Composite interests' exploration thanks to on-the-fly linked data spreading activation

International audienceExploratory search systems are built specifically to help the user in his cognitive consuming search tasks like learning or topic investigation. Some of these systems are built on the top of linked data and use semantics to provide cognitively-optimized search experiences. Thanks to their richness and to their connected nature linked data datasets can serve as a ground for advanced exploratory search. We propose to address the case of mixed interests' exploration in the form of composite queries (several unitary interests combined) e.g. exploring results and make discoveries related to both The Beatles and Ken Loach. The main contribution of this paper is the proposition of a novel method that processes linked-data for exploratory search purpose. It makes use of a semantic spreading activation algorithm coupled with a sampling technique. Its particularity is to not require any results preprocessing. Consequently this method offers a high level of flexibility for querying and allows, among others, the expression of composite interests' queries on remote linked data sources. This paper also details the analysis of the algorithm behavior over DBpedia and describes an implementation: the Discovery Hub application. It is an exploratory search engine that notably supports composite queries. Finally the results of a user evaluation are presented

The role of roX RNA in dosage compensation during Drosophila melanogaster embryogenesis

Dosage compensation (DC) in male Drosophila melanogaster flies is done through hypertranscription of the X chromosome. This involves the dosage compensation complex (DCC), a ribonucleoprotein complex of five protein subunits, Male-specific-lethal 1 (MSL1), MSL2, MSL3, Males-absent-on-the-first (MOF) and Maleless (MLE), and long noncoding RNA, RNA-on-the-X (roX), encoded by either roX1 or roX2 gene. DC is interlinked with the process of sex determination. A hypothesis suggests that upon hybridization of roX1 and roX2 RNAs, a miRNA is produced that is implicated in a feedback mechanism of sex determination. Different approaches were used to reproduce hybridization and validate putative miRNA; however, such observations could not be seen. As differential function of roX RNAs have been proposed, characterization of roX1 and roX2 RNAs in fractionated extracts were done by rt-qPCR. Long isoforms of roX, roX1-RE and roX2-RB, tended to be polyadenylated and enriched in the cytoplasm suggesting differential post-transcriptional processing and possible shuttling mechanism. A preliminary experiment of direct-RNA nanopore sequencing detected major parts of roX RNAs important for DC. With improved protocol of RNA preservation and library preparation, it may prove to be a potent tool to further characterize the lncRNAs and profile its isoforms. Additionally, a detailed study on the establishment of dosage compensation during early embryogenesis was done. MSL2 binding to DNA was evident 4 hours after egg laying when least compensation of X-linked genes is observed. Concurrent detection of MOF on the X chromosome signified assembly of DCC in early development. This complex was active in its function to acetylate H4K16. Nevertheless, accumulation of H4K16ac on the X chromosome proceeded in a time- and space-dependent manner, coinciding with the progression of dosage compensation. Specifically, genes defined as constitutive were closer to DCC binding sites, more acetylated, and first compensated. Meanwhile, genes characterized as developmental were farther from DCC binding sites, lowly acetylated, and slowly compensated.Die Dosiskompensation bei männlichen Drosophila melanogaster Fliegen erfolgt durch Übertranskription des X-Chromosoms. Dies wird durch den Dosiskompensationskomplex (DCC) ermöglicht. Dieser Ribonukleoproteinkomplex besteht aus fünf Proteinuntereinheiten, Male-specific-lethal 1 (MSL1), MSL2, MSL3, Males-absent-on-the-first (MOF) und Maleless (MLE), und einer langen nichtkodierenden RNA, RNA-on-the-X (roX), die entweder durch das roX1- oder das roX2-Gen kodiert wird. Die Dosiskompensation ist mit dem Prozess der Geschlechtsdetermination verbunden. Die Hypothese, dass bei Hybridisierung von roX1- und roX2-RNAs eine miRNA erzeugt wird, die an einem Rückkopplungsmechanismus der Geschlechtsdetermination beteiligt ist, wurde in dieser Arbeit getestet. Leider konnten vorangegangene, hypothesenstützende Beobachtungen nicht reproduziert werden. Für die roX-RNAs wurde eine redundante Rolle in der Dosiskompensation sowie zusätzliche Funktionen außerhalb dieses Prozesses vorgeschlagen. Diese Dissertation umfasst die Charakterisierung von roX1- und roX2-RNAs in fraktionierten Embryoextrakten durch RT-qPCR. Die Ergebnisse deuten auf eine differenzielle posttranskriptionale Verarbeitung der RNAs hin. Lange Isoformen von roX, roX1-RE und roX2-RB sind polyadenyliert. Darüber hinaus sind sie im Zytoplasma angereichert, was auf einen möglichen Austausch mit dem Nucleus hindeutet. Definierende Abschnitte der für DC wichtigen roX-RNAs wurden in einem explorativen Experiment durch direct-RNA nanopore Sequenzieren nachgewiesen. Mit einem verbesserten Protokoll zur Extraktion der RNA, sowie deren Konservation und Bibliotheksvorbereitung könnte es sich als wirksames Instrument zur weiteren Charakterisierung der langen nichtkodierenden RNA und auch in Bezug auf die Selektion der RNA-Isoformen erweisen. Zudem wurde im Rahmen dieser Arbeit eine detaillierte Studie zur Etablierung der Dosiskompensation während der frühen Embryogenese durchgeführt. Die Bindung von MSL2 an DNA war bereits 4 Stunden nach der Eiablage messbar. Zu diesem Zeitpinkt ist nur eine geringe Dosiskompensation von X-Chromosom gekoppelten Genen vorhanden. Gleichzeitig ließ sich ebenfalls MOF bereits in derselben Region auf dem X-Chromosom nachweisen. Dies zeigte die Bildung des DCC in der frühen Embryogenese. Der Komplex war bereits aktiv und acetylierte H4K16. Trotzdem verlief die Akkumulation von H4K16ac auf dem X-Chromosom nachfolgend zeit- und positionsabhängig, übereinstimmend mit dem Fortschreiten der Dosiskompensation. So wurden Gene, die als konstitutiv definiert wurden und näher an DCC-Bindungsstellen lagen, stärker acetyliert und zuerst kompensiert. Als Entwicklungsgene definierte Gene hingegen, lagen weiter von DCC-Bindungsstellen entfernt, wurden nur schwach acetyliert und langsam kompensiert

Local and chromosome-wide regulation of gene expression in Drosophila melanogaster

Within animal species, phenotypic variation is striking both between sexes and among individuals of the same sex. Much of this variation can be attributed to diverse gene expression patterns that evolved due to selection pressures specific to the external physical environment or to the internal chromosomal environment. Mechanisms that regulate expression can act on individual genes (local regulation) or on whole chromosomes (chromosome-wide). This dissertation seeks to examine the evolution of local and chromosome-wide expression regulation using the fruit fly Drosophila melanogaster as a model organism. When sex chromosomes determine sex, usually their ploidy differs between the sexes. In the XY system, present in both mammals and Drosophila, males are hemizygous for the X chromosome. This disparity between sexes exposes the X chromosome to unique selective forces that cause it to evolve different gene content and regulatory mechanisms from the autosomes. Notably, D. melanogaster tissue-specific genes, with the exception of ovary-specific genes, are underrepresented on the X chromosome. Furthermore, in the male soma gene expression is equalized between the single X chromosome and the autosomes through a mechanism known as dosage compensation. In contrast, in the male germline the expression of testis-specific genes residing on the X chromosome is suppressed through a mechanism known as X suppression. The main aim of this thesis is to investigate these aspects of gene regulation on the X chromosome in D. melanogaster. Chapter 1 and part of Chapter 2 focus on the phenomenon of X suppression. In Chapter 1, using testis- and other tissue-specific constructs, I survey autosomal and X-linked reporter gene expression in whole flies and carcasses with the tissue of interest removed. First, by reanalyzing the expression of the testis-specific reporter genes for which X suppression was initially described, I confirm the occurrence of X suppression in testis. Second, I show that X suppression is not a general property of tissue-specific genes, and that the X chromosome is neither a restrictive nor an unrestrictive environment for the expression of genes expressed specifically in the accessory gland (analogous to the mammalian prostate gland), ovary, or Malpighian tubule (analogous to the mammalian kidney). Moreover, I show that X-linkage has no impact on the tissue-specificity of gene expression. These findings suggest that the observed genomic distribution of tissue-specific genes is not the consequence of a chromosome-wide regulatory mechanism. This is the first study to functionally investigate the effect of X-linkage on the expression of tissue-specific genes, other than those specific to the testis. Chapter 2 investigates further the extent of X suppression. Using a ubiquitously-expressed reporter gene with an exogenous promoter in order to exclude any sex- or tissue-specific effects, I survey the expression of X-linked and autosomal reporter genes in testes and male somatic tissues. As expected, X suppression is absent in somatic tissues, which indicates that X suppression exclusively affects testis-expressed genes. Surprisingly, I find that the exogenous reporter gene, which has a basal level of expression in testis, shows no sign of X suppression in the male germline. This demonstrates that the expression level of a gene, together with its sex- and tissue-specificity, can be a major factor that influences the extent of X suppression. Thus, the present work makes a valuable contribution to the characterization of this newly-discovered regulatory mechanism. In Chapter 2, I also perform a pilot study regarding the effect the dosage compensation, which is mediated via the dosage compensation complex (DCC), on the chromosomal distribution of sex-biased genes in various tissues. I use X-linked insertions of the above mentioned ubiquitously-expressed reporter gene and correlate its expression in testis and male somatic tissues (heads and carcasses) with the proximity to different DCC binding sites. I find that the expression level of the X-linked reporter genes is not correlated with their distance to a binding site of DCC components, with the exception of maleless protein (MLE), for which there was a positive correlation between expression level and MLE distance in somatic tissues. Based on my findings, I provide recommendations that will serve as a foundation for a future study of this topic. Chapter 3 examines a candidate gene for local regulatory adaptation. The Metallothionein A (MtnA) gene exhibits expression variation in brains of natural populations of D. melanogaster. By collecting flies and analyzing the deletion frequency in an additional population (Cyprus), I provide further evidence that this expression variation is associated with a 49-bp deletion in the MtnA 3’ untranslated region (UTR), which is present at intermediate frequency in derived populations of the species. These results, supported with population genetic analysis, suggest that the deletion allele has been a target of local adaptation. By performing hydrogen peroxide tolerance assays, I show that the deletion is associated with increased oxidative stress tolerance, which suggests that the deletion (and increased MtnA expression) is an adaption to oxidative stress

Spinoff 1997: 25 Years of Reporting Down-to-Earth Benefits

The 25th annual issue of NASA's report on technology transfer and research and development (R&D) from its ten field centers is presented. The publication is divided into three sections. Section 1 comprises a summary of R&D over the last 25 years. Section 2 presents details of the mechanisms NASA uses to transfer technology to private industry as well as the assistance NASA provides in commercialization efforts. Section 3, which is the focal point of the publication, features success stories of manufacturers and entrepreneurs in developing commercial products and services that improve the economy and life in general

Explaining Data Patterns using Knowledge from the Web of Data

Knowledge Discovery (KD) is a long-tradition field aiming at developing methodologies to detect hidden patterns and regularities in large datasets, using techniques from a wide range of domains, such as statistics, machine learning, pattern recognition or data visualisation. In most real world contexts, the interpretation and explanation of the discovered patterns is left to human experts, whose work is to use their background knowledge to analyse, refine and make the patterns understandable for the intended purpose. Explaining patterns is therefore an intensive and time-consuming process, where parts of the knowledge can remain unrevealed, especially when the experts lack some of the required background knowledge. In this thesis, we investigate the hypothesis that such interpretation process can be facilitated by introducing background knowledge from the Web of (Linked) Data. In the last decade, many areas started publishing and sharing their domain-specific knowledge in the form of structured data, with the objective of encouraging information sharing, reuse and discovery. With a constantly increasing amount of shared and connected knowledge, we thus assume that the process of explaining patterns can become easier, faster, and more automated. To demonstrate this, we developed Dedalo, a framework that automatically provides explanations to patterns of data using the background knowledge extracted from the Web of Data. We studied the elements required for a piece of information to be considered an explanation, identified the best strategies to automatically find the right piece of information in the Web of Data, and designed a process able to produce explanations to a given pattern using the background knowledge autonomously collected from the Web of Data. The final evaluation of Dedalo involved users within an empirical study based on a real-world scenario. We demonstrated that the explanation process is complex when not being familiar with the domain of usage, but also that this can be considerably simplified when using the Web of Data as a source of background knowledge

Impact of geogenic degassing on C-isotopic composition of dissolved carbon in karst systems of Greece

The Earth C-cycle is complex, where endogenic and exogenic sources are interconnected, operating in a multiple spatial and temporal scale (Lee et al., 2019). Non-volcanic CO2 degassing from active tectonic structures is one of the less defined components of this cycle (Frondini et al., 2019). Carbon mass-balance (Chiodini et al., 2000) is a useful tool to quantify the geogenic carbon output from regional karst hydrosystems. This approach has been demonstrated for central Italy and may be valid also for Greece, due to the similar geodynamic settings. Deep degassing in Greece has been ascertained mainly at hydrothermal and volcanic areas, but the impact of geogenic CO2 released by active tectonic areas has not yet been quantified. The main aim of this research is to investigate the possible deep degassing through the big karst aquifers of Greece. Since 2016, 156 karst springs were sampled along most of the Greek territory. To discriminate the sources of carbon, the analysis of the isotopic composition of carbon was carried out. δ13CTDIC values vary from -16.61 to -0.91‰ and can be subdivided into two groups characterized by (a) low δ13CTDIC, and (b) intermediate to high δ13CTDIC with a threshold value of -6.55‰. The composition of the first group can be related to the mixing of organic-derived CO2 and the dissolution of marine carbonates. Springs of the second group, mostly located close to Quaternary volcanic areas, are linked to possible carbon input from deep sources

EVOLUTION OF THE SUBCONTINENTAL LITHOSPHERE DURING MESOZOIC TETHYAN RIFTING: CONSTRAINTS FROM THE EXTERNAL LIGURIAN MANTLE SECTION (NORTHERN APENNINE, ITALY)

Our study is focussed on mantle bodies from the External Ligurian ophiolites, within the Monte Gavi and Monte Sant'Agostino areas. Here, two distinct pyroxenite-bearing mantle sections were recognized, mainly based on their plagioclase-facies evolution. The Monte Gavi mantle section is nearly undeformed and records reactive melt infiltration under plagioclase-facies conditions. This process involved both peridotites (clinopyroxene-poor lherzolites) and enclosed spinel pyroxenite layers, and occurred at 0.7–0.8 GPa. In the Monte Gavi peridotites and pyroxenites, the spinel-facies clinopyroxene was replaced by Ca-rich plagioclase and new orthopyroxene, typically associated with secondary clinopyroxene. The reactive melt migration caused increase of TiO2 contents in relict clinopyroxene and spinel, with the latter also recording a Cr2O3 increase. In the Monte Gavi peridotites and pyroxenites, geothermometers based on slowly diffusing elements (REE and Y) record high temperature conditions (1200-1250 °C) related to the melt infiltration event, followed by subsolidus cooling until ca. 900°C. The Monte Sant'Agostino mantle section is characterized by widespread ductile shearing with no evidence of melt infiltration. The deformation recorded by the Monte Sant'Agostino peridotites (clinopyroxene-rich lherzolites) occurred at 750–800 °C and 0.3–0.6 GPa, leading to protomylonitic to ultramylonitic textures with extreme grain size reduction (10–50 μm). Compared to the peridotites, the enclosed pyroxenite layers gave higher temperature-pressure estimates for the plagioclase-facies re-equilibration (870–930 °C and 0.8–0.9 GPa). We propose that the earlier plagioclase crystallization in the pyroxenites enhanced strain localization and formation of mylonite shear zones in the entire mantle section. We subdivide the subcontinental mantle section from the External Ligurian ophiolites into three distinct domains, developed in response to the rifting evolution that ultimately formed a Middle Jurassic ocean-continent transition: (1) a spinel tectonite domain, characterized by subsolidus static formation of plagioclase, i.e. the Suvero mantle section (Hidas et al., 2020), (2) a plagioclase mylonite domain experiencing melt-absent deformation and (3) a nearly undeformed domain that underwent reactive melt infiltration under plagioclase-facies conditions, exemplified by the the Monte Sant'Agostino and the Monte Gavi mantle sections, respectively. We relate mantle domains (1) and (2) to a rifting-driven uplift in the late Triassic accommodated by large-scale shear zones consisting of anhydrous plagioclase mylonites. Hidas K., Borghini G., Tommasi A., Zanetti A. & Rampone E. 2021. Interplay between melt infiltration and deformation in the deep lithospheric mantle (External Liguride ophiolite, North Italy). Lithos 380-381, 105855