bluuebunny/crossref_metadata_2025_split huggingface dataset:
An empirical pipeline to derive gaze prediction heuristics for 3D action games
Authors: Bernhard Matthias , Stavrakis Efstathios , Wimmer Michael 
Published: November 2010

Gaze analysis and prediction in interactive virtual environments, such as games, is a challenging topic since the 3D perspective and variations of the viewpoint as well as the current task introduce many variables that affect the distribution of gaze. In this article, we present a novel pipeline to study eye-tracking data acquired from interactive 3D applications. The result of the pipeline is an importance map which scores the amount of gaze spent on each object. This importance map is then used as a heuristic to predict a user's visual attention according to the object properties present at runtime. The novelty of this approach is that the analysis is performed in object space and the importance map is defined in the feature space of high-level properties. High-level properties are used to encode task relevance and other attributes, such as eccentricity, which may have an impact on gaze behavior.
The pipeline has been tested with an exemplary study on a first-person shooter game. In particular, a protocol is presented describing the data acquisition procedure, the learning of different importance maps from the data, and finally an evaluation of the performance of the derived gaze predictors. A metric measuring the degree of correlation between attention predicted by the importance map and the actual gaze yielded clearly positive results. The correlation becomes particularly strong when the player is attentive to an in-game task.
Use of object oriented technologies in high reliability system
Authors: Rosen Jean-Pierre 
Published: November 2010

This tutorial presents the new challenges brought by the advent of object oriented technologies (OOT) into the realm of high reliability systems.
For a long time, OOP was deemed too dynamic a model for highly reliable systems, especially levels A/B of the DO178B, although the standard in itself does not preclude the use of any technology. However, interest for introducing OO techniques is growing in the community; the FAA sponsored OOTiA (Object-Oriented Technology in Aviation), a handbook intended to identify and address these issues. Although not an official policy of the FAA, this handbook is a major input for the upcoming revision of DO178B (DO178C).
The tutorial provides an overview of software safety related standards (DO178B in airborne systems, EN5018 for railway systems). Based on the extensive work of the OOTiA, it explains the issues of object oriented technologies in high reliability systems, and how such technologies can be used while ensuring the high degree of control, review, and testing mandated by these systems. Finally, it shows how Ada's object oriented model differs from the traditional model, and brings better solutions for introducing OOP to high reliability systems.
The tutorial will help participants to understand what software safety standards are about, discover the issues of object oriented technologies in high reliability systems, get an up to date view of current trends with regard to OOT and the DO178B, and learn how Ada's model of object oriented programming is especially appropriate for secure systems
Experience report
Authors: Schmidt Richard B. 
Published: November 2010

The Ada language has been architected to provide a strong foundation for building software at the heart of safety critical, real-time, and long-maintained programs. The benefits of Ada in such environments have led to its use in a wide range of systems where correctness and predictability are critical. The current trend in our industry is to loosely tie systems together to share data that previously required manual re-entry, simply was not available, or worse could have been inconsistent between systems. This trend is resulting in a need to connect previously closed systems over in-house and external networks to perform that loose linkage.
The FAA has embraced this technology and has been developing an architecture, code framework, and standards for sharing data across their entire spectrum of Air Traffic Control systems and consumers. The FAA's overall umbrella for this is termed SWIM (System Wide Information Management), and programs participating in the architecture are called "SWIM implementing programs". The ERAM (EnRoute Automation Modernization) program I work on and previously presented at SIG Ada 2009 is one of the first SWIM implementing programs. ERAM has recently entered the test phase of the first increment of SWIM functionality. ERAM SWIM faced many of the same hurdles as other legacy Ada systems around the globe. The new interfaces are built on standard web protocols and need to provide secure reliable information flow to both other internal FAA systems, and external customers such as the major commercial air carriers.
In an effort to use best industry practices Lockheed Martin and the FAA chose Java and other web-standard technologies to implement much of the new SWIM interface. Java has gained a strong foothold in the internet environment and the classrooms for a variety of reasons. The result is that Java enjoys a large amount of FOSS and commercial support that makes it a natural choice for such a web interface, even in a high stakes environment such as ATC. ERAM SWIM development has encountered several issues with bridging the gap between Ada and Java and the quickly evolving world of FOSS/COTS SW.
Performance issues and command and control issues have dominated our internal discussions and been the focus of much of our effort to achieve test readiness. Efficient data representation, baseline control (remember much of it is FOSS), and debugging have also received a lot of attention. We had a lot of prior experience with mixed languages having several hundred thousand lines of C and C++ and considered ourselves prepared. However, integrating with Java is completely unlike integrating with those others, and we have had to adapt across the board to this new challenge. My talk will focus on the challenges we have encountered, and the lessons we have learned about the strengths and weaknesses of the various languages and other technology elements we have used implementing ERAM SWIM.
Gene Expression Profiles of Estrogen Receptor–Positive and Estrogen Receptor–Negative Breast Cancers Are Detectable in Histologically Normal Breast Epithelium
Authors: Graham Kelly , Ge Xijin , de las Morenas Antonio , Tripathi Anusri , Rosenberg Carol L. 
Published: November 2010

Abstract
Purpose: Previously, we found that gene expression in histologically normal breast epithelium (NlEpi) from women at high breast cancer risk can resemble gene expression in NlEpi from cancer-containing breasts. Therefore, we hypothesized that gene expression characteristic of a cancer subtype might be seen in NlEpi of breasts containing that subtype.
Experimental Design: We examined gene expression in 46 cases of microdissected NlEpi from untreated women undergoing breast cancer surgery. From 30 age-matched cases [15 estrogen receptor (ER)+, 15 ER−] we used Affymetryix U133A arrays. From 16 independent cases (9 ER+, 7 ER−), we validated selected genes using quantitative real-time PCR (qPCR). We then compared gene expression between NlEpi and invasive breast cancer using four publicly available data sets.
Results: We identified 198 genes that are differentially expressed between NlEpi from breasts with ER+ (NlEpiER+) compared with ER− cancers (NlEpiER−). These include genes characteristic of ER+ and ER− cancers (e.g., ESR1, GATA3, and CX3CL1, FABP7). qPCR validated the microarray results in both the 30 original cases and the 16 independent cases. Gene expression in NlEpiER+ and NlEpiER− resembled gene expression in ER+ and ER− cancers, respectively: 25% to 53% of the genes or probes examined in four external data sets overlapped between NlEpi and the corresponding cancer subtype.
Conclusions: Gene expression differs in NlEpi of breasts containing ER+ compared with ER− breast cancers. These differences echo differences in ER+ and ER− invasive cancers. NlEpi gene expression may help elucidate subtype-specific risk signatures, identify early genomic events in cancer development, and locate targets for prevention and therapy. Clin Cancer Res; 17(2); 236–46. ©2010 AACR.
Corticosteroids and Outcome in Children Undergoing Congenital Heart Surgery
Authors: Pasquali Sara K. , Hall Matthew , Li Jennifer S. , Peterson Eric D. , Jaggers James , Lodge Andrew J. , Marino Bradley S. , Goodman Denise M. , Shah Samir S. 
Published: November 2010

Background—
Children undergoing congenital heart surgery often receive corticosteroids with the aim of reducing the inflammatory response after cardiopulmonary bypass; however, the value of this approach is unclear.

Methods and Results—
The Pediatric Health Information Systems Database was used to evaluate outcomes associated with corticosteroids in children (0 to 18 years of age) undergoing congenital heart surgery at 38 US centers from 2003 to 2008. Propensity scores were constructed to account for potential confounders: age, sex, race, prematurity, genetic syndrome, type of surgery (Risk Adjustment in Congenital Heart Surgery [RACHS-1] category), center, and center volume. Multivariable analysis, adjusting for propensity score and individual covariates, was performed to evaluate in-hospital mortality, postoperative length of stay, duration of ventilation, infection, and use of insulin. A total of 46 730 children were included; 54% received corticosteroids. In multivariable analysis, there was no difference in mortality among corticosteroid recipients and nonrecipients (odds ratio, 1.13; 95% confidence interval, 0.98 to 1.30). Corticosteroids were associated with longer length of stay (least square mean difference, 2.18 days; 95% confidence interval, 1.62 to 2.74 days), greater infection (odds ratio, 1.27; 95% confidence interval, 1.10 to 1.46), and greater use of insulin (odds ratio, 2.45; 95% confidence interval, 2.24 to 2.67). There was no difference in duration of ventilation. In analysis stratified by RACHS-1 category, no significant benefit was seen in any group, and the association of corticosteroids with increased morbidity was most prominent in RACHS-1 categories 1 through 3.

Conclusion—
In this observational analysis of children undergoing congenital heart surgery, we were unable to demonstrate a significant benefit associated with corticosteroids and found that corticosteroids may be associated with increased morbidity, particularly in lower-risk patients.
Silent Information Regulator 1 Protects the Heart From Ischemia/Reperfusion
Authors: Hsu Chiao-Po , Zhai Peiyong , Yamamoto Takanobu , Maejima Yasuhiro , Matsushima Shouji , Hariharan Nirmala , Shao Dan , Takagi Hiromitsu , Oka Shinichi , Sadoshima Junichi 
Published: November 2010

Background—
Silent information regulator 1 (Sirt1), a class III histone deacetylase, retards aging and protects the heart from oxidative stress. We here examined whether Sirt1 is protective against myocardial ischemia/reperfusion (I/R).

Methods and Results—

Protein and mRNA expression of Sirt1 is significantly reduced by I/R. Cardiac-specific Sirt1
−/−
mice exhibited a significant increase (44±5% versus 15±5%;
P
=0.01) in the size of myocardial infarction/area at risk. In transgenic mice with cardiac-specific overexpression of Sirt1, both myocardial infarction/area at risk (15±4% versus 36±8%;
P
=0.004) and terminal deoxynucleotidyl transferase dUTP nick end labeling–positive nuclei (4±3% versus 10±1%;
P
<0.003) were significantly reduced compared with nontransgenic mice. In Langendorff-perfused hearts, the functional recovery during reperfusion was significantly greater in transgenic mice with cardiac-specific overexpression of Sirt1 than in nontransgenic mice. Sirt1 positively regulates expression of prosurvival molecules, including manganese superoxide dismutase, thioredoxin-1, and Bcl-xL, whereas it negatively regulates the proapoptotic molecules Bax and cleaved caspase-3. The level of oxidative stress after I/R, as evaluated by anti-8-hydroxydeoxyguanosine staining, was negatively regulated by Sirt1. Sirt1 stimulates the transcriptional activity of FoxO1, which in turn plays an essential role in mediating Sirt1-induced upregulation of manganese superoxide dismutase and suppression of oxidative stress in cardiac myocytes. Sirt1 plays an important role in mediating I/R-induced increases in the nuclear localization of FoxO1 in vivo.

Conclusions—
These results suggest that Sirt1 protects the heart from I/R injury through upregulation of antioxidants and downregulation of proapoptotic molecules through activation of FoxO and decreases in oxidative stress.
Factors Associated With Pulseless Electric Activity Versus Ventricular Fibrillation
Authors: Teodorescu Carmen , Reinier Kyndaron , Dervan Celia , Uy-Evanado Audrey , Samara Mershed , Mariani Ronald , Gunson Karen , Jui Jonathan , Chugh Sumeet S. 
Published: November 2010

Background—
Corresponding with a continuing decline in the prevalence of sudden cardiac arrest cases presenting with ventricular fibrillation (VF), there has been a significant rise in the prevalence of pulseless electrical activity (PEA). Given significantly lower survival from PEA versus VF, we comprehensively investigated PEA correlates by incorporating first-responder data with lifetime clinical history information.

Methods and Results—

In the Portland, Ore, metropolitan area (population ≈1 million), cases of out-of-hospital sudden cardiac arrest who underwent attempted resuscitation were identified prospectively (2002–2007). Those presenting with PEA versus VF and asystole were compared with χ
2
tests, ANOVA, and logistic regression. A total of 1277 cases aged ≥18 years underwent resuscitation by first responders (mean age, 65±16 years; 67% male). Presenting arrhythmia was VF in 48%, PEA in 25%, and asystole/other in the remainder. Compared with VF cases, PEA cases were older (mean age, 68 versus 63 years;
P
=0.0002), more likely to be female (37% versus 26%;
P
=0.0008), and less likely to survive to hospital discharge (6% versus 25%;
P
<0.0001). A history of syncope was strongly associated with PEA (odds ratio, 2.6; confidence interval, 1.3 to 5.3) after adjustment for age, gender, response time, and arrest circumstances. Black race was also independently associated with PEA (odds ratio, 2.6; confidence interval, 1.3 to 5.4). Pulmonary disease and female gender were significant factors associated with PEA (
P
for interaction=0.04). In a subgroup analysis of resting ECGs (n=391), there were no differences in cardiac clinical history or prevalence of cardiac conduction system disease (PEA, 31.6% versus VF, 32.2%;
P
=0.48).

Conclusions—
PEA cases had a significantly higher prevalence of syncope in their lifetime, with other correlates, including black race, that were distinct from VF cases. Potential mechanistic links between syncope and future manifestation with PEA warrant further exploration.
Understanding Negative Impacts of Perceived Cognitive Load on Job Learning Effectiveness: A Social Capital Solution
Authors: Lin Chieh-Peng 
Published: November 2010

Objective: This study proposes a model explaining how social capital helps ease excessively required mental effort. Background: Although organizational researchers have studied both social capital and cognitive load, no prior research has critically examined the role of social capital in improving individuals’ mental load and effort and consequently enhancing job learning effectiveness. Method: This study surveys participants made up of professionals in Taiwan’s information technology industry. It measures the constructs with the use of 5-point Likert-type scale items modified from existing literature. The survey data were analyzed with the use of structural equation modeling. Results: Job learning effectiveness is negatively influenced by role ambiguity and role conflict. Time pressure has a positive influence on role ambiguity and role conflict. Although the relationship between task complexity and role ambiguity is insignificant, task complexity has a positive influence on role conflict. Because the relationship between network ties and role conflict is insignificant, trust has a negative influence on role conflict. Last, shared vision has a negative influence on role ambiguity. Conclusion: This study provides an example of how social capital can be applied as a useful remedy to ease the negative impact of perceived cognitive load on job learning effectiveness. Application: The negative relationship between shared vision and role ambiguity suggests that a shared vision helps in disseminating organizationally common goals and directions among employees to alleviate individuals’ mental efforts in dealing with the ambiguity of their job roles. A firm’s management team should take actions to decrease role conflict by strengthening trust among employees.
In Vivo Measurement of Humeral Elevation Angles and Exposure Using a Triaxial Accelerometer
Authors: Amasay Tal , Latteri Michael , Karduna Andrew R. 
Published: November 2010

Objective: The aim of this study was to measure the capability of a triaxial accelerometer (Virtual Corset) to collect humeral elevation angles and exposure parameters in a simulated occupational environment. Background: There is a need for an economical ambulatory device to estimate elevation angles and exposure parameters in occupational groups. Method: A magnetic tracking device was used to assess the ability of the Virtual Corset to evaluate humeral elevation angles and identify exposure parameters with in vivo dynamic conditions for 16 female dental hygienists. Results: Significant differences were found for the reaching task with the Virtual Corset, underestimating the means of the average humeral elevation angle by 10° and the means for the range of the humeral elevation by 4°. Furthermore, significant differences were found for the exposure parameters with the Virtual Corset, overestimating the jerk by 4% and underestimating the percentage time above 40° and 60° by 9% and 4%, respectively. However, the Virtual Corset was able to identify similar kinematics patterns and exposure data when compared with a magnetic tracking device. Conclusion: The outcomes of the study suggest that the Virtual Corset may be useful for data collection during a dental hygienist workday. Professions that have similar patterns of angular velocity and acceleration and humeral range of elevation as the dental hygienist flossing technique may benefit from the use of the Virtual Corset. Application: This study provides evidence that the Virtual Corset can be used to reconstruct humeral elevation angles and identify exposure parameters in some tasks of dental hygienists.
Autoimmune lymphoproliferative syndrome–like disease with somatic KRAS mutation
Authors: Takagi Masatoshi , Shinoda Kunihiro , Piao Jinhua , Mitsuiki Noriko , Takagi Mari , Matsuda Kazuyuki , Muramatsu Hideki , Doisaki Sayoko , Nagasawa Masayuki , Morio Tomohiro , Kasahara Yoshihito , Koike Kenichi , Kojima Seiji , Takao Akira , Mizutani Shuki 
Published: November 2010

Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is classically defined as a disease with defective FAS-mediated apoptosis (type I-III). Germline NRAS mutation was recently identified in type IV ALPS. We report 2 cases with ALPS-like disease with somatic KRAS mutation. Both cases were characterized by prominent autoimmune cytopenia and lymphoadenopathy/splenomegaly. These patients did not satisfy the diagnostic criteria for ALPS or juvenile myelomonocytic leukemia and are probably defined as a new disease entity of RAS-associated ALPS-like disease (RALD).
On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations
Authors: Sangaralingam Ajanthah , Susko Edward , Bryant David , Spencer Matthew 
Published: November 2010

Abstract

Background
Phylogenetic reconstruction methods based on gene content often place all the parasitic and endosymbiotic eubacteria (parasites for short) together in a clan. Many other lines of evidence point to this parasites clan being an artefact. This artefact could be a consequence of the methods used to construct ortholog databases (due to some unknown bias), the methods used to estimate the phylogeny, or both.
We test the idea that the parasites clan is an ortholog identification artefact by analyzing three different ortholog databases (COG, TRIBES, and OFAM), which were constructed using different methods, and are thus unlikely to share the same biases. In each case, we estimate a phylogeny using an improved version of the conditioned logdet distance method. If the parasites clan appears in trees from all three databases, it is unlikely to be an ortholog identification artefact.
Accelerated loss of a subset of gene families in parasites (a form of heterotachy) may contribute to the difficulty of estimating a phylogeny from gene content data. We test the idea that heterotachy is the underlying reason for the estimation of an artefactual parasites clan by applying two different mixture models (phylogenetic and non-phylogenetic), in combination with conditioned logdet. In these models, there are two categories of gene families, one of which has accelerated loss in parasites. Distances are estimated separately from each category by conditioned logdet. This should reduce the tendency for tree estimation methods to group the parasites together, if heterotachy is the underlying reason for estimation of the parasites clan.

Results
The parasites clan appears in conditioned logdet trees estimated from all three databases. This makes it less likely to be an artefact of database construction. The non-phylogenetic mixture model gives trees without a parasites clan. However, the phylogenetic mixture model still results in a tree with a parasites clan. Thus, it is not entirely clear whether heterotachy is the underlying reason for the estimation of a parasites clan. Simulation studies suggest that the phylogenetic mixture model approach may be unsuccessful because the model of gene family gain and loss it uses does not adequately describe the real data.

Conclusions
The most successful methods for estimating a reliable phylogenetic tree for parasitic and endosymbiotic eubacteria from gene content data are still ad-hoc approaches such as the SHOT distance method. however, the improved conditioned logdet method we developed here may be useful for non-parasites and can be accessed at http://www.liv.ac.uk/~cgrbios/cond_logdet.html