TViz : a taxonomy visualization tool

The Semantic Web is an emerging science in the world of computer information processing. RACER, a robust semantic web engine, represents the core of a semantic web system. The engine offers various inference services that return information about a given ontology, for instance, to compute its associated taxonomy of concept names. The taxonomy is generated in a form called the "TBox subsumption hierarchy" although it is not necessarily a true hierarchy. Since humans are more comfortable reading a graphical structure than a textual one, RACER needs a visualization tool in order to visualize taxonomies after processing them. Also, a graph delivers statistical information in addition to its easy interaction capabilities. In this thesis, we present TViz, a tool capable of visualizing large numbers of nodes representing the TBox subsumption hierarchy, using the Cone Tree layout. TViz, customized for taxonomy visualizations, gets its input from a text file that is created after streaming the information from RACER. TViz consists of three components: (1) a parser that parses the information obtained from the RACER server using a specific grammar, (2) an engine that simplifies and changes the non-hierarchical structure into a hierarchical tree, and (3) a graphics engine that graphs the hierarchical tree using the Cone Tree layout. The graphics engine handles the graphics, the user interface, and tools and is written using OpenGL and GLUI multiplatform libraries. TViz implements useful tools for an easy exploration of a dense environment such as the Compass, the Local View and the Information Window and is implemented using standard C/C++ multiplatform librarie

A Knowledge-based Approach for Creating Detailed Landscape Representations by Fusing GIS Data Collections with Associated Uncertainty

Geographic Information Systems (GIS) data for a region is of different types and collected from different sources, such as aerial digitized color imagery, elevation data consisting of terrain height at different points in that region, and feature data consisting of geometric information and properties about entities above/below the ground in that region. Merging GIS data and understanding the real world information present explicitly or implicitly in that data is a challenging task. This is often done manually by domain experts because of their superior capability to efficiently recognize patterns, combine, reason, and relate information. When a detailed digital representation of the region is to be created, domain experts are required to make best-guess decisions about each object. For example, a human would create representations of entities by collectively looking at the data layers, noting even elements that are not visible, like a covered overpass or underwater tunnel of a certain width and length. Such detailed representations are needed for use by processes like visualization or 3D modeling in applications used by military, simulation, earth sciences and gaming communities. Many of these applications are increasingly using digitally synthesized visuals and require detailed digital 3D representations to be generated quickly after acquiring the necessary initial data. Our main thesis, and a significant research contribution of this work, is that this task of creating detailed representations can be automated to a very large extent using a methodology which first fuses all Geographic Information System (GIS) data sources available into knowledge base (KB) assertions (instances) representing real world objects using a subprocess called GIS2KB. Then using reasoning, implicit information is inferred to define detailed 3D entity representations using a geometry definition engine called KB2Scene. Semantic Web is used as the semantic inferencing system and is extended with a data extraction framework. This framework enables the extraction of implicit property information using data and image analysis techniques. The data extraction framework supports extraction of spatial relationship values and attribution of uncertainties to inferred details. Uncertainty is recorded per property and used under Zadeh fuzzy semantics to compute a resulting uncertainty for inferred assertional axioms. This is achieved by another major contribution of our research, a unique extension of the KB ABox Realization service using KB explanation services. Previous semantics based research in this domain has concentrated more on improving represented details through the addition of artifacts like lights, signage, crosswalks, etc. Previous attempts regarding uncertainty in assertions use a modified reasoner expressivity and calculus. Our work differs in that separating formal knowledge from data processing allows fusion of different heterogeneous data sources which share the same context. Imprecision is modeled through uncertainty on assertions without defining a new expressivity as long as KB explanation services are available for the used expressivity. We also believe that in our use case, this simplifies uncertainty calculations. The uncertainties are then available for user-decision at output. We show that the process of creating 3D visuals from GIS data sources can be more automated, modular, verifiable, and the knowledge base instances available for other applications to use as part of a common knowledge base. We define our method’s components, discuss advantages and limitations, and show sample results for the transportation domain

Appropriate use of red blood cell transfusion in emergency departments: A study in five emergency departments

BACKGROUND: Transfusion of blood components continues to be an important therapeutic resource into the 21st century. Between 5 and 58% of transfusions carried out are estimated to be unnecessary. According to several studies, at least 20% of packed red blood cell transfusions (RBCT) are administered in hospital emergency departments (ED), but few data are available about the appropriateness of RBCT in this setting. This multicentre, cross-sectional observational study aims to assess the appropriateness of RBCT indications and transfused volumes in patients who attend ED. MATERIALS AND METHODS: The study cohort is made up of consecutive consenting adult patients (≥18 years old) who received RBCT in ED over a 3-month period and for whom relevant clinical data were collected and analysed. RESULTS: Data from 908 RBCT episodes (2±1 units per transfused patient) were analysed. RBCT was considered appropriate in 21.4% (n=195), with significant differences according to RBCT indication (p<0.001), hospital level (p<0.001) and prescribing physician (p=0.002). Pre-transfusion haemoglobin level (Hb) negatively correlated with RBCT appropriateness (r=-0.616; p<0.01). Only 72.4% of appropriate RBCT had a post-transfusion Hb assessment (n=516). Of these, 45% were considered to be over-transfused (n=232), with significant differences according to RBCT indication (p=0.012) and prescribing physician (p=0.047). Overall, 584/1,433 (41%) of evaluable RBC units were unnecessarily transfused. DISCUSSION: The appropriateness of RBCT in ED is similar to other hospital departments, but the rate of over-transfusion was high. These data support the need for a reassessment after transfusion of each RBC unit before further units are prescribed. In view of these results, we recommend that physicians should be made more aware of the need to prescribe RBCT appropriately in order to reduce over-transfusionThis project has received funding from the Spanish Ministry of Health, Social Policy and Equality through the SAS/2377/2010 call for granting aid for the promotion of independent clinical research (Department of Pharmacy and Health Products), file n. EC10-21

A system dynamics model to predict the human monocyte response to endotoxins

System dynamics is a powerful tool that allows modeling of complex and highly networked systems such as those found in the human immune system. We have developed a model that reproduces how the exposure of human monocytes to lipopolysaccharides (LPSs) induces an inflammatory state characterized by high production of tumor necrosis factor alpha (TNFα), which is rapidly modulated to enter into a tolerant state, known as endotoxin tolerance (ET). The model contains two subsystems with a total of six states, seven flows, two auxiliary variables, and 14 parameters that interact through six differential and nine algebraic equations. The parameters were estimated and optimized to obtain a model that fits the experimental data obtained from human monocytes treated with various LPS doses. In contrast to publications on other animal models, stimulation of human monocytes with super-low-dose LPSs did not alter the response to a second LPSs challenge, neither inducing ET, nor enhancing the inflammatory response. Moreover, the model confirms the low production of TNFα and increased levels of C-C motif ligand 2 when monocytes exhibit a tolerant state similar to that of patients with sepsis. At present, the model can help us better understand the ET response and might offer new insights on sepsis diagnostics and prognosis by examining the monocyte response to endotoxins in patients with sepsisThis work was supported by grants from the “Instituto de Salud Carlos III” (ISCiii), “Fondo de Investigación Sanitaria” (FIS), and Fondos FEDER (PI14/01234, PIE15/00065) to EL-C. EA work contract is supported by the Torres Quevedo program from “Ministerio de Economía y Competitividad” (SPTQ1300X006175XV0). VT work contract is supported by the “Ministerio de Economía y Competitividad” (PTA2013-8265-I

Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis

Background: Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is not well understood but is known to involve epigenetic and transcriptional dysregulation. Methods: Bead arrays were used to compare global DNA methylation changes in patients with sepsis, noninfectious systemic inflammatory response syndrome, and healthy controls. Bioinformatic analyses were performed to dissect functional reprogramming and signaling pathways related to the acquisition of these specific DNA methylation alterations. Finally, in vitro experiments using human monocytes were performed to test the induction of similar DNA methylation reprogramming. Results: Here, we focused on DNA methylation changes associated with sepsis, given their potential role in stabilizing altered phenotypes. Tolerized monocytes from patients with sepsis display changes in their DNA methylomes with respect to those from healthy controls, affecting critical monocyte-related genes. DNA methylation profiles correlate with IL-10 and IL-6 levels, significantly increased in monocytes in sepsis, as well as with the Sequential Organ Failure Assessment score; the observed changes associate with TFs and pathways downstream to toll-like receptors and inflammatory cytokines. In fact, in vitro stimulation of toll-like receptors in monocytes results in similar gains and losses of methylation together with the acquisition of tolerance. Conclusion: We have identified a DNA methylation signature associated with sepsis that is downstream to the response of monocytes to inflammatory signals associated with the acquisition of a tolerized phenotype and organic dysfunction

Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis

Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is not well understood but is known to involve epigenetic and transcriptional dysregulation. Bead arrays were used to compare global DNA methylation changes in patients with sepsis, non-infectious systemic inflammatory response syndrome, and healthy controls. Bioinformatic analyses were performed to dissect functional reprogramming and signaling pathways related to the acquisition of these specific DNA methylation alterations. Finally, in vitro experiments using human monocytes were performed to test the induction of similar DNA methylation reprogramming. Here, we focused on DNA methylation changes associated with sepsis, given their potential role in stabilizing altered phenotypes. Tolerized monocytes from patients with sepsis display changes in their DNA methylomes with respect to those from healthy controls, affecting critical monocyte-related genes. DNA methylation profiles correlate with IL-10 and IL-6 levels, significantly increased in monocytes in sepsis, as well as with the Sequential Organ Failure Assessment score; the observed changes associate with TFs and pathways downstream to toll-like receptors and inflammatory cytokines. In fact, in vitro stimulation of toll-like receptors in monocytes results in similar gains and losses of methylation together with the acquisition of tolerance. We have identified a DNA methylation signature associated with sepsis that is downstream to the response of monocytes to inflammatory signals associated with the acquisition of a tolerized phenotype and organic dysfunction

The HIV-1 Integrase α4-Helix Involved in LTR-DNA Recognition Is also a Highly Antigenic Peptide Element

Monoclonal antibodies (MAbas) constitute remarkable tools to analyze the relationship between the structure and the function of a protein. By immunizing a mouse with a 29mer peptide (K159) formed by residues 147 to 175 of the HIV-1 integrase (IN), we obtained a monoclonal antibody (MAba4) recognizing an epitope lying in the N-terminal portion of K159 (residues 147–166 of IN). The boundaries of the epitope were determined in ELISA assays using peptide truncation and amino acid substitutions. The epitope in K159 or as a free peptide (pep-a4) was mostly a random coil in solution, while in the CCD (catalytic core domain) crystal, the homologous segment displayed an amphipathic helix structure (α4-helix) at the protein surface. Despite this conformational difference, a strong antigenic crossreactivity was observed between pep-a4 and the protein segment, as well as K156, a stabilized analogue of pep-a4 constrained into helix by seven helicogenic mutations, most of them involving hydrophobic residues. We concluded that the epitope is freely accessible to the antibody inside the protein and that its recognition by the antibody is not influenced by the conformation of its backbone and the chemistry of amino acids submitted to helicogenic mutations. In contrast, the AA →Glu mutations of the hydrophilic residues Gln148, Lys156 and Lys159, known for their interactions with LTRs (long terminal repeats) and inhibitors (

Oxygen Saturation on Admission Is a Predictive Biomarker for PD-L1 Expression on Circulating Monocytes and Impaired Immune Response in Patients With Sepsis

Sepsis is a pathology in which patients suffer from a proinflammatory response and a dysregulated immune response, including T cell exhaustion. A number of therapeutic strategies to treat human sepsis, which are different from antimicrobial and fluid resuscitation treatments, have failed in clinical trials, and solid biomarkers for sepsis are still lacking. Herein, we classified 85 patients with sepsis into two groups according to their blood oxygen saturation (SaO2): group I (SaO2 ≤ 92%, n = 42) and group II (SaO2 &gt; 92%, n = 43). Blood samples were taken before any treatment, and the immune response after ex vivo LPS challenge was analyzed, as well as basal expression of PD-L1 on monocytes and levels of sPD-L1 in sera. The patients were followed up for 1 month. Taking into account reinfection and exitus frequency, a significantly poorer evolution was observed in patients from group I. The analysis of HLA-DR expression on monocytes, T cell proliferation and cytokine profile after ex vivo LPS stimulation confirmed an impaired immune response in group I. In addition, these patients showed both, high levels of PD-L1 on monocytes and sPD-L1 in serum, resulting in a down-regulation of the adaptive response. A blocking assay using an anti-PD-1 antibody reverted the impaired response. Our data indicated that SaO2 levels on admission have emerged as a potential signature for immune status, including PD-L1 expression. An anti-PD-1 therapy could restore the T cell response in hypoxemic sepsis patients with SaO2 ≤ 92% and high PD-L1 levels