bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Z Proteins of Pathogenic but Not Nonpathogenic Arenaviruses Inhibit RIG-i-Like Receptor-Dependent Interferon Production
Authors: Xing Junji , Ly Hinh , Liang Yuying 
Published: January 2015

ABSTRACT
Arenavirus pathogens cause a wide spectrum of diseases in humans ranging from central nervous system disease to lethal hemorrhagic fevers with few treatment options. The reason why some arenaviruses can cause severe human diseases while others cannot is unknown. We find that the Z proteins of all known pathogenic arenaviruses, lymphocytic choriomeningitis virus (LCMV) and Lassa, Junin, Machupo, Sabia, Guanarito, Chapare, Dandenong, and Lujo viruses, can inhibit retinoic acid-inducible gene 1 (RIG-i) and Melanoma Differentiation-Associated protein 5 (MDA5), in sharp contrast to those of 14 other nonpathogenic arenaviruses. Inhibition of the RIG-i-like receptors (RLRs) by pathogenic Z proteins is mediated by the protein-protein interactions of Z and RLRs, which lead to the disruption of the interactions between RLRs and mitochondrial antiviral signaling (MAVS). The Z-RLR interactive interfaces are located within the N-terminal domain (NTD) of the Z protein and the N-terminal CARD domains of RLRs. Swapping of the LCMV Z NTD into the nonpathogenic Pichinde virus (PICV) genome does not affect virus growth in Vero cells but significantly inhibits the type I interferon (IFN) responses and increases viral replication in human primary macrophages. In summary, our results show for the first time an innate immune-system-suppressive mechanism shared by the diverse pathogenic arenaviruses and thus shed important light on the pathogenic mechanism of human arenavirus pathogens.

IMPORTANCE
We show that all known human-pathogenic arenaviruses share an innate immune suppression mechanism that is based on viral Z protein-mediated RLR inhibition. Our report offers important insights into the potential mechanism of arenavirus pathogenesis, provides a convenient way to evaluate the pathogenic potential of known and/or emerging arenaviruses, and reveals a novel target for the development of broad-spectrum therapies to treat this group of diverse pathogens. More broadly, our report provides a better understanding of the mechanisms of viral immune suppression and host-pathogen interactions.
Parainfluenza Virus 5 Expressing the G Protein of Rabies Virus Protects Mice after Rabies Virus Infection
Authors: Huang Ying , Chen Zhenhai , Huang Junhua , Fu ZhenFang , He Biao 
Published: January 2015

ABSTRACT
Rabies remains a major public health threat around the world. Once symptoms appear, there is no effective treatment to prevent death. In this work, we tested a recombinant parainfluenza virus 5 (PIV5) strain expressing the glycoprotein (G) of rabies (PIV5-G) as a therapy for rabies virus infection: we have found that PIV5-G protected mice as late as 6 days after rabies virus infection. PIV5-G is a promising vaccine for prevention and treatment of rabies virus infection.
The epidemiology of competence: protocol for a scoping review
Authors: Glover Takahashi Susan , Herold Jodi , Nayer Marla , Bance Sheena 
Published: January 2015

IntroductionFactors that are important to the competence of healthcare providers have important consequences for quality of healthcare. Although some previous research has discussed risks or supports to the competence of clinicians, a thorough exploration is currently lacking. The purpose of this review is to examine the literature examining risks and supports to clinical competence of healthcare practitioners and trainees engaged in field-based education. In this study, field-based education refers to teaching or training in a real-world/work-based setting.Methods and analysisWe will employ an established scoping review methodology. Eligible studies will include those that mention (1) a healthcare professional, (2) competence from field-based education throughout the lifespan/career and (3) a risk or support to competence. Four authors will independently apply the inclusion criteria to all studies, regardless of study design. Our data extraction will include information on study design, location and type of study and we will develop a comprehensive list of risks and supports that are discussed in the literature.Ethics and disseminationSince this is a review of the literature, ethics approval is not indicated. We will disseminate the findings from this study in publications in peer-reviewed journals as well as presentations at relevant national and international conferences.
Location- and Query-Aware Modeling of Browsing and Click Behavior in Sponsored Search
Authors: Ashkan Azin , Clarke Charles L. A. 
Published: January 2015

An online advertisement’s clickthrough rate provides a fundamental measure of its quality, which is widely used in ad selection strategies. Unfortunately, ads placed in contexts where they are rarely viewed—or where users are unlikely to be interested in commercial results—may receive few clicks regardless of their quality. In this article, we model the variability of a user’s browsing behavior for the purpose of click analysis and prediction in sponsored search. Our model incorporates several important contextual factors that influence ad clickthrough rates, including the user’s query and ad placement on search engine result pages. We formally model these factors with respect to the list of ads displayed on a result page, the probability that the user will initiate browsing of this list, and the persistence of the user in browsing the list. We incorporate these factors into existing click models by augmenting them with appropriate query and location biases. Using expectation maximization, we learn the parameters of these augmented models from click signals recorded in the logs of a commercial search engine.To evaluate the performance of the models and to compare them with state-of-the-art performance, we apply standard evaluation metrics, including log-likelihood and perplexity. Our evaluation results indicate that, through the incorporation of query and location biases, significant improvements can be achieved in predicting browsing and click behavior in sponsored search. In addition, we explore the extent to which these biases actually reflect varying behavioral patterns. Our observations confirm that correlations exist between the biases and user search behavior.
Dynamic Energy, Performance, and Accuracy Optimization and Management Using Automatically Generated Constraints for Separable 2D FIR Filtering for Digital Video Processing
Authors: Llamocca Daniel , Pattichis Marios 
Published: January 2015

There is strong interest in the development of dynamically reconfigurable systems that can meet real-time constraints on energy, performance, and accuracy. The generation of real-time constraints will significantly expand the applicability of dynamically reconfigurable systems to new domains, such as digital video processing.
We develop a dynamically reconfigurable 2D FIR filtering system that can meet real-time constraints in energy, performance, and accuracy (EPA). The real-time constraints are automatically generated based on user input, image types associated with video communications, and video content. We first generate a set of Pareto-optimal realizations, described by their EPA values and associated 2D FIR hardware description bitstreams. Dynamic management is then achieved by selecting Pareto-optimal realizations that meet the automatically generated time-varying EPA constraints.
We validate our approach using three different 2D Gaussian filters. Filter realizations are evaluated in terms of the required energy per frame, accuracy of the resulting image, and performance in frames per second. We demonstrate dynamic EPA management by applying a Difference of Gaussians (DOG) filter to standard video sequences. For video frame sizes that are equal to or larger than the VGA resolution, compared to a static implementation, our dynamic system provides significant reduction in the total energy consumption (>30%).
Dehazing Using Color-Lines
Authors: Fattal Raanan 
Published: January 2015

Photographs of hazy scenes typically suffer having low contrast and offer a limited visibility of the scene. This article describes a new method for single-image dehazing that relies on a generic regularity in natural images where pixels of small image patches typically exhibit a 1D distribution in RGB color space, known as color-lines. We derive a local formation model that explains the color-lines in the context of hazy scenes and use it for recovering the scene transmission based on the lines' offset from the origin. The lack of a dominant color-line inside a patch or its lack of consistency with the formation model allows us to identify and avoid false predictions. Thus, unlike existing approaches that follow their assumptions across the entire image, our algorithm validates its hypotheses and obtains more reliable estimates where possible.
In addition, we describe a Markov random field model dedicated to producing complete and regularized transmission maps given noisy and scattered estimates. Unlike traditional field models that consist of local coupling, the new model is augmented with long-range connections between pixels of similar attributes. These connections allow our algorithm to properly resolve the transmission in isolated regions where nearby pixels do not offer relevant information.
An extensive evaluation of our method over different types of images and its comparison to state-of-the-art methods over established benchmark images show a consistent improvement in the accuracy of the estimated scene transmission and recovered haze-free radiances.
Interactive Exploration of Multi-Dimensional Information Spaces with Preference Support
Authors: Papadakos Panagiotis 
Published: January 2015

Users access large amounts of information resources mainly through search functions, where they type a few keywords and the web search or query engine returns a linear list of hits. While this is often satisfactory for focalized search, it does not provide enough support for exploratory information needs. Faceted and Dynamic Taxonomies (FDT) is a highly prevalent model for exploratory search, which allows users to get an overview of the information space and offer them various groupings of the results based on their attributes, metadata, or other dynamically mined information, enabling them to gradually restrict their focus through clicks and locate low ranked resources. The enrichment of such mechanisms with preferences could be proven useful for exploratory tasks. However, the current preference-based approaches seem to ignore the fact that users should be acquainted with the information space and the available choices for describing effectively their preferences.
In this dissertation we extend the interaction model of FDT with preference actions that allow users to express their preferences interactively, gradually, and in a simple way. We introduce a preference framework appropriate for information spaces comprising resources described by attributes whose values can be hierarchically valued and/or multi-valued. We define the language, its semantics and the required algorithms. The framework supports preference inheritance in the hierarchies, automatic conflict resolution, as well as preference composition. Subsequently, we enrich the FDT model with preference actions and we propose logical optimizations and methods for exploiting the intrinsic characteristics of the FDT-based interaction, aiming at making it applicable to large amounts of information. We present the design and the implementation of the web-based system Hippalus, which realizes the extended interaction model. Regarding user benefits, we theoretically analyze user gain in terms of the number and difficulty of choices, and we describe and analyze three user-based evaluations. The first investigates the degree of effectiveness of preferences when users are not aware of the available choices. We found that only 20% of the users managed to express effective preferences without knowing the available choices. The second comparatively evaluates FDT with other exploratory models, and shows that the majority of users preferred FDT, was more satisfied by FDT and achieved higher rates of task completion with FDT. The last one evaluates the preference-enriched FDT as realized by Hippalus. The results were impressive. Even in a very small dataset, with the preference-enriched FDT all users successfully completed all tasks in 1/3 of the time and with 1/3 of the actions in comparison to the plain FDT. Moreover all of the users preferred the preference-enriched interfac.
Available: http://www.ics.forth.gr/_publications/Papadakos_Dissertation.pdf.
Chisel
Authors: Misailovic Sasa , Carbin Michael , Achour Sara , Qi Zichao , Rinard Martin C. 
Published: January 2015

The accuracy of an approximate computation is the distance between the result that the computation produces and the corresponding fully accurate result. The reliability of the computation is the probability that it will produce an acceptably accurate result. Emerging approximate hardware platforms provide approximate operations that, in return for reduced energy consumption and/or increased performance, exhibit reduced reliability and/or accuracy.
We present Chisel, a system for reliability- and accuracy-aware optimization of approximate computational kernels that run on approximate hardware platforms. Given a combined reliability and/or accuracy specification, Chisel automatically selects approximate kernel operations to synthesize an approximate computation that minimizes energy consumption while satisfying its reliability and accuracy specification.
We evaluate Chisel on five applications from the image processing, scientific computing, and financial analysis domains. The experimental results show that our implemented optimization algorithm enables Chisel to optimize our set of benchmark kernels to obtain energy savings from 8.7% to 19.8% compared to the fully reliable kernel implementations while preserving important reliability guarantees.
Staged parser combinators for efficient data processing
Authors: Jonnalagedda Manohar , Coppey Thierry , Stucki Sandro , Rompf Tiark , Odersky Martin 
Published: January 2015

Parsers are ubiquitous in computing, and many applications depend on their performance for decoding data efficiently. Parser combinators are an intuitive tool for writing parsers: tight integration with the host language enables grammar specifications to be interleaved with processing of parse results. Unfortunately, parser combinators are typically slow due to the high overhead of the host language abstraction mechanisms that enable composition.
We present a technique for eliminating such overhead. We use staging, a form of runtime code generation, to dissociate input parsing from parser composition, and eliminate intermediate data structures and computations associated with parser composition at staging time. A key challenge is to maintain support for input dependent grammars, which have no clear stage distinction.
Our approach applies to top-down recursive-descent parsers as well as bottom-up non-deterministic parsers with key applications in dynamic programming on sequences, where we auto-generate code for parallel hardware. We achieve performance comparable to specialized, hand-written parsers.
Sonic Hedgehog and Gli1 Expression Predict Outcome in Resected Pancreatic Adenocarcinoma
Authors: Maréchal Raphaël , Bachet Jean-Baptiste , Calomme Annabelle , Demetter Pieter , Delpero Jean Robert , Svrcek Magali , Cros Jérôme , Bardier-Dupas Armelle , Puleo Francesco , Monges Geneviève , Hammel Pascal , Louvet Christophe , Paye François , Bachelier Philippe , Le Treut Yves Patrice , Vaillant Jean-Christophe , Sauvanet Alain , André Thierry , Salmon Isabelle , Devière Jacques , Emile Jean-François , Van Laethem Jean-Luc 
Published: January 2015

Abstract
Purpose: Aberrant activation of the hedgehog (Hh) pathway is implicated in pancreatic ductal adenocarcinoma (PDAC) tumorigenesis. We investigated the prognostic and predictive value of four Hh signaling proteins and of the tumor stromal density.
Experimental Design: Using tissue microarray and immunohistochemistry, the expression of Shh, Gli1, SMO, and PTCH1 was assessed in 567 patients from three independent cohorts who underwent surgical resection for PDAC. In 82 patients, the tumor stromal index (SI) was calculated, and its association with overall survival (OS) and disease-free survival (DFS) was investigated.
Results: Shh and Gli1 protein abundance were independent prognostic factors in resected PDACs; low expressors for those proteins experiencing a better OS and DFS. The combination of Shh and Gli1 levels was the most significant predictor for OS and defined 3 clinically relevant subgroups of patients with different prognosis (Gli1 and Shh low; HR set at 1 vs. 3.08 for Shh or Gli1 high vs. 5.69 for Shh and Gli1 high; P &lt; 0.001). The two validating cohorts recapitulated the findings of the training cohort. After further stratification by lymph node status, the prognostic significance of combined Shh and Gli1 was maintained. The tumor SI was correlated with Shh levels and was significantly associated with OS (P = 0.023).
Conclusions: Shh and Gli1 are prognostic biomarkers for patients with resected PDAC. Clin Cancer Res; 21(5); 1215–24. ©2014 AACR.
Radiotherapy Combined with the Immunocytokine L19-IL2 Provides Long-lasting Antitumor Effects
Authors: Zegers Catharina M.L. , Rekers Nicolle H. , Quaden Dana H.F. , Lieuwes Natasja G. , Yaromina Ala , Germeraad Wilfred T.V. , Wieten Lotte , Biessen Erik A.L. , Boon Louis , Neri Dario , Troost Esther G.C. , Dubois Ludwig J. , Lambin Philippe 
Published: January 2015

AbstractPurpose: Radiotherapy modifies the tumor microenvironment and causes the release of tumor antigens, which can enhance the effect of immunotherapy. L19 targets the extra domain B (ED-B) of fibronectin, a marker for tumor neoangiogenesis, and can be used as immunocytokine when coupled to IL2. We hypothesize that radiotherapy in combination with L19-IL2 provides an enhanced antitumor effect, which is dependent on ED-B expression.Experimental Design: Mice were injected with syngeneic C51 colon carcinoma, Lewis lung carcinoma (LLC), or 4T1 mammary carcinoma cells. Tumor growth delay, underlying immunologic parameters, and treatment toxicity were evaluated after single-dose local tumor irradiation and systemic administration of L19-IL2 or equimolar controls.Results: ED-B expression was high, intermediate, and low for C51, LLC, and 4T1, respectively. The combination therapy showed (i) a long-lasting synergistic effect for the C51 model with 75% of tumors being cured, (ii) an additive effect for the LLC model, and (iii) no effect for the 4T1 model. The combination treatment resulted in a significantly increased cytotoxic (CD8+) T-cell population for both C51 and LLC. Depletion of CD8+ T cells abolished the benefit of the combination therapy.Conclusions: These data provide the first evidence for an increased therapeutic potential by combining radiotherapy with L19-IL2 in ED-B–positive tumors. This new opportunity in cancer treatment will be investigated in a phase I clinical study for patients with an oligometastatic solid tumor (NCT02086721). An animation summarizing our results is available at https://www.youtube.com/watch?v=xHbwQuCTkRc. Clin Cancer Res; 21(5); 1151–60. ©2014 AACR.
Echocardiography in Pediatric Pulmonary Arterial Hypertension
Authors: Ploegstra Mark-Jan , Roofthooft Marcus T.R. , Douwes Johannes M. , Bartelds Beatrijs , Elzenga Nynke J. , van de Weerd Dick , Hillege Hans L. , Berger Rolf M.F. 
Published: January 2015

Background—
The value of echocardiography in assessing disease severity and predicting outcome in pediatric pulmonary arterial hypertension (PAH) is insufficiently defined. The aim of this study was to describe correlations between echocardiography and disease severity and outcome in pediatric PAH.

Methods and Results—

Forty-three consecutive children (median age, 8.0 years; range, 0.4–21.5) with idiopathic/hereditary PAH (n=25) or PAH associated with congenital heart disease (n=18) were enrolled in a prospective single-center observational study. Anatomic and right ventricular-functional variables were obtained by two-dimensional echocardiography and Doppler-echocardiography at presentation and at standardized follow-up and were correlated with measures of disease severity (World Health Organization functional class [WHO-FC], N-terminal-pro-B-type natriuretic peptide, hemodynamics) and lung-transplantation–free survival. Right atrial and right ventricular dimensions correlated with WHO-FC and hemodynamics (
P
<0.05), whereas left ventricular dimensions correlated with hemodynamics and survival (
P
<0.05). Right-to-left ventricular dimension ratiocorrelated with WHO-FC, hemodynamics and survival (
P
<0.05). Right ventricular ejection time correlated with hemodynamics and survival (
P
<0.05) and tended to correlate with WHO-FC (
P
=0.071). Tricuspid annular plane systolic excursion correlated with WHO-FC, mean right atrial pressure and survival (
P
<0.05).

Conclusions—
This early descriptive study shows that echocardiographic chararacteristics of both the right and the left heart correlate with disease severity and outcome in pediatric PAH, both at presentation and during the course of the disease. The preliminary data from this study support the potential value of echocardiography as a tool in guiding management in children with PAH.
Association of a Favorable Cardiovascular Health Profile With the Presence of Coronary Artery Calcification
Authors: Saleem Yasir , F. DeFina Laura , B. Radford Nina , Willis Benjamin L. , Barlow Carolyn E. , Gibbons Larry W. , Khera Amit 
Published: January 2015

Background—
To examine the association between the American Heart Association’s 7 metrics of ideal cardiovascular health (ICH) and the presence of subclinical coronary atherosclerosis as assessed by coronary artery calcification (CAC) using electron-beam computed tomography.

Methods and Results—
This study is a cross-sectional analysis of data obtained on 3121 male and female patients evaluated at the Cooper Clinic in Dallas, Texas, between 1997 and 2007. We included men aged ≥45 and women aged ≥55 without known cardiovascular disease and for whom information on all ICH metrics and a CAC score were available. Patients were grouped into 3 categories according to their number of ICH metrics: favorable (4–7 ICH metrics), intermediate (3 metrics), and unfavorable (0–2 metrics). Patients with favorable ICH profiles had a lower prevalence and severity of subclinical atherosclerosis than those with unfavorable or intermediate ICH profiles as estimated by CAC. This inverse association of CAC with ICH metrics was evident whether the presence of coronary calcium was defined as CAC score >0, CAC score >100, or CAC score >400. Patients with favorable ICH profiles had odds of coronary calcium (CAC>0) less than half of those for patients with unfavorable profiles (odds ratio 0.41; 95% confidence interval, 0.34–0.50) and patients with intermediate ICH profiles had odds of detectable CAC 32% lower (odds ratio 0.68; 95% confidence interval, 0.57–0.82).

Conclusions—
A statistically significant association was found between a favorable level of ICH metrics and less or absent subclinical atherosclerosis as measured by CAC underscoring the importance of primordial prevention.