologous point tracking. The displacement maps highlight that both DIC algorithms succeed in identifying and quantifying slope movements of multi-pixel magnitude in non-densely vegetated areas, while they struggle to quantify displacement patterns in areas characterized by movements of sub-pixel magnitude, especially if densely vegetated. Nonetheless, in all three landslides, they proved to be able to differentiate stable and active parts at the slope scale, thus representing a useful integration of punctual ground-based monitoring systems

The genomic organisation of the tra/trd locus validates the peculiar characteristics of dromedary δ-chain expression

The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) account for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage of the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR α (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site

New insight into the genomic structure of dog T cell receptor beta (TRB) locus inferred from expression analysis

Here is an updated report on the genomic organization of T cell receptor beta (TRB) locus in the domestic dog (Canis lupus familiaris) as inferred from comparative genomics and expression analysis. The most interesting results we found were a second TRBD–J–C cluster, which is absent from the reference genome sequence, and the annotation of two additional TRBV genes. In dogs, TRB locus consists of a library of 37 TRBV genes positioned at the 50 end of two in tandem aligned D–J–C gene clusters, each composed of a single TRBD, 6 TRBJ and one TRBC genes, followed by a single TRBV gene with an inverted transcriptional orientation. The TRB genes are distributed in less than 300 kb, making the canine locus, one of the smaller mammalian TRB locus studied so far. The small size may be ascribed to reduced gene duplication occurrences and a lower density of total interspersed repeats compared to humans and mice. Despite the low TRBV gene content, a large and diversified beta chain repertoire is displayed in the dog peripheral blood. A full usage of TRBV and TRBJ genes, including pseudogenes, and a high level of allelic polymorphism contribute to generate diversity. Finally, this study suggests that the overall TRB locus organization is evolutionarily conserved supporting the dog as a highly suited model system for immune development and diseases

MICROPILES TRIPODS SHIELDS (MTS) AS UNCONVENTIONAL BREAKERS FOR THE CONTROL OF MODERATELY RAPID EARTHFLOWS (SASSI NERI LANDSLIDE, NORTHERN APENNINES)

The paper deals with the idea, design and implementation of unconventional one-of-a-kind Micropiles Tripods Shields (MTS) intended to break and decelerate moderately rapid earthflows surges in the track zone of the Sassi Neri landslide (Nure Valley, Northern Apennines, Province of Piacenza, Italy). The MTS are inspired to floating anchors and “chevaux de fries” used in wartime. The basic elements are tripods of 193 mm diameter steel micropiles laid out at triangle, driven into the stable bedrock and emerging some meters aboveground. Each tripod consists of a vertical upslope central pile and two lateral oblique piles, linked by two transversal beams and connection plates aboveground. Multiple tripods are spaced along transversal rows to form Micropiles Tripods Shields (MTS) to advancing earthflows. The design of MTS has been based on field investigations such as boreholes and geophysics, that indicated a limited thickness of landslide deposits in the track zone where MTS have been installed. The forces resulting from active earthflows fronts have been estimated both with geotechnical and hydraulic computations. The analysis of vertical and transversal forces as well as bending moments acting on a single tripod versus the characteristic resistances was carried out using a bi-dimensional scheme with finite-elements software Plaxis, that indicated that the stress levels were compatible with the structural resistance of the tripods. The construction of MTS took place in 2018, involving working site preparation with partial lime-treatment of the surficial layers, underground micropiles drilling and installation, aboveground micropiles welding, tripods completion with connection beams and plates. Some tripods have been instrumented with load cells for monitoring earth pressures against micropiles, electric transducers for groundwater monitoring next to the piles, tiltmeters for tripods rotations and a total station for slope and tripods movements monitoring. Results show that the acceleration of slope movements corresponds to a generalized increase of pore water pressure at all the monitored tripods and to temporary slight tilting of the tripods which has so far being fully recovered when the landside slowed down and pressure decreased. This pioneering application indicates that once the characteristics of the earthflows are carefully considered, the depth to the bedrock in the installation zone is limited, and the logistical conditions in the field during construction are adequate, the MTS can be taken into consideration as a possible unconventional solution to break down and control moderately rapid earthflow

Evolution of the T-cell receptor (TR) Loci in the adaptive immune response: The tale of the TRG locus in mammals

T lymphocytes are the principal actors of vertebrates’ cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response