bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems biology approaches to enhance our understanding of drug hypersensitivity reactions
Authors: Perkins J. R. , Barrionuevo E. , Ranea J. A. , Blanca M. , Cornejo‐Garcia J. A. 
Published: July 2014

SummaryHypersensitivity drug reactions (HDRs) encompass a wide spectrum of unpredictable clinical entities. They represent an important health problem, affecting people of all ages, and lead to a large strain on the public health system. Here, we summarize experiments that use high‐throughput genomics technologies to investigate HDRs. We also introduce the field of systems biology as a relatively recent discipline concerned with the integration and analysis of high‐throughput data sets such as DNA microarrays and next‐generation sequencing data. We describe previous studies that have applied systems biology techniques to related fields such as allergy and asthma. Finally, we present a number of potential applications of systems biology to the study of HDRs, in order to make the reader aware of the types of analyses that can be performed and the insights that can be gained through their application.
Extracting Features from Time‐Dependent Vector Fields Using Internal Reference Frames
Authors: Bhatia H. , Pascucci V. , Kirby R. M. , Bremer P.‐T. 
Published: July 2014

AbstractExtracting features from complex, time‐dependent flow fields remains a significant challenge despite substantial research efforts, especially because most flow features of interest are defined with respect to a given reference frame. Pathline‐based techniques, such as the FTLE field, are complex to implement and resource intensive, whereas scalar transforms, such as λ2, often produce artifacts and require somewhat arbitrary thresholds. Both approaches aim to analyze the flow in a more suitable frame, yet neither technique explicitly constructs one.This paper introduces a new data‐driven technique to compute internal reference frames for large‐scale complex flows. More general than uniformly moving frames, these frames can transform unsteady fields, which otherwise require substantial processing of resources, into a sequence of individual snapshots that can be analyzed using the large body of steady‐flow analysis techniques. Our approach is simple, theoretically well‐founded, and uses an embarrassingly parallel algorithm for structured as well as unstructured data. Using several case studies from fluid flow and turbulent combustion, we demonstrate that internal frames are distinguished, result in temporally coherent structures, and can extract well‐known as well as notoriously elusive features one snapshot at a time.
4D MRI Flow Coupled to Physics‐Based Fluid Simulation for Blood‐Flow Visualization
Authors: de Hoon N. , van Pelt R. , Jalba A. , Vilanova A. 
Published: July 2014

AbstractModern MRI measurements deliver volumetric and time‐varying blood‐flow data of unprecedented quality. Visual analysis of these data potentially leads to a better diagnosis and risk assessment of various cardiovascular diseases. Recent advances have improved the speed and quality of the imaging data considerably. Nevertheless, the data remains compromised by noise and a lack of spatiotemporal resolution. Besides imaging data, also numerical simulations are employed. These are based on mathematical models of specific features of physical reality. However, these models require realistic parameters and boundary conditions based on measurements. We propose to use data assimilation to bring measured data and physically‐based simulation together, and to harness the mutual benefits. The accuracy and noise robustness of the coupled approach is validated using an analytic flow field. Furthermore, we present a comparative visualization that conveys the differences between using conventional interpolation and our coupled approach.
Line Integral Convolution for Real‐Time Illustration of Molecular Surface Shape and Salient Regions
Authors: Lawonn Kai , Krone Michael , Ertl Thomas , Preim Bernhard 
Published: July 2014

AbstractWe present a novel line drawing algorithm that illustrates surfaces in real‐time to convey their shape. We use line integral convolution (LIC) and employ ambient occlusion for illustrative surface rendering. Furthermore, our method depicts salient regions based on the illumination gradient. Our method works on animated surfaces in a frame‐coherent manner. Therefore, it yields an illustrative representation of time‐dependent surfaces as no preprocessing step is needed. In this paper, the method is used to highlight the structure of molecular surfaces and to illustrate important surface features like cavities, channels, and pockets. The benefit of our method was evaluated with domain experts. We also demonstrate the applicability of our method to medical visualization.
Networks of Names: Visual Exploration and Semi‐Automatic Tagging of Social Networks from Newspaper Articles
Authors: Kochtchi A. , Landesberger T. von , Biemann C. 
Published: July 2014

AbstractUnderstanding relationships between people and organizations by reading newspaper articles is difficult to manage for humans due to the large amount of data. To address this problem, we present and evaluate a new visual analytics system, which offers interactive exploration and tagging of social networks extracted from newspapers. For the visual exploration of the network, we extract “interesting” neighbourhoods of nodes, using a new degree of interest (DOI) measure based on edges instead of nodes. It improves the seminal definition of DOI, which we find to produce the same “globally interesting” neighbourhoods in our use case, regardless of the query. Our approach allows answering different user queries appropriately, avoiding uniform search results.We propose a user‐driven pattern‐based classifier for discovery and tagging of non‐taxonomic semantic relations. Our approach does not require any a‐priori user knowledge, such as expertise in syntax or pattern creation. An evaluation shows that our classifier is capable of identifying known lexico‐syntactic patterns as well as various domain‐specific patters. Our classifier yields good results already with a small amount of training, and continuously improves through user feedback.We conduct a user study to evaluate whether our visual interactive system has an impact on how users tag relationships, as compared to traditional text‐based interfaces. Study results suggest that users of the visual system tend to tag more concisely, avoiding too abstract or overly specific relationship labels.
Visual Multiplexing
Authors: Chen M. , Walton S. , Berger K. , Thiyagalingam J. , Duffy B. , Fang H. , Holloway C. , Trefethen A. E. 
Published: July 2014

AbstractThe majority of display devices used in visualization are 2D displays. Inevitably, it is often necessary to overlay one piece of visual information on top of another, especially in applications such as multi‐field visualization and geo‐spatial information visualization. In this paper, we present a conceptual framework for studying the mechanisms for overlaying multiple pieces of visual information while allowing users to recover occluded information. We adopt the term ‘multiplexing’ from tele‐ and data communication to encompass all such overlapping mechanisms. We establish 10 categories of visual multiplexing mechanisms. We draw support evidence from both perception literature and existing works in visualization to support this conceptual framework. We examine the relationships between multiplexing and information theoretic measures. This new conceptual categorization provides the much‐needed theory of visualization with an integral component.
Many Plans: Multidimensional Ensembles for Visual Decision Support in Flood Management
Authors: Waser J. , Konev A. , Sadransky B. , Horváth Z. , Ribičić H. , Carnecky R. , Kluding P. , Schindler B. 
Published: July 2014

AbstractUncertainties in flood predictions complicate the planning of mitigation measures. There is a consensus that many possible incident scenarios should be considered. For each scenario, a specific response plan should be prepared which is optimal with respect to criteria such as protection, costs, or realization time. None of the existing software tools is capable of creating large scenario pools, nor do they provide means for quick exploration and assessment of the associated plans. In this paper, we present an integrated solution that is based on multidimensional, time‐dependent ensemble simulations of incident scenarios and protective measures. We provide scalable interfaces which facilitate and accelerate setting up multiple time‐varying parameters for generating a pool of pre‐cooked scenarios. In case of an emergency, disaster managers can quickly extract relevant information from the pool to deal with the situation at hand. An interactive 3D‐view conveys details about how a response plan has to be executed. Linked information visualization and ranking views allow for a quick assessment of many plans. In collaboration with flood managers, we demonstrate the practical applicability of our solution. We tackle the challenges of planning mobile water barriers for protecting important infrastructure. We account for real‐world limitations of available resources and handle the involved logistics problems.
LoVis: Local Pattern Visualization for Model Refinement
Authors: Zhao Kaiyu , Ward Matthew O. , Rundensteiner Elke A. , Higgins Huong N. 
Published: July 2014

AbstractLinear models are commonly used to identify trends in data. While it is an easy task to build linear models using pre‐selected variables, it is challenging to select the best variables from a large number of alternatives. Most metrics for selecting variables are global in nature, and thus not useful for identifying local patterns. In this work, we present an integrated framework with visual representations that allows the user to incrementally build and verify models in three model spaces that support local pattern discovery and summarization: model complementarity, model diversity, and model representivity. Visual representations are designed and implemented for each of the model spaces. Our visualizations enable the discovery of complementary variables, i.e., those that perform well in modeling different subsets of data points. They also support the isolation of local models based on a diversity measure. Furthermore, the system integrates a hierarchical representation to identify the outlier local trends and the local trends that share similar directions in the model space. A case study on financial risk analysis is discussed, followed by a user study.
Semi‐Automatic Editing of Graphs with Customized Layouts
Authors: Gladisch S. , Schumann H. , Ernst M. , Füllen G. , Tominski C. 
Published: July 2014

AbstractUsually visualization is applied to gain insight into data. Yet consuming the data in form of visual representation is not always enough. Instead, users need to edit the data, preferably through the same means used to visualize them. In this work, we present a semi‐automatic approach to visual editing of graphs. The key idea is to use an interactive EditLens that defines where an edit operation affects an already customized and established graph layout. Locally optimal node positions within the lens and edge routes to connected nodes are calculated according to different criteria. This spares the user much manual work, but still provides sufficient freedom to accommodate application‐dependent layout constraints. Our approach utilizes the advantages of multi‐touch gestures, and is also compatible with classic mouse and keyboard interaction. Preliminary user tests have been conducted with researchers from bio‐informatics who need to manually maintain a slowly, but constantly growing molecular network. As the user feedback indicates, our solution significantly improves the editing procedure applied so far.
In vitro color evaluation of esthetic coatings for metallic dental implants and implant prosthetic appliances
Authors: Pecnik Christina M. , Roos Malgorzata , Muff Daniel , Spolenak Ralph , Sailer Irena 
Published: July 2014

AbstractObjectivesThe aim of this study was to characterize the optical properties of newly developed esthetic coatings for metallic implants and components for an improved peri‐implant soft tissue appearance.Material and methodsPig maxillae (n = 6) were used for the in vitro color evaluation of coated and uncoated samples. Three different coating systems (Ti–ZrO2, Ti–Al–ZrO2, and Ti–Ag–ZrO2) were deposited on titanium substrates, which exhibited different roughness (polished, machined, and sand‐blasted) and interference colors (pink, yellow, and white). Spectrophotometric measurements were made of samples below three different mucosa thicknesses (1 mm, 2 mm, and 3 mm) and titanium served as negative control. Color difference ΔE was calculated using ΔL, Δa, and Δb values for each sample (in total 30 samples).ResultsΔE values were significantly above the threshold value of 3.70 for sand‐blasted Ti and Ti–ZrO2 samples when tested below 1 mm thick soft tissue, hence resulted in a dark appearance of the soft tissues. In contrast, Ti–Al–ZrO2 and Ti–Ag–ZrO2 samples showed significant ΔL values below 1 mm, which indicates a brightening of the covering tissue. In general, ΔE values decreased with increasing thickness of the tissue. At 3 mm thick tissue, ΔE values were significantly below 3.70 for Ti–Al–ZrO2 and Ti–Ag–ZrO2 samples. The preferable substrate surface should be machined due increased color brightness, good soft tissue integration and improved adhesion between coating and substrates. Improvement of the optical appearance of the metal was achieved with the coating systems Ti–Al–ZrO2 and Ti–Ag–ZrO2. Darkening effects could not be observed for these systems, and partially light brightening of the tissue was observed. Advantageous colors were suggested to be pink and yellow.
Histopathological comparative analysis of peri‐implant soft tissue response after dental implant placement with flap and flapless surgical technique. Experimental study in pigs
Authors: Vlahovic Zoran , Markovic Aleksa , Golubovic Mileta , Scepanovic Miodrag , Kalanovic Milena , Djinic Ana 
Published: July 2014

AbstractAimThe aim of this study was comparing the effect of flapless vs. flap technique of implant placement on inflammation degree of peri‐implant soft tissue, through histopathological analysis.MethodThe experiment was conducted on five domestic pigs. Nine weeks after tooth extraction, implants were installed. Each animal received six implants in mandible. According to split‐mouth design, randomly one side was used for flapless technique using mini‐incision, while on the other side, flap was raised. After 7, 14, 21, 28, and 90 days, the experimental animals were sacrificed. Samples for histopathological analyzes were taken from the buccal side of peri‐implant mucosa next to the neck of implants, from three levels. The degree of inflammatory response in the peri‐implant soft tissue was estimated through ordinal scores from 0 to 3.ResultsIn the flap group Score 3 indicating high degree of inflammation was present from day 7 to day 21, in contrast to flapless group where Score 3 was not recorded during the entire follow‐up. Three months after implantation, there were no signs of inflammation neither around flap nor around flapless implants.ConclusionFlapless surgical implantation technique using mini‐incision decreases peri‐implant soft tissue inflammatory reaction compared with flap surgery.
Reliable Identification of Declining Populations in an Uncertain World
Authors: d’Eon‐Eggertson Faye , Dulvy Nicholas K. , Peterman Randall M. 
Published: July 2014

AbstractAssessments of extinction risk based on population declines are widely used, yet scientists have little quantitative understanding of their reliability. Incorrectly classifying whether a population is declining or not can lead to inappropriate conservation actions or management measures, with potentially profound societal costs. Here we evaluate key causes of misclassification of decline status and assess the reliability of 20 decline metrics using a stochastic model to simulate time series of population abundance of sockeye salmon (Oncorhynchus nerka). We show that between‐year variability in population productivity (process variation) and, to a lesser extent, variability in abundance estimates (observation error) are important causes of unreliable identification of population status. We found that using all available data, rather than just the most recent three generations, consistently improved the reliability of risk assessments. The approach outlined here can improve understanding of the reliability of risk assessments, thereby reducing concerns that may impede their use for exploited taxa such as marine fishes.
Bojale Drum: Material Culture in Living Contexts
Authors: Setlhabi Keletso Gaone 
Published: July 2014

AbstractThis paper discusses the three phases of the lifecycle of the bojale drum: its custodianship by the queen of Bakgatla‐baga‐Kgafela; the drum's use in bojale (girls’ initiation ceremony); and its presence in Phuthadikobo Museum, a community institution. This lifecycle was observed by the author prior, during, and post initiation in bojale, a girls’ initiation school in 2009. The drum's use, its royal significance and sacredness, is barely documented in its museum record, which can result in its misinterpretation. The recommendations are that the drum's documentation, preservation, handling, and storage in the museum should incorporate its intangible cultural attributes if the museum is to be relevant to the Bakgatla‐baga‐Kgafela community. In conclusion, bojale drum is an example of how material culture can connect a museum with its community through the living culture of bojale.
A new twist on old ideas: how sitting reorients crawlers
Authors: Soska Kasey C. , Robinson Scott R. , Adolph Karen E. 
Published: July 2014

AbstractTraditionally, crawling and sitting are considered distinct motor behaviors with different postures and functions. Ten‐ to 12‐month‐old infants were observed in the laboratory or in their homes while being coaxed to crawl continuously over long, straight walkways (Study 1; N = 20) and during spontaneous crawling during free play (Study 2; N = 20). In every context, infants stopped crawling to sit 3–6 times per minute. Transitions from crawling to sitting frequently turned infants' bodies away from the direction of heading; subsequent transitions back to crawling were offset by as much as 180° from the original direction of heading. Apparently, body reorientations result from the biomechanics of transitioning between crawling and sitting. Findings indicate that sustained, linear crawling is likely an epiphenomenon of how gait is studied in standard paradigms. Postural transitions between crawling and sitting are ubiquitous and can represent a functional unit of action. These transitions and the accompanying body reorientations likely have cascading effects for infants' exploration, visual perception, and spatial cognition.
Variation in mouthguard thickness due to different heating conditions during fabrication: Part 2
Authors: Takahashi Mutsumi , Koide Kaoru , Mizuhashi Fumi 
Published: July 2014

AbstractThe purpose of this study was to determine changes in the thickness of mouthguard sheets under different heating conditions during fabrication. Mouthguards were fabricated with polyolefin–polystyrene co‐polymer (OS) and olefin co‐polymer (OL) sheets (4.0‐mm thick) utilizing a vacuum‐forming machine under the following three conditions: (A) the sheet was moulded when it sagged 15 mm below the sheet frame (i.e. the normally used position); (B) the sheet frame was lowered to and heated at 30 mm below the top of the post and moulded when it sagged by 15 mm; and (C) the sheet frame was lowered to and heated at 50 mm below the top of the post and moulded when it sagged by 15 mm. The working model was trimmed to a height of 20 mm at the incisor and 15 mm at the first molar. Post‐moulding thickness was determined for the incisal portion (incisal edge and labial surface) and molar portion (cusp, central groove and buccal surface). Dimensions were measured, and differences in the change in thickness due to heating condition were analysed using the Kruskal–Wallis test. Under condition C, OS and OL decreased in thickness from 0.36–0.54 mm to 0.26–0.30 mm, respectively, at the incisal portion and from 0.34–0.66 mm to 0.17–0.47 mm, respectively, at the molar portion. It may be clinically useful when moulding a mouthguard to maintain the thickness of the incisal and molar portions by adjusting the height of the sheet frame.
A molecular diagnostic assay for the detection and identification of wood decay fungi of conifers
Authors: Gonthier P. , Guglielmo F. , Sillo F. , Giordano L. , Garbelotto M. 
Published: July 2014

SummaryTen taxon‐specific primers were designed to amplify the Internal Transcribed Spacer of the rRNA operon of several important decay fungi of coniferous wood, including Armillaria spp., Echinodontium spp., Fomitopsis pinicola, Fuscoporia torulosa, Heterobasidion annosum sensu lato (s.l.), Onnia spp., Phaeolus schweinitzii, Phellinus weirii s.l., Pholiota spp. and Porodaedalea spp. Primers designed in this study and in a previous one for the identification of Laetiporus sulphureus and Stereum spp. were combined in two multiplex PCRs, which were tested for efficiency and specificity, and detected at least 1 pg of fungal target DNA. Target DNA at concentrations of 10−1 pg or lower can be detected with this assay using SYBR® Green Real‐Time PCR. Validation assays performed on 129 naturally infected wood samples or fruiting bodies confirmed the reliability of the multiplex PCR‐based diagnostic method. This method represents a simple and rapid diagnostic tool for the detection of a number of destructive wood decay fungi of conifer wood.
Rituximab, Gemcitabine, Cisplatin and Methylprednisolone (R‐GEM‐P) is an effective regimen in relapsed diffuse large B‐cell lymphoma
Authors: Barton Sarah , Hawkes Eliza A. , Cunningham David , Peckitt Clare , Chua Sue , Wotherspoon Andrew , Attygalle Ayoma , Horwich Alan , Potter Mike , Ethell Mark , Dearden Claire , Gleeson Mary , Chau Ian 
Published: July 2014

AbstractBackgroundPatients with relapsed diffuse large B‐cell lymphoma (DLBCL) have a poor prognosis. Gemcitabine, methylprednisolone, cisplatin +/− rituximab (GEM‐P+/−R) is a salvage regimen with limited overlap in toxicity with first‐line therapy and short duration of inpatient delivery.MethodsWe assessed the efficacy and safety of GEM‐P+/−R in a retrospective single‐centre analysis including patients meeting criteria of ≥18 yr of age, histologically proven DLBCL, treated between 2001 and 2011 in second‐line with gemcitabine 1000 mg/m2 day 1, 8 and 15, methylprednisolone 1000 mg day 1–5, cisplatin 100 mg/m2 day 15 (replaced with carboplatin AUC5 if contraindication/toxicity) +/− rituximab 375 mg/m2 day 1 and 15, every 28 d.ResultsForty‐five patients aged 25–74 received a median of three cycles of GEM‐P+/−R; 64% received rituximab. In 44 evaluable patients receiving GEM‐P+/−R, overall response rate (ORR) was 48%; in 28 evaluable patients treated with rituximab + GEM‐P (R‐GEM‐P), ORR was 61%. With median follow‐up of 50.5 months (95% CI: 28.3–72.7), 3‐yr overall survival (OS) from start of GEM‐P+/−R was 31.4% (95% CI: 16.5–46.3); in patients treated with R‐GEM‐P, 3‐yr OS was 49.1% (95% CI: 28.7–69.5). Predominant grade ≥ 3 toxicities were haematological; thrombocytopenia 69%, neutropenia 60% and febrile neutropenia 7%.ConclusionR‐GEM‐P is a deliverable regimen with useful activity in second‐line treatment of DLBCL. Our data suggest that rituximab should be given concurrently.