Preparing DARIAH

In this paper, a preparatory project for an integrated European research infrastructure in the humanities is presented. This project, Preparing for the construction of the Digital Research Infrastructure for the Arts and Humanities - or Preparing DARIAH for short, is part of the ESFRI e-infrastructures programme and supports the emergence of a new collaborative framework in which researchers are able to maximise the impact of their work on the international stage and aims at providing the foundations for the timely construction of the infrastructure requisite for the arts, humanities and cultural heritage communities in the digital age. DARIAH uses an interdisciplinary approach and involves tackling a number of interrelated issues such as strategic, organisational, financial, technical and conceptual in order to facilitate long-term access to and use of all European humanities and cultural heritage information for the purposes of enhancing and expanding research, thereby increasing our knowledge and understanding of our histories, heritage, languages and cultures. The DARIAH network will act as a place where the incubation of new ideas and ways of working can be facilitated and developed, and then transitioned into established organisations thus ensuring long-term sustainability and stability and the integration of these methods and techniques into everyday research practice. DARIAH will support research practitioners at all stages in the research process, and at differing levels of sophistication, from beginners through to those employing advanced techniques and methodologies

Inherited Cardiomyopathies: From Genotype to Phenotype

The heart undergoes extensive morphological, metabolic, and energetic remodeling in response to inherited, or familial, hypertrophic cardiomyopathies (FHC). Myocyte contractile perturbations downstream of Ca2+, the so-called sarcomere-controlled mechanisms, may represent the earliest indicators of this remodeling. We can now state that the dynamics of cardiac contraction and relaxation during the progression of FHC are governed by downstream mechanisms, particularly the kinetics and energetics of actin and myosin interaction to drive the trajectory of pathological cardiac remodeling. This notion is unambiguously supported by elegant studies above linking inheritable FHC-causing mutations to cardiomyopathies, known to disturb contractile function and alter the energy landscape of the heart. Although studies examining the biophysical properties of cardiac myocytes with FHC-causing mutations have yielded a cellular and molecular understanding of myofilament function, this knowledge has had limited translational success. This is driven by a critical failure in elucidating an integrated and sequential link among the changing energy landscape, myofilament function, and initiated signaling pathways in response to FHC. Similarly, there continues to be a major gap in understanding the cellular and molecular mechanisms contributing to sex differences in FHC development and progression. The primary reason for this gap is a lack of a “unifying” or “central” hypothesis that integrates signaling cascades, energetics, sex and FHC

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

International audienceIncreasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system

Immediate post-operative effects of tracheotomy on respiratory function during mechanical ventilation

INTRODUCTION: Tracheotomy is widely performed in the intensive care unit after long-term oral intubation. The present study investigates the immediate influence of tracheotomy on respiratory mechanics and blood gases during mechanical ventilation. METHODS: Tracheotomy was performed in 32 orally intubated patients for 10.5 ± 4.66 days (all results are means ± standard deviations). Airway pressure, flow and arterial blood gases were recorded immediately before tracheotomy and half an hour afterwards. Respiratory system elastance (E(rs)), resistance (R(rs)) and end-expiratory pressure (EEP) were evaluated by multiple linear regression. Respiratory system reactance (X(rs)), impedance (Z(rs)) and phase angle (φ(rs)) were calculated from E(rs )and R(rs). Comparisons of the mechanical parameters, blood gases and pH were performed with the aid of the Wilcoxon signed-rank test (P = 0.05). RESULTS: E(rs )increased (7 ± 11.3%, P = 0.001), whereas R(rs )(-16 ± 18.4%, P = 0.0003), X(rs )(-6 ± 11.6%, P = 0.006) and φ (rs )(-14.3 ± 16.8%, P = <0.001) decreased immediately after tracheotomy. EEP, Z(rs), blood gases and pH did not change significantly. CONCLUSION: Lower R(rs )but also higher E(rs )were noted immediately after tracheotomy. The net effect is a non-significant change in the overall R(rs )(impedance) and the effectiveness of respiratory function. The extra dose of anaesthetics (beyond that used for sedation at the beginning of the procedure) or a higher FiO(2 )(fraction of inspired oxygen) during tracheotomy or aspiration could be related to the immediate elastance increase

XTraQue: traceability for product line systems

Product line engineering has been increasingly used to support the development and deployment of software systems that share a common set of features and are developed based on the reuse of core assets. The large number and heterogeneity of documents generated during the development of product line systems may cause difficulties to identify common and variable aspects among applications, and to reuse core assets that are available under the product line. In this paper, we present a traceability approach for product line systems. Traceability has been recognised as an important task in in software system development. Traceability relations can improve the quality of the product being developed and reduce development time and cost. We present a rule-based approach to support automatic generation of traceability relations between feature-based object-oriented documents. The traceability rules used in our work are classified into two groups namely (a) direct rules, which support the creation of traceability relations that do not depend on the existence of other relations, and (b) indirect rules, which require the existence of previously generated relations. The documents are represented in XML and the rules are represented in an extension of XQuery. A prototype tool called XTraQue has been implemented. This tool, together with a mobile phone product line case study, has been used to demonstrate and evaluate our work in various experiments. The results of these experiments are encouraging and comparable with other approaches that support automatic generation of traceability relations

Immediate post-operative effects of tracheotomy on respiratory function during mechanical ventilation

INTRODUCTION: Tracheotomy is widely performed in the intensive care unit after long-term oral intubation. The present study investigates the immediate influence of tracheotomy on respiratory mechanics and blood gases during mechanical ventilation. METHODS: Tracheotomy was performed in 32 orally intubated patients for 10.5 +/- 4.66 days (all results are means +/- standard deviations). Airway pressure, flow and arterial blood gases were recorded immediately before tracheotomy and half an hour afterwards. Respiratory system elastance (Ers), resistance (Rrs) and end-expiratory pressure (EEP) were evaluated by multiple linear regression. Respiratory system reactance (Xrs), impedance (Zrs) and phase angle (phirs) were calculated from Ers and Rrs. Comparisons of the mechanical parameters, blood gases and pH were performed with the aid of the Wilcoxon signed-rank test (P = 0.05). RESULTS: Ers increased (7 +/- 11.3%, P = 0.001), whereas Rrs (-16 +/- 18.4%, P = 0.0003), Xrs (-6 +/- 11.6%, P = 0.006) and phi rs (-14.3 +/- 16.8%, P = <0.001) decreased immediately after tracheotomy. EEP, Zrs, blood gases and pH did not change significantly. CONCLUSION: Lower Rrs but also higher Ers were noted immediately after tracheotomy. The net effect is a non-significant change in the overall Rrs (impedance) and the effectiveness of respiratory function. The extra dose of anaesthetics (beyond that used for sedation at the beginning of the procedure) or a higher FiO2 (fraction of inspired oxygen) during tracheotomy or aspiration could be related to the immediate elastance increase.Crit Car

As time goes by

A rather simple and non-technical exposition of our new approach to {\em Time, Quantum Physics, Black-Hole dynamics}, and {\em Cosmology}, based on non-critical string theory, is provided. A new fundamental principle, the {\em Procrustean Principle}, that catches the essence of our approach is postulated: the low-energy world is {\em unavoidably} an ``open" system due to the spontaneous truncation of the {\em delocalized, topological} string modes in continuous interaction with the low-lying-{\em localized} string modes. The origin of space-time, the expansion of the Universe, the entropy increase and accompanied irreversibility of time, as well as the collapse of the wavefunction are all very neatly tied together. Possible observable consequences include: quantum relaxation with time of the Universal, fundamental constants, like the velocity of light $c$ and the Planck constant $\hbar$ decreasing towards their asymptotic values, and the cosmological constant $\Lambda_C$ diminishing towards zero; possible violation of {\em CPT} invariance in the $K^0-\bar K^0$ system, possible apparent non-conservation of angular momentum, and possible loss of quantum coherence in SQUID-type experiments.Comment: CERN-TH.7260/94, 84 pages Latex (no figures

Assessment of splenic function

Hyposplenic patients are at risk of overwhelming post-splenectomy infection (OPSI), which carries mortality of up to 70%. Therefore, preventive measures are warranted. However, patients with diminished splenic function are difficult to identify. In this review we discuss immunological, haematological and scintigraphic parameters that can be used to measure splenic function. IgM memory B cells are a potential parameter for assessing splenic function; however, more studies are necessary for its validation. Detection of Howell–Jolly bodies does not reflect splenic function accurately, whereas determining the percentage of pitted erythrocytes is a well-evaluated method and seems a good first-line investigation for assessing splenic function. When assessing spleen function, 99mTc-labelled, heat-altered, autologous erythrocyte scintigraphy with multimodality single photon emission computed tomography (SPECT)-CT technology is the best approach, as all facets of splenic function are evaluated. In conclusion, although scintigraphic methods are most reliable, they are not suitable for screening large populations. We therefore recommend using the percentage of pitted erythrocytes, albeit suboptimal, as a first-line investigation and subsequently confirming abnormal readings by means of scintigraphy. More studies evaluating the value of potentially new markers are needed