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A variety of schemas and ontologies are currently used for the machine-readable description of bibliographic entities and citations. This diversity, and the reuse of the same ontology terms with different nuances, generates inconsistencies in data. Adoption of a single data model would facilitate data integration tasks regardless of the data supplier or context application. In this paper we present the OpenCitations Data Model (OCDM), a generic data model for describing bibliographic entities and citations, developed using Semantic Web technologies. We also evaluate the effective reusability of OCDM according to ontology evaluation practices, mention existing users of OCDM, and discuss the use and impact of OCDM in the wider open science community., Comment: ISWC 2020 Conference proceedings

Presentiamo i risultati del progetto Linked Books, che ha portato alla creazione di un prototipo per un indice citazionale capace di collegare il catalogo bibliotecario nazionale italiano (Opac SBN) con il sistema informativo dell’Archivio di Stato di Venezia e con i portali d’autorità e “metamotori” di ricerca internazionali (VIAF.org, Europeana). Il prototipo include 3.850.581 citazioni estratte da un corpus di 2.475 volumi, di cui 1.905 monografie e 552 numeri di rivista, da cui 5.496 articoli, riguardanti la storia di Venezia. Il progetto Linked Books ha permesso di esplorare la fattibilità e l’opportunità della creazione di un indice citazionale per discipline umanistiche, e di affrontare e risolvere ostacoli tecnici quali la creazione di un corpus rappresentativo a partire da risorse e competenze bibliografiche, la digitalizzazione dei materiali nel rispetto dei diritti d’autore, l’estrazione automatica di citazionie lo sviluppo di interfacce di ricerca per il pubblico.

Citation indexes are by now part of the research infrastructure in use by most scientists: a necessary tool in order to cope with the increasing amounts of scientific literature being published. Commercial citation indexes are designed for the sciences and have uneven coverage and unsatisfactory characteristics for humanities scholars, while no comprehensive citation index is published by a public organisation. We argue that an open citation index for the humanities is desirable, for four reasons: it would greatly improve and accelerate the retrieval of sources, it would offer a way to interlink collections across repositories (such as archives and libraries), it would foster the adoption of metadata standards and best practices by all stakeholders (including publishers) and it would contribute research data to fields such as bibliometrics and science studies. We also suggest that the citation index should be informed by a set of requirements relevant to the humanities. We discuss four such requirements: source coverage must be comprehensive, including books and citations to primary sources; there needs to be chronological depth, as scholarship in the humanities remains relevant over time; the index should be collection driven, leveraging the accumulated thematic collections of specialised research libraries; and it should be rich in context in order to allow for the qualification of each citation, for example, by providing citation excerpts. We detail the fit-for-purpose research infrastructure which can make the Humanities Citation Index a reality. Ultimately, we argue that a citation index for the humanities can be created by humanists, via a collaborative, distributed and open effort.

The Early Growth Response protein (Egr-1) is a C(2)H(2)-zinc finger-containing transcriptional regulator involved in the control of cell proliferation and apoptosis. Its DNA-binding activity is redox regulated in vitro through the oxidation-reduction of Cys residues within its DNA-binding domain. APE/Ref-1 is a DNA-repair enzyme with redox modulating activities on several transcription factors. In this study, by evaluating the effects of different stimuli, we found a similar timing of activation being suggestive for a common and co-linear regulation for the two proteins. Indeed, we show that APE/Ref-1 increases the Egr-1 DNA-binding activity in unstimulated osteoblastic HOBIT cells. H(2)O(2) stimulation induces a strong interaction between Egr-1 and APE/Ref-1 at early times upon activation, as assayed by immunoprecipitation experiments. By using a cell transfection approach, we demonstrated the functional role of this interaction showing that two specific Egr-1 target genes, the PTEN phosphatase and the thymidine kinase (TK) genes promoters, are activated by contransfection of APE/Ref-1. Interestingly, by using a cell transfection approach and Chromatin immunoprecipitation assays, we were able to demonstrate that Egr-1 stimulates the transcriptional activity of APE/Ref-1 gene promoter by a direct interaction with specific DNA-binding site on its promoter. Taken together, our data delineate a new molecular mechanism of Egr-1 activation occurring soon after H(2)O(2) stimulation in osteoblastic cells and suggest a model for a positive loop between APE/Ref-1 and Egr-1 that could explain the early transcriptional activation of APE/Ref-1 gene expression.

Extracellular ATP is a widespread autocrine/paracrine signal since many animal cells release ATP in the extracellular medium; often this release is mechanosensitive, but the molecular mechanism is still unclear. The involvement of vesicular release, conductive channels, or ABC transporters has been suggested in different cell types. We investigated the mechanism of ATP release in human HOBIT osteoblastic cells, in which mechanical stimulation induced intercellular calcium waves sustained by both cell-to-cell coupling through gap junctions and ATP release. In this study we employed a luciferin-luciferase bioluminescence assay to measure the amount of ATP released under different stimulatory conditions. Given the role of connexin hemichannels in favoring passive NAD(+) transport [Bruzzone, S., et al. (2001) FASEB J. 15, 10-12], the involvement of connexin hemichannels as putative ATP transporters was initially investigated. In HOBIT cells overexpressing connexin43 the amount of nucleotide released under basal and stimulated conditions was similar to non-transfected cells, ruling out a major involvement of connexin hemichannels in ATP transport. In nontransfected HOBIT cells mechanical stimulations induced by medium displacement and hypotonic stress consistently enhanced ATP efflux. Cytochalsin D treatment did not alter basal and stimulated ATP release, while elevated cAMP levels consistently reduced efflux in both cases. ATP released by hypotonic stress and medium displacement evoked intracellular Ca(2+) transients in fura2-loaded HOBIT cells, indicating that different mechanical stimuli activate physiological cell responses.

Extracellular nucleotides such as ATP and UTP are released in response to mechanical stimulation in different cell systems. It is becoming increasingly evident that ATP release plays a role in autocrine and paracrine stimulation of osteoblasts. Mechanical stimulation, as shear stress, membrane stretch or hypo-osmotic swelling, as well as oscillatory fluid flow, stimulates ATP release from different osteoblastic cell lines. Human osteoblast-like initial transfectant (HOBIT) cells release ATP in response to mechanical stimulation. In the present study, we show that HOBIT cells are activated by nanomolar levels of extracellular ATP, concentrations that can be detected under resting conditions and increase following hypotonic shock. Cell activation by hypotonic medium induced intracellular Ca2+ oscillations, and Egr-1 synthesis and DNA-binding activity. Quinacrine staining of living, resting cells revealed a granular fluorescence, typical of ATP-storing vesicles. Monensin prevented quinacrine staining and considerably inhibited hypotonic- induced ATP release. Finally, elevated levels of cytosolic Ca2+ activated massive ATP release and a dose-dependent loss of quinacrine granules. The contribution of a vesicular mechanism for ATP release is proposed to sustain paracrine osteoblast activation.

Dynamic mechanical loading increases bone density and strength and promotes osteoblast proliferation, differentiation and matrix production, by acting at the gene expression level. Molecular mechanisms through which mechanical forces are conversed into biochemical signalling in bone are still poorly understood. A growing body of evidence point to extracellular nucleotides (i.e., ATP and UTP) as soluble factors released in response to mechanical stimulation in different cell systems. Runx2, a fundamental transcription factor involved in controlling osteoblasts differentiation, has been recently identified as a target of mechanical signals in osteoblastic cells. We tested the hypothesis that these extracellular nucleotides could be able to activate Runx2 in the human osteoblastic HOBIT cell line. We found that ATP and UTP treatments, as well as hypotonic stress, promote a significant stimulation of Runx2 DNA-binding activity via a mechanism involving PKC and distinct mitogen-activated protein kinase cascades. In fact, by using the specific inhibitors SB203580 (specific for p38 MAPK) and PD98059 (specific for ERK-1/2 MAPK), we found that ERK-1/2, but not p38, play a major role in Runx2 activation. On the contrary, another important transcription factor, i.e., Egr-1, that we previously demonstrated being activated by extracellular released nucleotides in this osteoblastic cell line, demonstrated to be susceptible to both ERK-1/2 and p38 kinases. These data suggest a possible differential involvement of these two transcription factors in response to extracellularly released nucleotides. The biological relevance of our data is strengthened by the finding that a target gene of Runx2, i.e., Galectin-3, is up-regulated by ATP stimulation of HOBIT cells with a comparable kinetic of that found for Runx2. Since it is known that osteocytes are the primary mechanosensory cells of the bone, we hypothesize that they may signal mechanical loading to osteoblasts through release of extracellular nucleotides. Altogether, these data suggest a molecular mechanism explaining the purinoreceptors-mediated activation of specific gene expression in osteoblasts and could be of help in setting up new pharmacological strategies for the intervention in bone loss pathologies.

Extracellular nucleotides exert an important role in controlling cell physiology by activating intracellular signalling cascades. Osteoblast HOBIT cells express P2Y1 and P2Y2 G-protein-coupled receptors, and respond to extracellular ATP by increasing cytosolic calcium concentrations. Early growth response protein 1 (Egr-1) is a C2H2-zinc-finger-containing transcriptional regulator responsible for the activation of several genes involved in the control of cell proliferation and apoptosis, and is thought to have a central role in osteoblast biology. We show that ATP treatment of HOBIT cells increases Egr-1 protein levels and binding activity via a mechanism involving a Ca2+-independent protein kinase C isoform. Moreover, hypotonic stress and increased medium turbulence, by inducing ATP release, result in a similar effect on Egr-1. Increased levels of Egr-1 protein expression and activity are achieved at very early times after stimulation (5 min), possibly accounting for a rapid way for changing the osteoblast gene-expression profile. A target gene for Egr-1 that is fundamental in osteoblast physiology, COL1A2, is up-regulated by ATP stimulation of HOBIT cells in a timescale that is compatible with that of Egr-1 activation.

Intercellular communication allows co-ordination of cell metabolism and sensitivity to extracellular stimuli. In bone cells, paracrine stimulation and cell-to-cell coupling through gap junctions induce the formation of complex intercellular networks, which favours the intercellular exchange of nutrients and second messengers, ultimately controlling the process of bone remodelling. The importance of local factors in bone remodelling is known since many years. Bone cells secrete and respond to a variety signals, among which include prostaglandins, cytokines, growth factors, and ATP. We here report evidence that extracellular NAD(+) is a novel extracellular signal stimulating osteoblast differentiation. We found that HOBIT human osteoblastic cells, which are known to express ADP-ribosyl cyclase/CD38 activity, respond to micromolar concentrations of extracellular NAD(+) with oscillatory increases of the cytosolic Ca(2+) concentration. The initial Ca(2+) response was followed by a time-dependent inhibition of cell growth, the appearance of an epithelial morphology, and by an increase of alkaline phosphatase and osteocalcin expression. Under resting condition HOBIT cells release NAD(+) in the extracellular medium and the release is significantly potentiated by mechanical stimulation. Taken together these results point to NAD(+) as a novel autocrine/paracrine factor involved in stimulation and maintenance of the osteoblast differentiated phenotype.

ADP-ribosyl cyclase/CD38 is a bifunctional enzyme that catalyzes at its ectocellular domain the synthesis from NAD(+) (cyclase) and the hydrolysis (hydrolase) of the calcium-mobilizing second messenger cyclic ADP ribose (cADPR). Furthermore, CD38 mediates cADPR influx inside a number of cells, thereby inducing Ca(2+) mobilization. Intracellularly, cADPR releases Ca(2+) from ryanodine-sensitive pools, thus activating several Ca(2+)-dependent functions. Among these, the inhibition of osteoclastic-mediated bone resorption has been demonstrated. We found that HOBIT human osteoblastic cells display ADP-ribosyl cyclase activity and we examined the effects of CD38 stimulation on osteoblasts function. Extracellular NAD(+) induced elevation of cytosolic calcium due to both Ca(2+) influx from the extracellular medium and Ca(2+) release from ryanodine-sensitive intracellular stores. Culturing these cells in the presence of NAD(+) caused a complete growth arrest with a time-dependent decrease of cell number and the appearance of apoptotic nuclei. The first changes could be observed after 24 h of treatment and became fully evident after 72-96 h. We propose a role of extracellular NAD(+) in bone homeostatic control.

Bone-forming cells are organized in a multicellular network interconnected by gap junctions. Direct intercellular communication via gap junctions is an important component of bone homeostasis, coordinating cellular responses to external signals and promoting osteoblast differentiation. The cAMP pathway, a major intercellular signal transduction mechanism, regulates osteoblastic function and metabolism. We investigated the effects of this second messenger on junctional communication and on the expression of differentiation markers in human HOBIT osteoblastic cells. Increased levels of cAMP induce posttranslational modifications (i.e., phosphorylations) of connexin43 and enhancement of gap junction assembly, resulting in an increased junctional permeance to Lucifer yellow and to a positive modulation of intercellular Ca2+ waves. Increased intercellular communication, however, was accompanied by a parallel decrease of alkaline phosphatase activity and by an increase of osteocalcin expression. cAMP-dependent stimulation of cell-to-cell coupling induces a complex modulation of bone differentiation markers.