Supporting and Enhancing Research on Cultural Heritage in France: the PATRIMA Project

In this paper, we first overview the French project on heritage called PATRIMA, launched in 2011 as one of the Projets d'investissement pour l'avenir, a French funding program meant to last for the next ten years. The overall purpose of the PATRIMA project is to promote and fund research on various aspects of heritage presentation and preservation. Such research being interdisciplinary, research groups in history, physics, chemistry, biology and computer science are involved in this project. The PATRIMA consortium involves research groups from universities and from the main museums or cultural heritage institutions in Paris and surroundings. More specifically, the main members of the consortium are the two universities of Cergy-Pontoise and Versailles Saint-Quentin and the following famous museums or cultural institutions: Musée du Louvre, Château de Versailles, Bibliothèque nationale de France, Musée du Quai Branly, Musée Rodin. In the second part of the paper, we focus on two projects funded by PATRIMA named EDOP and Parcours and dealing with data integration. The goal of the EDOP project is to provide users with a data space for the integration of heterogeneous information about heritage; Linked Open Data are considered for an effective access to the corresponding data sources. On the other hand, the Parcours project aims at building an ontology on the terminology about the techniques dealing with restoration and/or conservation. Such an ontology is meant to provide a common terminology to researchers using different databases and different vocabularies.

Petrologia e geocronologia U-Pb do plúton granítico Serra da Rajada, porção central do domínio Rio Piranhas - Seridó, Província Borborema, NE do Brasil

The ediacaran plutonic activity related to the Brasilian/Pan-African orogeny is one of the most important geological features in the Borborema Province, represented along its extension by numerous batholiths, stocks, and dikes.The object of this study, the Serra Rajada Granitic Pluton (SRGP), located in the central portion of the Piranhas-Seridó River Domain is an example of this activity. This pluton has been the subject of cartographic, petrographic, geochronological and lithogeochemical studies and its rocks were characterized by two facies. First, the granitic facies were described as monzogranites consisting of K-feldspar, plagioclase (oligoclase - An23-24%), quartz and biotite (main mafic) and opaque minerals such as titanite, allanite, apatite, and zircon as accessories. Alteration minerals are chlorite, white mica and carbonate. Second, the dioritic facies consist of rocks formed by quartz diorite containing plagioclase (dominant mineral phase), quartz and K-feldspar. Biotite and amphibole are the dominant mafic minerals; and titanite, opaque minerals, allanite, zircon and apatite are the accessories. However, previous geological mapping work in the region also identified the presence of other lithostratigraphic units. These were described as gneisses and migmatites with undifferentiated amphibolite lenses related to the Caicó Complex (Paleoproterozoic) and metasedimentary rocks of the Seridó Group (Neoproterozoic) composed of paragneiss with calc-silicate lenses, muscovite quartzite and biotite schist (respectively, the Jucurutu formations, Equador and Seridó), the host rocks for the SRGP rocks. Leucomicrogranite and pegmatite dikes have also been identified, both related to the end of the Ediacaran magmatism and colluvial- eluvial and alluvial deposits related to Neogene and Quaternary, respectively. Lithogeochemical data on the SRGP granite facies, highlighted quite evolved rocks (SiO2 69% to 75%), rich in alkalis (Na2O+K2O ≥ 8.0%), depleted of MgO (≤ 0.45%), CaO (≤ 1.42%) and TiO2 (≤ 0.36%) and moderate levels of Fe2O3t (2.16 to 3.53%). They display transitional nature between metaluminous and peraluminous (predominance of the latter) with sub-alkaline/monzonitic (High K calcium-alkali) affinity. Harker diagrams show negative correlations for Fe2O3t, MgO, and CaO, indicating mafic and plagioclase fractionation. REE spectrum shows enrichment of LREE relative to heavy REE (LaN/YbN = 23.70 to 10.13), with negative anomaly in the Eu (Eu/Eu* = 0.70 to 0.23), suggesting fractionation or accumulation in the feldspars source (plagioclase). Data integration allows to correlate the SRGP rocks with those described as Calcium-Alkaline Suite of equigranular High K. The crystallization conditions of the SRGP rocks were determined from the integration of petrographic and lithogeochemical data. These data indicated intermediate to high conditions of ƒO2 (mineral paragenesis titanite + magnetite + quartz), parent magma saturated in H2O (early biotite crystallization), tardi-magmatic processes of fluids rich in ƒCO2, H2O and O2 causing part of the mineral assembly to change (plagioclase carbonation and saussuritization, biotite chloritization and opaques Sphenitization). Thermobarometrical conditions were estimated based on geochemical parameters (Zr and P2O5) and CIPW normative minerals, with results showing the liquidus minimum temperature of about800°C and the solidus temperature of approximately 700°C. The final/minimum crystallization pressure are suggested to be between 3 and 5 Kbar. The presence of zoned minerals (plagioclase and allanite) associated with lithogeochemical data in bi-log diagrams for Rb vs. Ba and Rb vs. Sr suggest the role of fractional crystallization as the dominant process in the magmatic evolution of SRGP. U-Pb Geochronological and Sm-Nd isotope studies indicated, respectively, the crystallization age of biotite monzogranite as 557 ± 13 Ma, with TDM model age of 2.36 Ga, and εNd value of -20.10 to the crystallization age, allowing to infer paleoproterozoic crustal source for the magma.

Petrologia e geocronologia U-Pb do plúton granítico Serra da Rajada, porção central do domínio Rio Piranhas - Seridó, Província Borborema, NE do Brasil

The ediacaran plutonic activity related to the Brasilian/Pan-African orogeny is one of the most important geological features in the Borborema Province, represented along its extension by numerous batholiths, stocks, and dikes.The object of this study, the Serra Rajada Granitic Pluton (SRGP), located in the central portion of the Piranhas-Seridó River Domain is an example of this activity. This pluton has been the subject of cartographic, petrographic, geochronological and lithogeochemical studies and its rocks were characterized by two facies. First, the granitic facies were described as monzogranites consisting of K-feldspar, plagioclase (oligoclase - An23-24%), quartz and biotite (main mafic) and opaque minerals such as titanite, allanite, apatite, and zircon as accessories. Alteration minerals are chlorite, white mica and carbonate. Second, the dioritic facies consist of rocks formed by quartz diorite containing plagioclase (dominant mineral phase), quartz and K-feldspar. Biotite and amphibole are the dominant mafic minerals; and titanite, opaque minerals, allanite, zircon and apatite are the accessories. However, previous geological mapping work in the region also identified the presence of other lithostratigraphic units. These were described as gneisses and migmatites with undifferentiated amphibolite lenses related to the Caicó Complex (Paleoproterozoic) and metasedimentary rocks of the Seridó Group (Neoproterozoic) composed of paragneiss with calc-silicate lenses, muscovite quartzite and biotite schist (respectively, the Jucurutu formations, Equador and Seridó), the host rocks for the SRGP rocks. Leucomicrogranite and pegmatite dikes have also been identified, both related to the end of the Ediacaran magmatism and colluvial- eluvial and alluvial deposits related to Neogene and Quaternary, respectively. Lithogeochemical data on the SRGP granite facies, highlighted quite evolved rocks (SiO2 69% to 75%), rich in alkalis (Na2O+K2O ≥ 8.0%), depleted of MgO (≤ 0.45%), CaO (≤ 1.42%) and TiO2 (≤ 0.36%) and moderate levels of Fe2O3t (2.16 to 3.53%). They display transitional nature between metaluminous and peraluminous (predominance of the latter) with sub-alkaline/monzonitic (High K calcium-alkali) affinity. Harker diagrams show negative correlations for Fe2O3t, MgO, and CaO, indicating mafic and plagioclase fractionation. REE spectrum shows enrichment of LREE relative to heavy REE (LaN/YbN = 23.70 to 10.13), with negative anomaly in the Eu (Eu/Eu* = 0.70 to 0.23), suggesting fractionation or accumulation in the feldspars source (plagioclase). Data integration allows to correlate the SRGP rocks with those described as Calcium-Alkaline Suite of equigranular High K. The crystallization conditions of the SRGP rocks were determined from the integration of petrographic and lithogeochemical data. These data indicated intermediate to high conditions of ƒO2 (mineral paragenesis titanite + magnetite + quartz), parent magma saturated in H2O (early biotite crystallization), tardi-magmatic processes of fluids rich in ƒCO2, H2O and O2 causing part of the mineral assembly to change (plagioclase carbonation and saussuritization, biotite chloritization and opaques Sphenitization). Thermobarometrical conditions were estimated based on geochemical parameters (Zr and P2O5) and CIPW normative minerals, with results showing the liquidus minimum temperature of about800°C and the solidus temperature of approximately 700°C. The final/minimum crystallization pressure are suggested to be between 3 and 5 Kbar. The presence of zoned minerals (plagioclase and allanite) associated with lithogeochemical data in bi-log diagrams for Rb vs. Ba and Rb vs. Sr suggest the role of fractional crystallization as the dominant process in the magmatic evolution of SRGP. U-Pb Geochronological and Sm-Nd isotope studies indicated, respectively, the crystallization age of biotite monzogranite as 557 ± 13 Ma, with TDM model age of 2.36 Ga, and εNd value of -20.10 to the crystallization age, allowing to infer paleoproterozoic crustal source for the magma.

Role of ABL Family Kinases in Breast Cancer

The ABL family of non-receptor tyrosine kinases, ABL1 (also known as c-ABL) and ABL2 (also known as Arg), links diverse extracellular stimuli to signaling pathways that control cell growth, survival, adhesion, migration and invasion. ABL tyrosine kinases play an oncogenic role in human leukemias. However, the role of ABL kinases in solid tumors including breast cancer progression and metastasis is just emerging.

To evaluate whether ABL family kinases are involved in breast cancer development and metastasis, we first analyzed genomic data from large-scale screen of breast cancer patients. We found that ABL kinases are up-regulated in invasive breast cancer patients and high expression of ABL kinases correlates with poor prognosis and early metastasis. Using xenograft mouse models combined with genetic and pharmacological approaches, we demonstrated that ABL kinases are required for regulating breast cancer progression and metastasis to the bone. Using next generation sequencing and bioinformatics analysis, we uncovered a critical role for ABL kinases in promoting multiple oncogenic pathways including TAZ and STAT5 signaling networks and the epithelial to mesenchymal transition (EMT). These findings revealed a role for ABL kinases in regulating breast cancer tumorigenesis and bone metastasis and provide a rationale for targeting breast tumors with ABL-specific inhibitors.

Analysis of expression quantitative trait loci in D. melanogaster

Expression Quantitative Trait Loci (eQTL) analysis allows for the identification of genetic variation associated with variation in gene expression. It is often unclear however, which of the associated variants are causal, and by what mechanism. Integrating functional genomic data with eQTL data can provide insight into the impact of natural variation in the population, and the nature of the transcriptional machinery itself. In this thesis, I integrate functional genomic data with eQTL data derived from both 5’ CAGE and 3’ TagXseq expression assays, in developing embryos. I first use both datasets to analyse the transcription landscape in embryonic D., melanogaster, and then carry out an analysis of sequence motifs associated with transcription factor binding sites, promoters, and 3’ polyadenylation sites. Finally, I integrate functional genomic data, including these novel sequence motifs, to shed light on the mechanisms of gene expression variation in D.,melanogaster. I am able to demonstrate that some variants effecting gene regulation in Drosophila are found within haplotypes which buffer their effects.

UNDERSTANDING ESSAY RATING AS A SOCIALLY MEDIATED ACTIVITY: THE CASE OF A HIGH-STAKES ENGLISH TEST IN CHINA

Most essay rating research in language assessment has examined human raters’ essay rating as a cognitive process, thus overlooking or oversimplifying the interaction between raters and sociocultural contexts. Given that raters are social beings, their practices have social meanings and consequences. Hence it is important to situate essay rating within its sociocultural context for a more meaningful understanding. Drawing on Engeström’s (1987, 2001) cultural-historical activity theory (CHAT) framework with a sociocultural perspective, this study reconceptualized essay rating as a socially mediated activity with both cognitive (individual raters’ goal-directed decision-making actions) and social layers (raters’ collective object-oriented essay rating activity at related settings). In particular, this study explored raters’ essay rating at one provincial rating centre in China within the context of a high-stakes university entrance examination, the National Matriculation English Test (NMET). This study adopted a multiple-method multiple-perspective qualitative case study design. Think-aloud protocols, stimulated recalls, interviews, and documents served as the data sources. This investigation involved 25 participants at two settings (rating centre and high schools), including rating centre directors, team leaders, NMET essay raters who were high school teachers, and school principals and teaching colleagues of these essay raters. Data were analyzed using Strauss and Corbin’s (1990) open and axial coding techniques, and CHAT for data integration. The findings revealed the interaction between raters and the NMET sociocultural context. Such interaction can be understood through a surface structure (cognitive layer) and a deep structure (social layer) concerning how raters assessed NMET essays, where the surface structure reflected the “what” and the deep structure explained the “how” and “why” in raters’ decision-making. This study highlighted the roles of goals and rules in rater decision-making, rating tensions and raters’ solutions, and the relationship between essay rating and teaching. This study highlights the value of a sociocultural view to essay rating research, demonstrates CHAT as a sociocultural approach to investigate essay rating, and proposes a direction for future washback research on the effect of essay rating. This study also provides support for NMET rating practices that can potentially bring positive washback to English teaching in Chinese high schools.

Exploring molecular variation in Schistosoma japonicum in China

Schistosomiasis is a neglected tropical disease that affects more than 200 million people worldwide. The main disease-causing agents, Schistosoma japonicum, S. mansoni and S. haematobium, are blood flukes that have complex life cycles involving a snail intermediate host. In Asia, S. japonicum causes hepatointestinal disease (schistosomiasis japonica) and is challenging to control due to a broad distribution of its snail hosts and range of animal reservoir hosts. In China, extensive efforts have been underway to control this parasite, but genetic variability in S. japonicum populations could represent an obstacle to eliminating schistosomiasis japonica. Although a draft genome sequence is available for S. japonicum, there has been no previous study of molecular variation in this parasite on a genome-wide scale. In this study, we conducted the first deep genomic exploration of seven S. japonicum populations from mainland China, constructed phylogenies using mitochondrial and nuclear genomic data sets, and established considerable variation between some of the populations in genes inferred to be linked to key cellular processes and/or pathogen-host interactions. Based on the findings from this study, we propose that verifying intraspecific conservation in vaccine or drug target candidates is an important first step toward developing effective vaccines and chemotherapies against schistosomiasis.

Unraveling flp-11/flp-32 dichotomy in nematodes

FMRFamide-like peptide (FLP) signalling systems are core to nematode neuromuscular function. Novel drug discovery efforts associated with nematode FLP/FLP receptor biology are advanced through the accumulation of basic biological data that can reveal subtle complexities within the neuropeptidergic system. This study reports the characterisation of FMRFamide-like peptide encoding gene-11 (flp-11) and FMRFamide-like peptide encoding gene-32 (flp-32), two distinct flp genes which encode the analogous peptide, AMRN(A/S)LVRFamide, in multiple nematode species - the only known example of this phenomenon within the FLPergic system of nematodes. Using bioinformatics, in situ hybridisation, immunocytochemistry and behavioural assays we show that: (i) flp-11 and -32 are distinct flp genes expressed individually or in tandem across multiple nematode species, where they encode a highly similar peptide; (ii) flp-11 does not appear to be the most widely expressed flp in Caenorhabditis elegans; (iii) in species expressing both flp-11 and flp-32, flp-11 displays a conserved, restricted expression pattern across nematode clades and lifestyles; (iv) in species expressing both flp-11 and flp-32, flp-32 expression is more widespread and less conserved than flp-11; (v) in species expressing only flp-11, the flp-11 expression profile is more similar to the flp-32 profile observed in species expressing both; and (vi) FLP-11 peptides inhibit motor function in multiple nematode species. The biological significance and evolutionary origin of flp-11 and -32 peptide duplication remains unclear despite attempts to identify a common ancestor; this may become clearer as the availability of genomic data improves. This work provides insight into the complexity of the neuropeptidergic system in nematodes, and begins to examine how nematodes may compensate for structural neuronal simplicity. From a parasite control standpoint this work underscores the importance of basic biological data, and has wider implications for the utility of C. elegans as a model for parasite neurobiology.

Phylum-wide transcriptome analysis of oogenesis and early embryogenesis in selected nematode species

Oogenesis is a prerequisite for embryogenesis in Metazoa. During both biological processes important decisions must be made to form the embryo and hence ensure the next generation: (1) Maternal gene products (mRNAs, proteins and nutrients) must be supplied to the embryo. (2) Polarity must be established and axes must be specified. While incorporation of maternal gene products occurs during oogenesis, the time point of polarity establishment and axis specification varies among species, as it is accomplished either prior, during, or after fertilisation. But not only the time point when these events take place varies among species but also the underlying mechanisms by which they are triggered. For the nematode model Caenorhabditis elegans the underlying pathways and gene regulatory networks (GRNs) are well understood. It is known that there the sperm entry point initiates a primary polarity in the 1-celled egg and with it the establishment of the anteroposterior axis. However, studies of other nematodes demonstrated that polarity establishment can be independent of sperm entry (Goldstein et al., 1998; Lahl et al., 2006) and that cleavage patterns, symmetry formation and cell specification also differ from C. elegans. In contrast to the studied Chromadorea (more derived nematodes including C. elegans), embryos of some marine Enoplea (more basal representatives) even show no discernible early polarity and blastomeres can adopt variable cell fates (Voronov and Panchin 1998). The underlying pathways controlling the obviously variant embryonic processes in non-Caenorhabditis nematodes are essentially unknown. In this thesis I addressed this issue by performing a detailed unbiased comparative transcriptome analysis based on microarrays and RNA sequencing of selected developmental stages in a variety of nematodes from different phylogenetic branches with C. elegans as a reference system and a nematomorph as an outgroup representative. In addition, I made use of available genomic data to determine the presence or absence of genes for which no expression had been detected. In particular, I focussed on components of selected pathways or GRNs which are known to play essential roles during C. elegans development and/or other invertebrate or vertebrate model systems. Oogenesis must be regulated differently in non-Caenorhabditis nematodes, as crucial controlling components of Wnt and sex determination signaling are absent in these species. In this respect, I identified female-specific expression of potential polarity associated genes during gonad development and oogenesis in the Enoplean nematode Romanomermis culicivorax. I could show that known downstream components of the polarity complexes PAR-3/-6/PKC-3 and PAR-1/-2 are absent in non-Caenorhabditis species. Even PAR-2 as part of the polarity complex does not exist in these nematodes. Instead, transcriptomes of nematodes (including C. elegans), show expression of other polarity-associated complexes such as the Lgl (Lethal giant larvae) complex. This result could pose an alternative route for nematodes and nematomorphs to initiate polarity during early embryogenesis. I could show that crucial pathways of axis specification, such as Wnt and BMP are very different in C. elegans compared to other nematodes. In the former, Wnt signaling, for instance, is mediated by four paralogous beta-catenins, while other Chromadorea have fewer and Enoplea only one beta-catenin. The transcriptomes of R. culicivorax and the nematomorph show that regulators of BMP (e.g. Chordin), are specifically expressed during early embryogenesis only in Enoplea and the close outgroup of nematomorphs. In conclusion, my results demonstrate that the molecular machinery controlling oogenesis and embryogenesis in nematodes is unexpectedly variable and C. elegans cannot be taken as a general model for nematode development. Under this perspective, Enoplean nematodes show more similarities with outgroups than with C. elegans. It appears that certain pathway components were lost or gained during evolution and others adopted new functions. Based on my findings I can conjecture, which pathway components may be ancestral and which were newly acquired in the course of nematode evolution.

Towards a Workflow Management Approach for Health Monitoring of Bridges

Part 14: Interoperability and Integration

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Background: Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results: We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

Harmonised framework for ecological risk assessment of sediments from ports and estuarine zones of North and South Atlantic

This paper presents a harmonised framework of sediment quality assessment and dredging material characterisation for estuaries and port zones of North and South Atlantic. This framework, based on the weight-of-evidence approach, provides a structure and a process for conducting sediment/dredging material assessment that leads to a decision. The main structure consists of step 1 (examination of available data); step 2 (chemical characterisation and toxicity assessment); decision 1 (any chemical level higher than reference values? are sediments toxic?); step 3 (assessment of benthic community structure); step 4 (integration of the results); decision 2 (are sediments toxic or benthic community impaired?); step 5 (construction of the decision matrix) and decision 3 (is there environmental risk?). The sequence of assessments may be interrupted when the information obtained is judged to be sufficient for a correct characterisation of the risk posed by the sediments/dredging material. This framework brought novel features compared to other sediment/dredging material risk assessment frameworks: data integration through multivariate analysis allows the identification of which samples are toxic and/or related to impaired benthic communities; it also discriminates the chemicals responsible for negative biological effects; and the framework dispenses the use of a reference area. We demonstrated the successful application of this framework in different port and estuarine zones of the North (Gulf of Cadiz) and South Atlantic (Santos and Paranagua Estuarine Systems).

Integrated sediment quality assessment in Paranagua Estuarine System, Southern Brazil

Sediment quality from Paranagua Estuarine System (PES), a highly important port and ecological zone, was evaluated by assessing three lines of evidence: (1) sediment physical-chemical characteristics; (2) sediment toxicity (elutriates, sediment-water interface, and whole sediment); and (3) benthic community structure. Results revealed a gradient of increasing degradation of sediments (i.e. higher concentrations of trace metals, higher toxicity, and impoverishment of benthic community structure) towards inner PES. Data integration by principal component analysis (PCA) showed positive correlation between some contaminants (mainly As, Cr, Ni, and Pb) and toxicity in samples collected from stations located in upper estuary and one station placed away from contamination sources. Benthic community structure seems to be affected by both pollution and natural fine characteristics of the sediments, which reinforces the importance of a weight-of-evidence approach to evaluate sediments of PES. (C) 2008 Elsevier B.V. All rights reserved.

A ética e a utilidade da contabilidade

Dissertação de Mestrado, Contabilidade, Faculdade de Economia, Universidade do Algarve, 2016

UNDERSTANDING ESSAY RATING AS A SOCIALLY MEDIATED ACTIVITY: THE CASE OF A HIGH-STAKES ENGLISH TEST IN CHINA

Thesis (Ph.D, Education) -- Queen's University, 2016-09-22 22:05:24.246