Functional Genomic Screen Identifies Klebsiella pneumoniae Factors Implicated in Blocking Nuclear Factor κB (NF-κB) Signaling

Klebsiella pneumoniae is etiologic agent of community-acquired and nosocomial pneumonia. It has been shown that K. pneumoniae infections are characterized by reduced early inflammatory response. Recently our group have shown that K. pneumoniae dampens the activation of inflammatory responses by antagonizing the activation of the NF-κB canonical pathway. Our results revealed that K. pneumoniae capsule (CPS) was necessary but not sufficient to attenuate inflammation. To identify additional Klebsiella factors required to dampen inflammation, we standardized and applied a high-throughput gain-on-function screen to examine a Klebsiella transposon mutant library. We identified 114 mutants that triggered the activation of NF-κB. Two gene ontology categories accounted for half of the loci identified in the screening, that of metabolism and transport (32% of the mutants), and of enveloperelated genes (17%). Characterization of the mutants revealed that the lack of the enterobactin siderophore was linked to a reduced CPS expression which in turn underlined the NF- κB activation induced by the mutant. The lipopolysaccharide (LPS) O-polysaccharide and the pullulanase (PulA) type 2 secretion system (T2SS) are required for full effectiveness of immune evasion. Importantly, these factors do not play a redundant role. The fact that LPS Opolysaccharide and T2SS mutants-induced responses were dependent on TLR2-TLR4- MyD88 activation suggested that LPS Opolysaccharide and PulA perturbed TLRdependent recognition of K. pneumoniae. Finally, we demonstrate that LPS O-polysaccharide and pulA mutants are attenuated in the pneumonia mouse model. We propose that LPS Opolysaccharide and PulA T2SS could be new targets for designing new antimicrobials. Increasing TLR-governed defence responses might provide also selective alternatives for the management of K. pneumoniae pneumonia.

Genome-wide gene pathway analysis of psychotic illness symptom dimensions based on a new schizophrenia-specific model of the OPCRIT

Empirically derived phenotypic measurements have the potential to enhance gene-finding efforts in schizophrenia. Previous research based on factor analyses of symptoms has typically included schizoaffective cases. Deriving factor loadings from analysis of only narrowly defined schizophrenia cases could yield more sensitive factor scores for gene pathway and gene ontology analyses. Using an Irish family sample, this study 1) factor analyzed clinician-rated Operational Criteria Checklist items in cases with schizophrenia only, 2) scored the full sample based on these factor loadings, and 3) implemented genome-wide association, gene-based, and gene-pathway analysis of these SCZ-based symptom factors (final N= 507). Three factors emerged from the analysis of the schizophrenia cases: a manic, a depressive, and a positive symptom factor. In gene-based analyses of these factors, multiple genes had q<. 0.01. Of particular interest are findings for PTPRG and WBP1L, both of which were previously implicated by the Psychiatric Genomics Consortium study of SCZ; results from this study suggest that variants in these genes might also act as modifiers of SCZ symptoms. Gene pathway analyses of the first factor indicated over-representation of glutamatergic transmission, GABA-A receptor, and cyclic GMP pathways. Results suggest that these pathways may have differential influence on affective symptom presentation in schizophrenia.

Integrative analysis of chemo-transcriptomic profiles for drug-feature specific gene expression signatures

One of the major challenges in systems biology is to understand the complex responses of a biological system to external perturbations or internal signalling depending on its biological conditions. Genome-wide transcriptomic profiling of cellular systems under various chemical perturbations allows the manifestation of certain features of the chemicals through their transcriptomic expression profiles. The insights obtained may help to establish the connections between human diseases, associated genes and therapeutic drugs. The main objective of this study was to systematically analyse cellular gene expression data under various drug treatments to elucidate drug-feature specific transcriptomic signatures. We first extracted drug-related information (drug features) from the collected textual description of DrugBank entries using text-mining techniques. A novel statistical method employing orthogonal least square learning was proposed to obtain drug-feature-specific signatures by integrating gene expression with DrugBank data. To obtain robust signatures from noisy input datasets, a stringent ensemble approach was applied with the combination of three techniques: resampling, leave-one-out cross validation, and aggregation. The validation experiments showed that the proposed method has the capacity of extracting biologically meaningful drug-feature-specific gene expression signatures. It was also shown that most of signature genes are connected with common hub genes by regulatory network analysis. The common hub genes were further shown to be related to general drug metabolism by Gene Ontology analysis. Each set of genes has relatively few interactions with other sets, indicating the modular nature of each signature and its drug-feature-specificity. Based on Gene Ontology analysis, we also found that each set of drug feature (DF)-specific genes were indeed enriched in biological processes related to the drug feature. The results of these experiments demonstrated the pot- ntial of the method for predicting certain features of new drugs using their transcriptomic profiles, providing a useful methodological framework and a valuable resource for drug development and characterization.

Natural Killer Cell-like signature observed in locally advanced rectal cancer after neoadjuvant chemoradiotherapy in a tumour regression grade dependent manner

Background: Around 10-15% of patients with locally advanced rectal cancer (LARC) undergo a pathologically complete response (TRG4) to neoadjuvant chemoradiotherapy; the rest of patients exhibit a spectrum of tumour regression (TRG1-3). Understanding therapy-related genomic alterations may help us to identify underlying biology or novel targets associated with response that could increase the efficacy of therapy in patients that do not benefit from the current standard of care.
Methods: 48 FFPE rectal cancer biopsies and matched resections were analysed using the WG-DASL HumanHT-12_v4 Beadchip array on the illumina iScan. Bioinformatic analysis was conducted in Partek genomics suite and R studio. Limma and glmnet packages were used to identify genes differentially expressed between tumour regression grades. Validation of microarray results will be carried out using IHC, RNAscope and RT-PCR.
Results: Immune response genes were observed from supervised analysis of the biopsies which may have predictive value. Differential gene expression from the resections as well as pre and post therapy analysis revealed induction of genes in a tumour regression dependent manner. Pathway mapping and Gene Ontology analysis of these genes suggested antigen processing and natural killer mediated cytotoxicity respectively. The natural killer-like gene signature was switched off in non-responders and on in the responders. IHC has confirmed the presence of Natural killer cells through CD56+ staining.
Conclusion: Identification of NK cell genes and CD56+ cells in patients responding to neoadjuvant chemoradiotherapy warrants further investigation into their association with tumour regression grade in LARC. NK cells are known to lyse malignant cells and determining whether their presence is a cause or consequence of response is crucial. Interrogation of the cytokines upregulated in our NK-like signature will help guide future in vitro models.

Contextual Intrusion Alerts for SCADA Networks

The complexity of modern SCADA networks and their associated cyber-attacks requires an expressive but flexible manner for representing both domain knowledge and collected intrusion alerts with the ability to integrate them for enhanced analytical capabilities and better understanding of attacks. This paper proposes an ontology-based approach for contextualized intrusion alerts in SCADA networks. In this approach, three security ontologies were developed to represent and store information on intrusion alerts, Modbus communications, and Modbus attack descriptions. This information is correlated into enriched intrusion alerts using simple ontology logic rules written in Semantic Query-Enhanced Web Rules (SQWRL). The contextualized alerts give analysts the means to better understand evolving attacks and to uncover the semantic relationships between sequences of individual attack events. The proposed system is illustrated by two use case scenarios.

Label-free based quantitative proteomics analysis of primary neonatal porcine Leydig cells exposed to the persistent contaminant 3-methylsulfonyl-DDE

Evidence that persistent environmental pollutants may target the male reproductive system is increasing. The male reproductive system is regulated by secretion of testosterone by testicular Leydig cells, and perturbation of Leydig cell function may have ultimate consequences. 3-Methylsulfonyl-DDE (3-MeSO₂-DDE) is a potent adrenal toxicants formed from the persistent insecticide DDT. Although studies have revealed the endocrine disruptive effect of 3-MeSO₂-DDE, the underlying mechanisms at cellular level in steroidogenic Leydig cells remains to be established. The current study addresses the effect of 3-MeSO₂-DDE on viability, hormone production and proteome response of primary neonatal porcine Leydig cells. The AlamarBlue™ assay was used to evaluate cell viability. Solid phase radioimmunoassay was used to measure concentration of hormones produced by both unstimulated and Luteinizing hormone (LH)-stimulated Leydig cells following 48h exposure. Protein samples from Leydig cells exposed to a non-cytotoxic concentration of 3-MeSO₂-DDE (10μM) were subjected to nano-LC-MS/MS and analyzed on a Q Exactive mass spectrometer and quantified using label-free quantitative algorithm. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) were carried out for functional annotation and identification of protein interaction networks. 3-MeSO₂-DDE regulated Leydig cell steroidogenesis differentially depending on cell culture condition. Whereas its effect on testosterone secretion at basal condition was stimulatory, the effect on LH-stimulated cells was inhibitory. From triplicate experiments, a total of 6804 proteins were identified in which the abundance of 86 proteins in unstimulated Leydig cells and 145 proteins in LH-stimulated Leydig cells was found to be significantly regulated in response to 3-MeSO₂-DDE exposure. These proteins not only are the first reported in relation to 3-MeSO₂-DDE exposure, but also display small number of proteins shared between culture conditions, suggesting the action of 3-MeSO₂-DDE on several targeted pathways, including mitochondrial dysfunction, oxidative phosphorylation, EIF2-signaling, and glutathione-mediated detoxification. Further identification and characterization of these proteins and pathways may build our understanding to the molecular basis of 3-MeSO₂-DDE induced endocrine disruption in Leydig cells.

On the Ontological Quality and Logical Quality of Conceptual-Modeling Grammars: The Need for a Dual Perspective

A core activity in information systems development involves building a conceptual model of the domain that an information system is intended to support. Such models are created using a conceptual-modeling (CM) grammar. Just as high-quality conceptual models facilitate high-quality systems development, high-quality CM grammars facilitate high-quality conceptual modeling. This paper provides a new perspective on ways to improve the quality of the semantics of CM grammars. For many years, the leading approach to this topic has relied on ontological theory. We show, however, that the ontological approach captures only half the story. It needs to be coupled with a logical approach. We explain how the ontological quality and logical quality of CM grammars interrelate. Furthermore, we outline three contributions that a logical approach can make to evaluating the quality of CM grammars: a means of seeing some familiar conceptual-modeling problems in simpler ways; the illumination of new problems; and the ability to prove the benefit of modifying existing CM grammars in particular ways. We demonstrate these benefits in the context of the Entity-Relationship grammar. More generally, our paper opens up a new area of research with many opportunities for future research and practice.

Model of access to natural language sources in electronic government

For the actual existence of e-government it is necessary and crucial to provide public information and documentation, making its access simple to citizens. A portion, not necessarily small, of these documents is in an unstructured form and in natural language, and consequently outside of which the current search systems are generally able to cope and effectively handle. Thus, in thesis, it is possible to improve access to these contents using systems that process natural language and create structured information, particularly if supported in semantics. In order to put this thesis to test, this work was developed in three major phases: (1) design of a conceptual model integrating the creation of structured information and making it available to various actors, in line with the vision of e-government 2.0; (2) definition and development of a prototype instantiating the key modules of this conceptual model, including ontology based information extraction supported by examples of relevant information, knowledge management and access based on natural language; (3) assessment of the usability and acceptability of querying information as made possible by the prototype - and in consequence of the conceptual model - by users in a realistic scenario, that included comparison with existing forms of access. In addition to this evaluation, at another level more related to technology assessment and not to the model, evaluations were made on the performance of the subsystem responsible for information extraction. The evaluation results show that the proposed model was perceived as more effective and useful than the alternatives. Associated with the performance of the prototype to extract information from documents, comparable to the state of the art, results demonstrate the feasibility and advantages, with current technology, of using natural language processing and integration of semantic information to improve access to unstructured contents in natural language. The conceptual model and the prototype demonstrator intend to contribute to the future existence of more sophisticated search systems that are also more suitable for e-government. To have transparency in governance, active citizenship, greater agility in the interaction with the public administration, among others, it is necessary that citizens and businesses have quick and easy access to official information, even if it was originally created in natural language.

Charting Cartographies of Resistance: Line of Flight in Women Artists’ Narratives

In this paper I chart lines of flight in women artist’s narratives. In focusing on the complex interrelations between the social milieus of education and art, what I suggest is that they should be analysed as an assemblage where power relations and forces of desire are constantly at play in creating conditions of possibility for women to resist, imagine themselves becoming other and for new possibilities in their lives to be actualised. As a novel approach to social ontology the theory of assemblages offers an analytics of social complexity that accounts for open configurations, continuous connections and unstable hierarchies, structures and axes of difference. In reconsidering resistance as immanent in dispositifs of power and assemblages of desire, what I finally argue is that women artists’ narratives contribute to the constitution of minor knowledges and create archives of radical futurity.

Scholarly chronographics: can a timeline be useful in historiography?

Our paper is concerned with the visualisation of historical events and artefacts in the context of time. It arises from a project bringing together expertise in visualisation, historiography and software engineering. The work is the result of an extended enquiry over several years which has included investigation of the prior history of such chronographics and their grounding in the temporal ontology of the Enlightenment. Timelines - visual, spatial presentations of chronology - are generally regarded as being too simple, perhaps too childish, to be worthy of academic attention, yet such chronographics should be capable of supporting sophisticated thinking about history and historiography, especially if they take full advantage of the capabilities of digital technologies. They should enable even professional academic historians to 'make sense' of history in new ways, allowing them insights they would not otherwise have achieved. In our paper we highlight key findings from the history of such representations, principally from the eighteenth and nineteenth centuries, and show how, in a project to develop new digital chronographics for collections of cultural objects and events, we have explored new implementations of the important ideas we have extracted about timewise presentation and interaction. This includes the representation of uncertainty, of relations between events, and the epistemology of time as a 'space' for history. We present developed examples, in particular a chronographic presentation of a large database of works by a single author, a composer, and discuss the extent to which our ambitions for chronographics have been realised in practice. Keywords: timeline, chronographics

Image morphology: from perception to rendering

Complete image ontology can be obtained by formalising a top-down meta-language wich must address all possibilities, from global message and composition to objects and local surface properties.

Normdaten im Semantic Web - Konzept für eine Ontologie der Personennamendatei (PND)

Das Ziel dieser Arbeit ist es, ein Konzept für eine Darstellung der Personennamendatei(PND) in den Sprachen Resource Description Framework (RDF), Resource DescriptionFramework Schema Language (RDFS) und Web Ontology Language (OWL) zu entwickeln. Der Prämisse des Semantic Web folgend, Daten sowohl in menschenverständlicher als auch in maschinell verarbeitbarer Form darzustellen und abzulegen, wird eine Struktur für Personendaten geschaffen. Dabei wird von der bestehenden Daten- und Struktursituation im Pica-Format ausgegangen. Die Erweiterbarkeit und Anpassbarkeit des Modells im Hinblick auf zukünftige, im Moment gegebenenfalls noch nicht absehbare Anwendungen und Strukurveränderungen, muss aber darüber hinaus gewährleistet sein. Die Modellierung orientiert sich an bestehenden Standards wie Dublin Core, Friend Of A Friend (FOAF), Functional Requirements for Bibliographic Records (FRBR), Functional Requirements for Authority Data (FRAD) und Resource Description and Access (RDA).

Europa : paisagem e pensamento : um excurso sobre Teixeira de Pascoaes, Friedrich Hölderlin, José Marinho e Martin Heidegger

Tese de doutoramento, Filosofia (Filosofia em Portugal), Universidade de Lisboa, Faculdade de Letras, 2014

The sound of a breaking string: critical environmental law and ontological vulnerability

This is a thought-provoking contribution on the space of ontological vulnerability as the awareness of being existentially exposed. This space, conceptualised as a space of ‘the middle’ (as opposed, emphatically, to ‘the centre’) offers an opportunity to think away from the sterile debate on eco/anthropocentricity and from such limiting hierarchies as animal/human, human/environmental, natural/artificial. This new, vulnerable position of the middle allows the reconfiguration of ecological processes, and more specifically the position of environmental law in relation to them. Environmental law now finds itself amidst a new, moving, ‘open ecology’ of social, biological and ecological processes. This is a new, radical conceptualisation of what the author has called ‘critical environmental law,’ based upon an epistemology of observation and an ontology of being part of this open ecology. Environmental law, in this light, is simultaneously reformulated as an invitation to disciplinary and ontological openness and yet a call to remain immanent within existing legal structures. This finds expression in four critical environmental positions that set the stage for the further elaboration of a critical environmental law.