bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using statistical measures for automated comparison of in‐beam PET data
Authors: Kuess Peter , Birkfellner Wolfgang , Enghardt Wolfgang , Helmbrecht Stephan , Fiedler Fine , Georg Dietmar 
Published: September 2012

Purpose:Positron emission tomography (PET) is considered to be the state of the art technique to monitor particle therapyin vivo. To evaluate the beam delivery the measured PET image is compared to a predicted β+‐distribution. Nowadays the range assessment is performed by a group of experts via visual inspection. This procedure is rather time consuming and requires well trained personnel. In this study an approach is presented to support human decisions in an automated and objective way.Methods:The automated comparison presented uses statistical measures, namely, Pearsonˈs correlation coefficient (PCC), to detect ion beam range deviations. The study is based on 12 in‐beam PET patient data sets recorded at GSI and 70 artificial beam range modifications per data set. The range modifications were 0, 4, 6, and 10 mm water equivalent path length (WEPL) in positive and negative beam directions. The reference image to calculate the PCC was both an unmodified simulation of the activity distribution (Test 1) and a measured in‐beam PET image (Test 2). Based on the PCCs sensitivity and specificity were calculated. Additionally the difference between modified and unmodified data sets was investigated using the Wilcoxon rank sum test.Results:In Test 1 a sensitivity and specificity over 90% was reached for detecting modifications of ±10 and ±6 mm WEPL. Regarding Test 2 a sensitivity and specificity above 80% was obtained for modifications of ±10 and −6 mm WEPL. The limitation of the method was around 4 mm WEPL.Conclusions:The results demonstrate that the automated comparison using PCC provides similar results in terms of sensitivity and specificity compared to visual inspections of in‐beam PET data. Hence the method presented in this study is a promising and effective approach to improve the efficiency in the clinical workflow in terms of particle therapy monitoring by means of PET.
Revisiting the combining synchronization technique
Authors: Fatourou Panagiota , Kallimanis Nikolaos D. 
Published: September 2012

Fine-grain thread synchronization has been proved, in several cases, to be outperformed by efficient implementations of the combining technique where a single thread, called the
combiner
, holding a coarse-grain lock, serves, in addition to its own synchronization request, active requests announced by other threads while they are waiting by performing some form of spinning. Efficient implementations of this technique significantly reduce the cost of synchronization, so in many cases they exhibit much better performance than the most efficient finely synchronized algorithms.

In this paper, we revisit the combining technique with the goal to discover where its real performance power resides and whether or how ensuring some desired properties (e.g., fairness in serving requests) would impact performance. We do so by presenting two new implementations of this technique; the first (CC-Synch) addresses systems that support coherent caches, whereas the second (DSM-Synch) works better in cacheless NUMA machines. In comparison to previous such implementations, the new implementations (1) provide bounds on the number of remote memory references (RMRs) that they perform, (2) support a stronger notion of fairness, and (3) use simpler and less basic primitives than previous approaches. In all our experiments, the new implementations outperform by far all previous state-of-the-art combining-based and fine-grain synchronization algorithms. Our experimental analysis sheds light to the questions we aimed to answer.
Several modern multi-core systems organize the cores into clusters and provide fast communication within the same cluster and much slower communication across clusters. We present an hierarchical version of CC-Synch, called H-Synch which exploits the hierarchical communication nature of such systems to achieve better performance. Experiments show that H-Synch significantly outper forms previous state-of-the-art hierarchical approaches.
We provide new implementations of common shared data structures (like stacks and queues) based on CC-Synch, DSM-Synch and H-Synch. Our experiments show that these implementations outperform by far all previous (fine-grain or combined-based) implementations of shared stacks and queues.
Observations of an Inertial Peak in the Intrinsic Wind Spectrum Shifted by Rotation in the Antarctic Vortex
Authors: Gelinas L. J. , Walterscheid R. L. , Mechoso C. R. , Schubert G. 
Published: September 2012

Abstract
Spectral analyses of time series of zonal winds derived from locations of balloons drifting in the Southern Hemisphere polar vortex during the Vorcore campaign of the Stratéole program reveal a peak with a frequency near 0.10 h−1, more than 25% higher than the inertial frequency at locations along the trajectories. Using balloon data and values of relative vorticity evaluated from the Modern Era Retrospective-Analyses for Research and Applications (MERRA), the authors find that the spectral peak near 0.10 h−1 can be interpreted as being due to inertial waves propagating inside the Antarctic polar vortex. In support of this claim, the authors examine the way in which the low-frequency part of the gravity wave spectrum sampled by the balloons is shifted because of effects of the background flow vorticity. Locally, the background flow can be expressed as the sum of solid-body rotation and shear. This study demonstrates that while pure solid-body rotation gives an effective inertial frequency equal to the absolute vorticity, the latter gives an effective inertial frequency that varies, depending on the direction of wave propagation, between limits defined by the absolute vorticity plus or minus half of the background relative vorticity.
Circulation Response to Eurasian versus North American Anomalous Snow Scenarios in the Northern Hemisphere with an AGCM Coupled to a Slab Ocean Model
Authors: Henderson Gina R. , Leathers Daniel J. , Hanson Brian 
Published: September 2012

Abstract
The difference between snow-covered and snow-free conditions is the most climatically significant natural seasonal change the land surface can experience. Most GCM studies investigating snow–atmosphere interactions have focused on impacts of Eurasian snow anomalies caused by the magnitude of snow mass, while North American snow has been shown to have a weaker relationship with downstream climate. Experiment design of recent snow–atmosphere interactions studies has been limited to atmosphere-only models, with sea surface temperature (SST) and sea ice extent represented as boundary conditions. The authors explore the circulation response to anomalous snow scenarios, for both North America and Eurasia, using a slab ocean model. Surface response include significant SST cooling directly downstream of each individual forcing region in addition to upstream centers of remote cooling under maximum snow conditions. Atmospheric response to anomalous snow conditions is consistent through multiple levels in the lower troposphere under maximum snow conditions throughout much of the midlatitudes in both experiments during early winter. Areas of strengthened midtropospheric eddy kinetic energy correlate well with steep geopotential height gradient differences and increased zonal wind at 250 hPa over the western Pacific. Both experiments show similar atmospheric response pathways; however, circulation response to maximum Eurasian snow is focused downstream in early winter, whereas upstream response is particularly evident from the North American experiment. This paper focuses on differences as a result of Eurasian versus North American snow forcing in atmospheric circulation response using an AGCM with a slab ocean model.
ENSO-Like and ENSO-Induced Tropical Pacific Decadal Variability in CGCMs
Authors: Choi Jung , An Soon-Il , Yeh Sang-Wook , Yu Jin-Yi 
Published: September 2012

Abstract
Outputs from coupled general circulation models (CGCMs) are used in examining tropical Pacific decadal variability (TPDV) and their relationships with El Niño–Southern Oscillation (ENSO). Herein TPDV is classified as either ENSO-induced TPDV (EIT) or ENSO-like TPDV (ELT), based on their correlations with a decadal modulation index of ENSO amplitude and spatial pattern. EIT is identified by the leading EOF mode of the low-pass filtered equatorial subsurface temperature anomalies and is highly correlated with the decadal ENSO modulation index. This mode is characterized by an east–west dipole structure along the equator. ELT is usually defined by the first EOF mode of subsurface temperature, of which the spatial structure is similar to ENSO. Generally, this mode is insignificantly correlated with the decadal modulation of ENSO. EIT closely interacts with the residuals induced by ENSO asymmetries, both of which show similar spatial structures. On the other hand, ELT is controlled by slowly varying ocean adjustments analogous to a recharge oscillator of ENSO. Both types of TPDV have similar spectral peaks on a decadal-to-interdecadal time scale. Interestingly, the variances of both types of TPDV depend on the strength of connection between El Niño–La Niña residuals and EIT, such that the strong two-way feedback between them enhances EIT and reduces ELT. The strength of the two-way feedback is also related to ENSO variability. The flavors of El Niño–La Niña with respect to changes in the tropical Pacific mean state tend to be well simulated when ENSO variability is larger in CGCMs. As a result, stronger ENSO variability leads to intensified interactive feedback between ENSO residuals and enhanced EIT in CGCMs.
On the Dynamical Causes of Variability in the Rain-Shadow Effect: A Case Study of the Washington Cascades
Authors: Siler Nicholas , Roe Gerard , Durran Dale 
Published: September 2012

AbstractWashington State’s Cascade Mountains exhibit a strong orographic rain shadow, with much wetter western slopes than eastern slopes due to prevailing westerly flow during the winter storm season. There is significant interannual variability in the magnitude of this rain-shadow effect, however, which has important consequences for water resource management, especially where water is a critically limited resource east of the crest. Here the influence of the large-scale circulation on the Cascade rain shadow is investigated using observations from the Snowfall Telemetry (SNOTEL) monitoring network, supplemented by stream gauge measurements. Two orthogonal indices are introduced as a basis set for representing variability in wintertime Cascade precipitation. First, the total precipitation index is a measure of regionwide precipitation and explains the majority of the variance in wintertime precipitation everywhere. Second, the rain-shadow index is a measure of the east–west precipitation gradient. It explains up to 31% of the variance west and east of the crest. A significant correlation is found between the winter-mean rain shadow and ENSO, with weak (strong) rain shadows associated with El Niño (La Niña). The analysis is supported by streamflow data from eastern and western watersheds. A preliminary review of individual storms suggests that the strongest rain shadows are associated with warm-sector events, while the weakest rain shadows occur during warm-frontal passages. This is consistent with known changes in storm tracks associated with ENSO, and a variety of mechanisms likely contribute.
Modeling coding-sequence evolution within the context of residue solvent accessibility
Authors: Scherrer Michael P , Meyer Austin G , Wilke Claus O 
Published: September 2012

AbstractBackgroundProtein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues).ResultsHere, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratioωthat varies linearly with RSA provides a better model fit than an RSA-independentωor anωthat is estimated separately in individual RSA bins. We further show that the branch lengthtand the transition-transverion ratioκalso vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship betweenωand RSA, and gene expression level affects both the intercept and the slope.ConclusionsStructure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship betweenωand RSA implies that genes are better characterized by theirωslope and intercept than by just their meanω.
Transcriptome classification reveals molecular subtypes in psoriasis
Authors: Ainali Chrysanthi , Valeyev Najl , Perera Gayathri , Williams Andrew , Gudjonsson Johann E , Ouzounis Christos A , Nestle Frank O , Tsoka Sophia 
Published: September 2012

Abstract

Background
Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phenotypes, such as plaque psoriasis, are well defined, it is currently unclear whether there are molecular subtypes that might impact on prognosis or treatment outcomes.

Results
We present a pipeline for patient stratification through a comprehensive analysis of gene expression in paired lesional and non-lesional psoriatic tissue samples, compared with controls, to establish differences in RNA expression patterns across all tissue types. Ensembles of decision tree predictors were employed to cluster psoriatic samples on the basis of gene expression patterns and reveal gene expression signatures that best discriminate molecular disease subtypes. This multi-stage procedure was applied to several published psoriasis studies and a comparison of gene expression patterns across datasets was performed.

Conclusion
Overall, classification of psoriasis gene expression patterns revealed distinct molecular sub-groups within the clinical phenotype of plaque psoriasis. Enrichment for TGFb and ErbB signaling pathways, noted in one of the two psoriasis subgroups, suggested that this group may be more amenable to therapies targeting these pathways. Our study highlights the potential biological relevance of using ensemble decision tree predictors to determine molecular disease subtypes, in what may initially appear to be a homogenous clinical group. The R code used in this paper is available upon request.
A trans-disciplinary approach to the evaluation of social determinants of health in a hispanic population
Authors: Dulin Michael F , Tapp Hazel , Smith Heather A , de Hernandez Brisa Urquieta , Coffman Maren J , Ludden Tom , Sorensen Janni , Furuseth Owen J 
Published: September 2012

AbstractBackgroundIndividual and community health are adversely impacted by disparities in health outcomes among disadvantaged and vulnerable populations. Understanding the underlying causes for variations in health outcomes is an essential step towards developing effective interventions to ameliorate inequalities and subsequently improve overall community health. Working at the neighborhood scale, this study examines multiple social determinates that can cause health disparities including low neighborhood wealth, weak social networks, inadequate public infrastructure, the presence of hazardous materials in or near a neighborhood, and the lack of access to primary care services. The goal of this research is to develop innovative and replicable strategies to improve community health in disadvantaged communities such as newly arrived Hispanic immigrants.Methods/designThis project is taking place within a primary care practice-based research network (PBRN) using key principles of community-based participatory research (CBPR). Associations between social determinants and rates of hospitalizations, emergency department (ED) use, and ED use for primary care treatable or preventable conditions are being examined. Geospatial models are in development using both hospital and community level data to identify local areas where interventions to improve disparities would have the greatest impact. The developed associations between social determinants and health outcomes as well as the geospatial models will be validated using community surveys and qualitative methods. A rapidly growing and underserved Hispanic immigrant population will be the target of an intervention informed by the research process to impact utilization of primary care services and designed, deployed, and evaluated using the geospatial tools and qualitative research findings. The purpose of this intervention will be to reduce health disparities by improving access to, and utilization of, primary care and preventative services.DiscussionThe results of this study will demonstrate the importance of several novel approaches to ameliorating health disparities, including the use of CBPR, the effectiveness of community-based interventions to influence health outcomes by leveraging social networks, and the importance of primary care access in ameliorating health disparities.
Oral health conditions and frailty in Mexican community-dwelling elderly: a cross sectional analysis
Authors: Castrejón-Pérez Roberto Carlos , Borges-Yáñez S Aída , Gutiérrez-Robledo Luis M , Ávila-Funes J Alberto 
Published: September 2012

Abstract

Background
Oral health is an important component of general well-being for the elderly. Oral health-related problems include loss of teeth, nonfunctional removable dental prostheses, lesions of the oral mucosa, periodontitis, and root caries. They affect food selection, speaking ability, mastication, social relations, and quality of life. Frailty is a geriatric syndrome that confers vulnerability to negative health-related outcomes. The association between oral health and frailty has not been explored thoroughly. This study sought to identify associations between the presence of some oral health conditions, and frailty status among Mexican community-dwelling elderly.

Methods
Analysis of baseline data of the Mexican Study of Nutritional and Psychosocial Markers of Frailty, a cohort study carried out in a representative sample of people aged 70 and older residing in one district of Mexico City. Frailty was defined as the presence of three or more of the following five components: weight loss, exhaustion, slowness, weakness, and low physical activity. Oral health variables included self-perception of oral health compared with others of the same age; utilization of dental services during the last year, number of teeth, dental condition (edentate, partially edentate, or completely dentate), utilization and functionality of removable partial or complete dentures, severe periodontitis, self-reported chewing problems and xerostomia. Covariates included were gender, age, years of education, cognitive performance, smoking status, recent falls, hospitalization, number of drugs, and comorbidity. The association between frailty and dental variables was determined performing a multivariate logistic regression analysis. Final models were adjusted by socio-demographic and health factors

Results
Of the 838 participants examined, 699 had the information needed to establish the criteria for diagnosis of frailty. Those who had a higher probability of being frail included women (OR = 1.9), those who reported myocardial infarction (OR = 3.8), urinary incontinence (OR = 2.7), those who rated their oral health worse than others (OR = 3.2), and those who did not use dental services (OR = 2.1). For each additional year of age and each additional drug consumed, the probability of being frail increased 10% and 30%, respectively.

Conclusions
Utilization of dental services and self-perception of oral health were associated with a higher probability of being frail.
Personality of outpatients with malignant tumors: a cross-sectional study
Authors: Wang Zhuo , Sakakibara Toshihiko , Kasai Yuichi 
Published: September 2012

Abstract

Background
There have been scarce large-scale studies investigating the personality of patients with malignant tumors. The purpose of this study is to determine the characteristic personality in malignant tumors outpatients.

Methods
Three thousand and three among 5013 consecutive outpatients who consented to answer the Japanese Maudsley Personality Inventory questionnaires were divided into two groups. 603 outpatients diagnosed with malignant tumors (M group) and the other 2400 outpatients (non-M group) were enrolled in this study. We determined three scores such as introversion/extroversion (E-score), neuroticism (N-score), and lie detection (L-score). All data were used to compare the two groups.

Results
Average E-score was slightly higher, and average N-score was slightly lower in M group than that in non-M group, and no significant differences between the two groups. However, the average L-score in M group was significant higher than that in non-M group (p < 0.01).

Conclusion
Outpatients with malignant tumors showed a significantly higher L-score on MPI when compared with patients with non-malignant tumors. These results stress the importance of taking the mentality of patients with cancer into consideration when conducting treatment and care.
Clustering of energy balance-related behaviors in 5-year-old children: Lifestyle patterns and their longitudinal association with weight status development in early childhood
Authors: Gubbels Jessica S , Kremers Stef PJ , Stafleu Annette , Goldbohm R Alexandra , de Vries Nanne K , Thijs Carel 
Published: September 2012

Abstract

Background
This study identified lifestyle patterns by examining the clustering of eating routines (e.g. eating together as a family, having the television on during meals, duration of meals) and various activity-related behaviors (i.e. physical activity (PA) and sedentary screen-based behavior) in 5-year-old children, as well as the longitudinal association of these patterns with weight status (BMI and overweight) development up to age 8.

Methods
Data originated from the KOALA Birth Cohort Study (N = 2074 at age 5). Principal component analysis (PCA) was used to identify lifestyle patterns. Backward regression analyses were used to examine the association of lifestyle patterns with parent and child background characteristics, as well as the longitudinal associations between the patterns and weight status development.

Results
Four lifestyle patterns emerged from the PCA: a ‘Television–Snacking’ pattern, a ‘Sports–Computer’ pattern, a ‘Traditional Family’ pattern, and a “Fast’ Food’ pattern. Child gender and parental educational level, working hours and body mass index were significantly associated with the scores for the patterns. The Television–Snacking pattern was positively associated with BMI (standardized regression coefficient β = 0.05; p < 0.05), and children with this pattern showed a positive tendency toward being overweight at age 8 (Odds ratio (OR) = 1.27, p = 0.06). In addition, the Sports–Computer pattern was significantly positively associated with an increased risk of becoming overweight at age 7 (OR = 1.28, p < 0.05).

Conclusions
The current study showed the added value of including eating routines in cross-behavioral clustering analyses. The findings indicate that future interventions to prevent childhood overweight should address eating routines and activity/inactivity simultaneously, using the synergy between clustered behaviors (e.g. between television viewing and snacking).