bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Evaluation of the Role of Gene Expression in the Prediction and Diagnosis of Ventilator-associated Pneumonia
Authors: Textoris Julien , Loriod Béatrice , Benayoun Laurent , Gourraud Pierre-Antoine , Puthier Denis , Albanèse Jacques , Mantz Jean , Martin Claude , Nguyen Catherine , Leone Marc 
Published: June 2011

Background
The SepsiChip project explored transcriptional modulation associated with ventilator-associated pneumonia (VAP) in patients admitted to the intensive care unit for trauma. Genome-wide expression analysis may help to identify potential diagnostic markers for diseases. The current study examined the changes in blood transcriptome during VAP.

Methods
The authors prospectively included 165 trauma patients, and 41 developed VAP. Whole blood samples were collected at admission and at VAP. To predict VAP, the admission samples were compared by microarray in patients who did or did not develop VAP. To identify diagnosis markers, paired samples of 35 patients who developed VAP were analyzed. Using NanoString (Seattle, WA), the results were confirmed in the patients who developed VAP. Trauma patients who did not develop VAP served as controls to eliminate a time effect.

Results
The injury severity scores of the patients who did or did not develop VAP were 36 and 29, respectively. No predictive biomarker was identified. For patients who developed VAP, a transcriptional signature was identified between the two sampling times. However, this signature was a generalized pattern related to trauma, independent of the infectious process. Genes involved in the proinflammatory response were down-regulated in the patients who developed VAP, but this difference was not statistically significant.

Conclusions
In contrast to clinical assessment, transcriptional analysis of whole blood samples cannot predict or diagnose VAP in trauma patients. Differentiating infection from inflammation seems challenging.
No Clinical or Electrophysiologic Evidence of Nerve Injury after Intraneural Injection during Sciatic Popliteal Block
Authors: Sala-Blanch Xavier , López Ana M. , Pomés Jaume , Valls-Sole Josep , García Ana I. , Hadzic Admir 
Published: June 2011

Background
Intraneural injection during nerve-stimulator-guided sciatic block at the popliteal fossa may be a common occurrence. Although intraneural injections have not resulted in clinically detectable neurologic injury in small studies in human subjects, intraneural injections result in postinjection inflammation in animal models. This study used clinical, imaging, and electrophysiologic measures to evaluate the occurrence of any subclinical neurologic injury in patients with intraneural injection during sciatic popliteal block.

Methods
Twenty patients undergoing popliteal block were enrolled; 17 patients completed the study protocol. After tibial nerve response was achieved by nerve stimulation (0.3-0.5 mA; 2 Hz; 0.1 ms), 20 ml mixture of mepivacaine (1.25%) and radiopaque contrast (2 ml) were injected. Location and spread of the injectant were assessed by ultrasound measurements of the sciatic nerve area before and after injection, and by computed tomography. In addition to clinical neurologic evaluations, serial electrophysiologic studies (nerve conduction and late response studies using predefined criteria) were performed at baseline and at 1 week and 3 weeks after the block for signs of subclinical neurologic dysfunction.

Results
Sixteen injections (94%, 95% CI: 71-100%) met criteria for an intraneural injection. Postinjection nerve area on ultrasound increased by 45% (95% CI: 29-58%), P < 0.001. Computed tomography demonstrated fascicular separation in 70% (95% CI: 44-90%), air within the nerve in 29% (95% CI: 10-56%), contrast along bifurcations in 65% (95% CI: 38-86%), and concentric contrast layers in 100% (95% CI: 84-100%). Neither clinical nor electrophysiologic studies detected neurologic dysfunction indicating injury to the nerve.

Conclusions
Nerve-stimulator-guided sciatic block at the popliteal fossa often results in intraneural injection that may not lead to clinical or electrophysiologic nerve injury.
Exploring Collections of Tagged Text for Literary Scholarship
Authors: Correll M. , Witmore M. , Gleicher M. 
Published: June 2011

AbstractModern literary scholars must combine access to vast collections of text with the traditional close analysis of their field. In this paper, we discuss the design and development of tools to support this work. Based on analysis of the needs of literary scholars, we constructed a suite of visualization tools for the analysis of large collections of tagged text (i.e. text where one or more words have been annotated as belonging to a specific category). These tools unite the aspects of the scholars’ work: large scale overview tools help to identify corpus‐wide statistical patterns while fine scale analysis tools assist in finding specific details that support these observations. We designed visual tools that support and integrate these levels of analysis. The result is the first tool suite that can support the multilevel text analysis performed by scholars, combining standard visual elements with novel methods for selecting individual texts and identifying represenative passages in them.
Semantic‐Preserving Word Clouds by Seam Carving
Authors: Wu Yingcai , Provan Thomas , Wei Furu , Liu Shixia , Ma Kwan‐Liu 
Published: June 2011

AbstractWord clouds are proliferating on the Internet and have received much attention in visual analytics. Although word clouds can help users understand the major content of a document collection quickly, their ability to visually compare documents is limited. This paper introduces a new method to create semantic‐preserving word clouds by leveraging tailored seam carving, a well‐established content‐aware image resizing operator. The method can optimize a word cloud layout by removing a left‐to‐right or top‐to‐bottom seam iteratively and gracefully from the layout. Each seam is a connected path of low energy regions determined by a Gaussian‐based energy function. With seam carving, we can pack the word cloud compactly and effectively, while preserving its overall semantic structure. Furthermore, we design a set of interactive visualization techniques for the created word clouds to facilitate visual text analysis and comparison. Case studies are conducted to demonstrate the effectiveness and usefulness of our techniques.
A User Study of Visualization Effectiveness Using EEG and Cognitive Load
Authors: Anderson E. W. , Potter K. C. , Matzen L. E. , Shepherd J. F. , Preston G. A. , Silva C. T. 
Published: June 2011

AbstractEffectively evaluating visualization techniques is a difficult task often assessed through feedback from user studies and expert evaluations. This work presents an alternative approach to visualization evaluation in which brain activity is passively recorded using electroencephalography (EEG). These measurements are used to compare different visualization techniques in terms of the burden they place on a viewer's cognitive resources. In this paper, EEG signals and response times are recorded while users interpret different representations of data distributions. This information is processed to provide insight into the cognitive load imposed on the viewer. This paper describes the design of the user study performed, the extraction of cognitive load measures from EEG data, and how those measures are used to quantitatively evaluate the effectiveness of visualizations.
Dynamic Insets for Context‐Aware Graph Navigation
Authors: Ghani S. , Riche N. Henry , Elmqvist N. 
Published: June 2011

AbstractMaintaining both overview and detail while navigating in graphs, such as road networks, airline route maps, or social networks, is difficult, especially when targets of interest are located far apart. We present a navigation technique called Dynamic Insets that provides context awareness for graph navigation. Dynamic insets utilize the topological structure of the network to draw a visual inset for off‐screen nodes that shows a portion of the surrounding area for links leaving the edge of the screen. We implement dynamic insets for general graph navigation as well as geographical maps. We also present results from a set of user studies that show that our technique is more efficient than most of the existing techniques for graph navigation in different networks.
Assisted Descriptor Selection Based on Visual Comparative Data Analysis
Authors: Bremm Sebastian , von Landesberger Tatiana , Bernard Jürgen , Schreck Tobias 
Published: June 2011

AbstractExploration and selection of data descriptors representing objects using a set of features are important components in many data analysis tasks. Usually, for a given dataset, an optimal data description does not exist, as the suitable data representation is strongly use case dependent. Many solutions for selecting a suitable data description have been proposed. In most instances, they require data labels and often are black box approaches. Non‐expert users have difficulties to comprehend the coherency of input, parameters, and output of these algorithms. Alternative approaches, interactive systems for visual feature selection, overburden the user with an overwhelming set of options and data views. Therefore, it is essential to offer the users a guidance in this analytical process. In this paper, we present a novel system for data description selection, which facilitates the user's access to the data analysis process. As finding of suitable data description consists of several steps, we support the user with guidance. Our system combines automatic data analysis with interactive visualizations. By this, the system provides a recommendation for suitable data descriptor selections. It supports the comparison of data descriptors with differing dimensionality for unlabeled data. We propose specialized scores and interactive views for descriptor comparison. The visualization techniques are scatterplot‐based and grid‐based. For the latter case, we apply Self‐Organizing Maps as adaptive grids which are well suited for large multi‐dimensional data sets. As an example, we demonstrate the usability of our system on a real‐world biochemical application.
Structural Decomposition Trees
Authors: Engel D. , Rosenbaum R. , Hamann B. , Hagen H. 
Published: June 2011

AbstractResearchers and analysts in modern industrial and academic environments are faced with a daunting amount of multi‐dimensional data. While there has been significant development in the areas of data mining and knowledge discovery, there is still the need for improved visualizations and generic solutions. The state‐of‐the‐art in visual analytics and exploratory data visualization is to incorporate more profound analysis methods while focusing on fast interactive abilities. The common trend in these scenarios is to either visualize an abstraction of the data set or to better utilize screen‐space.This paper presents a novel technique that combines clustering, dimension reduction and multi‐dimensional data representation to form a multivariate data visualization that incorporates both detail and overview. This amalgamation counters the individual drawbacks of common projection and multi‐dimensional data visualization techniques, namely ambiguity and clutter. A specific clustering criterion is used to decompose a multi‐dimensional data set into a hierarchical tree structure. This decomposition is embedded in a novel Dimensional Anchor visualization through the use of a weighted linear dimension reduction technique. The resulting Structural Decomposition Tree (SDT) provides not only an insight of the data set's inherent structure, but also conveys detailed coordinate value information. Further, fast and intuitive interaction techniques are explored in order to guide the user in highlighting, brushing, and filtering of the data.
Probabilistic Marching Cubes
Authors: Pöthkow Kai , Weber Britta , Hege Hans‐Christian 
Published: June 2011

AbstractIn this paper we revisit the computation and visualization of equivalents to isocontours in uncertain scalar fields. We model uncertainty by discrete random fields and, in contrast to previous methods, also take arbitrary spatial correlations into account. Starting with joint distributions of the random variables associated to the sample locations, we compute level crossing probabilities for cells of the sample grid. This corresponds to computing the probabilities that the well‐known symmetry‐reduced marching cubes cases occur in random field realizations. For Gaussian random fields, only marginal density functions that correspond to the vertices of the considered cell need to be integrated. We compute the integrals for each cell in the sample grid using a Monte Carlo method. The probabilistic ansatz does not suffer from degenerate cases that usually require case distinctions and solutions of ill‐conditioned problems. Applications in 2D and 3D, both to synthetic and real data from ensemble simulations in climate research, illustrate the influence of spatial correlations on the spatial distribution of uncertain isocontours.
Visualizing the Positional and Geometrical Variability of Isosurfaces in Uncertain Scalar Fields
Authors: Pfaffelmoser Tobias , Reitinger Matthias , Westermann Rüdiger 
Published: June 2011

AbstractWe present a novel approach for visualizing the positional and geometrical variability of isosurfaces in uncertain 3D scalar fields. Our approach extends recent work by Pöthkow and Hege [PH10] in that it accounts for correlations in the data to determine more reliable isosurface crossing probabilities. We introduce an incremental update‐scheme that allows integrating the probability computation into front‐to‐back volume ray‐casting efficiently. Our method accounts for homogeneous and anisotropic correlations, and it determines for each sampling interval along a ray the probability of crossing an isosurface for the first time. To visualize the positional and geometrical uncertainty even under viewing directions parallel to the surface normal, we propose a new color mapping scheme based on the approximate spatial deviation of possible surface points from the mean surface. The additional use of saturation enables to distinguish between areas of high and low statistical dependence. Experimental results confirm the effectiveness of our approach for the visualization of uncertainty related to position and shape of convex and concave isosurface structures.
WaveMap: Interactively Discovering Features From Protein Flexibility Matrices Using Wavelet‐based Visual Analytics
Authors: Barlowe Scott , Liu Yujie , Yang Jing , Livesay Dennis R. , Jacobs Donald J. , Mottonen James , Verma Deeptak 
Published: June 2011

AbstractThe knowledge gained from biology datasets can streamline and speed‐up pharmaceutical development. However, computational models generate so much information regarding protein behavior that large‐scale analysis by traditional methods is almost impossible. The volume of data produced makes the transition from data to knowledge difficult and hinders biomedical advances. In this work, we present a novel visual analytics approach named WaveMap for exploring data generated by a protein flexibility model. WaveMap integrates wavelet analysis, visualizations, and interactions to facilitate the browsing, feature identification, and comparison of protein attributes represented by two‐dimensional plots. We have implemented a fully working prototype of WaveMap and illustrate its usefulness through expert evaluation and an example scenario.
Pathway Preserving Representation of Metabolic Networks
Authors: Lambert A. , Dubois J. , Bourqui R. 
Published: June 2011

AbstractImprovements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques. An efficient representation of such a network should preserve the topological information of metabolic pathways while respecting biological drawing conventions. These constraints complicate the automatic generation of such visualization as it raises graph drawing issues. In this paper we propose a method to lay out the entire metabolic network while preserving the pathway information as much as possible. That method is flexible as it enables the user to define whether or not node duplication should be performed, to preserve or not the network topology. Our technique combines partitioning, node placement and edge bundling to provide a pseudo‐orthogonal visualization of the metabolic network. To ease pathway information retrieval, we also provide complementary interaction tools that emphasize relevant pathways in the entire metabolic context.
Visualizing the Evolution of Community Structures in Dynamic Social Networks
Authors: Reda Khairi , Tantipathananandh Chayant , Johnson Andrew , Leigh Jason , Berger‐Wolf Tanya 
Published: June 2011

AbstractSocial network analysis is the study of patterns of interaction between social entities. The field is attracting increasing attention from diverse disciplines including sociology, epidemiology, and behavioral ecology. An important sociological phenomenon that draws the attention of analysts is the emergence of communities, which tend to form, evolve, and dissolve gradually over a period of time. Understanding this evolution is crucial to sociologists and domain scientists, and often leads to a better appreciation of the social system under study. Therefore, it is imperative that social network visualization tools support this task. While graph‐based representations are well suited for investigating structural properties of networks at a single point in time, they appear to be significantly less useful when used to analyze gradual structural changes over a period of time. In this paper, we present an interactive visualization methodology for dynamic social networks. Our technique focuses on revealing the community structure implied by the evolving interaction patterns between individuals. We apply our visualization to analyze the community structure in the US House of Representatives. We also report on a user study conducted with the participation of behavioral ecologists working with social network datasets that depict interactions between wild animals. Findings from the user study confirm that the visualization was helpful in providing answers to sociological questions as well as eliciting new observations on the social organization of the population under study.
Visualizing High‐Dimensional Structures by Dimension Ordering and Filtering using Subspace Analysis
Authors: Ferdosi Bilkis J. , Roerdink Jos B.T.M. 
Published: June 2011

AbstractHigh‐dimensional data visualization is receiving increasing interest because of the growing abundance of high‐dimensional datasets. To understand such datasets, visualization of the structures present in the data, such as clusters, can be an invaluable tool. Structures may be present in the full high‐dimensional space, as well as in its subspaces. Two widely used methods to visualize high‐dimensional data are the scatter plot matrix (SPM) and the parallel coordinate plot (PCP). SPM allows a quick overview of the structures present in pairwise combinations of dimensions. On the other hand, PCP has the potential to visualize not only bi‐dimensional structures but also higher dimensional ones. A problem with SPM is that it suffers from crowding and clutter which makes interpretation hard. Approaches to reduce clutter are available in the literature, based on changing the order of the dimensions. However, usually this reordering has a high computational complexity. For effective visualization of high‐dimensional structures, also PCP requires a proper ordering of the dimensions.In this paper, we propose methods for reordering dimensions in PCP in such a way that high‐dimensional structures (if present) become easier to perceive. We also present a method for dimension reordering in SPM which yields results that are comparable to those of existing approaches, but at a much lower computational cost. Our approach is based on finding relevant subspaces for clustering using a quality criterion and cluster information. The quality computation and cluster detection are done in image space, using connected morphological operators. We demonstrate the potential of our approach for synthetic and astronomical datasets, and show that our method compares favorably with a number of existing approaches.
Automatic Registration of Multi‐Projector Domes Using a Single Uncalibrated Camera
Authors: Sajadi B. , Majumder A. 
Published: June 2011

AbstractIn this paper we present a novel technique for easily calibrating multiple casually aligned projectors on spherical domes using a single uncalibrated camera. Using the prior knowledge of the display surface being a dome, we can estimate the camera intrinsic and extrinsic parameters and the projector to display surface correspondences automatically using a set of images. These images include the image of the dome itself and a projected pattern from each projector. Using these correspondences we can register images from the multiple projectors on the dome. Further, we can register displays which are not entirely visible in a single camera view using multiple pan and tilted views of an uncalibrated camera making our method suitable for displays of different size and resolution. We can register images from any arbitrary viewpoint making it appropriate for a single head‐tracked user in a 3D visualization system. Also, we can use several cartographic mapping techniques to register images in a manner that is appropriate for multi‐user visualization.Domes are known to produce a tremendous sense of immersion and presence in visualization systems. Yet, till date, there exists no easy way to register multiple projectors on a dome to create a high‐resolution realistic visualizations. To the best of our knowledge, this is the first method that can achieve accurate geometric registration of multiple projectors on a dome simply and automatically using a single uncalibrated camera.
Role of personal decontamination in preventing the spread of equine influenza
Authors: Frazer JL , Perkins NR , Pitt D 
Published: June 2011

Background  During the 2007 equine influenza (EI) outbreak, infected horses were quarantined at Morgan Park Recreational Grounds (MPRG) near Warwick, Queensland. Some individuals caring for horses were reported to have made return journeys between MPRG and home properties containing other horses during the time there was active infection at MPRG.Objective  A retrospective cohort study to assess the biosecurity and hygiene measures undertaken and their outcomes.Methods  All individuals recorded as being responsible for caring for one or more horses at MPRG, and who were also recorded on entry and exit logs at the gate to MPRG during the period of interest, and kept horses at their home property were contacted for a telephone questionnaire.Results  Of the 31 individuals identified, valid responses were obtained from 27 (87% response rate). Respondents had 2–25 horses at their home property, and 1–10 return trips were reported; 11 respondents reported contact with horses at home and provided information on biosecurity practices.Conclusion  Although horses at some home properties became infected with EI, it appears unlikely that this was the result of spread from MPRG via horse handlers. Simple preventive measures based on personal decontamination and other biosecurity measures are considered likely to have prevented spread of infection from MPRG to other properties.