bluuebunny/crossref_metadata_2025_split huggingface dataset:
Myocardial Tissue Characterization Using Magnetic Resonance Noncontrast T1 Mapping in Hypertrophic and Dilated Cardiomyopathy
Authors: Dass Sairia , Suttie Joseph J. , Piechnik Stefan K. , Ferreira Vanessa M. , Holloway Cameron J. , Banerjee Rajarshi , Mahmod Masliza , Cochlin Lowri , Karamitsos Theodoros D. , Robson Matthew D. , Watkins Hugh , Neubauer Stefan 
Published: October 2012

Background—
Noncontrast magnetic resonance T1 mapping reflects a composite of both intra- and extracellular signal. We hypothesized that noncontrast T1 mapping can characterize the myocardium beyond that achieved by the well-established late gadolinium enhancement (LGE) technique (which detects focal fibrosis) in both hypertrophic (HCM) and dilated (DCM) cardiomyopathy, by detecting both diffuse and focal fibrosis.

Methods and Results—

Subjects underwent Cardiovascular Magnetic Resonance imaging at 3T (28 HCM, 18 DCM, and 12 normals). Matching short-axis slices were acquired for cine, T1 mapping, and LGE imaging (0.1 mmol/kg). Circumferential strain was measured in the midventricular slice, and
31
P magnetic resonance spectroscopy was acquired for the septum of the midventricular slice. Mean T1 relaxation time was increased in HCM and DCM (HCM 1209±28 ms, DCM 1225±42 ms, normal 1178±13 ms,
P
<0.05). There was a weak correlation between mean T1 and LGE (
r
=0.32,
P
<0.001). T1 values were higher in segments with LGE than in those without (HCM with LGE 1228±41 ms versus no LGE 1192±79 ms,
P
<0.01; DCM with LGE 1254±73 ms versus no LGE 1217±52 ms,
P
<0.01). However, in both HCM and DCM, even in segments unaffected by LGE, T1 values were significantly higher than normal (
P
<0.01). T1 values correlated with disease severity, being increased as wall thickness increased in HCM; conversely, in DCM, T1 values were highest in the thinnest myocardial segments. T1 values also correlated significantly with circumferential strain (
r
=0.42,
P
<0.01). Interestingly, this correlation remained statistically significant even for the slices without LGE (
r
=0.56,
P
=0.04). Finally, there was also a statistically significant negative correlation between T1 values and phosphocreatine/adenosine triphosphate ratios (
r
=−0.59,
P
<0.0001).

Conclusions—
In HCM and DCM, noncontrast T1 mapping detects underlying disease processes beyond those assessed by LGE in relatively low-risk individuals.
The Neural Correlates of Cognitive Control: Successful Remembering and Intentional Forgetting
Authors: Rizio Avery A. , Dennis Nancy A. 
Published: October 2012

Abstract
The ability to control how we process information by remembering that which is important and forgetting that which is irrelevant is essential to maintain accurate, up-to-date memories. As such, memory success is predicated on both successful intentional encoding and successful intentional forgetting. The current study used an item-method directed forgetting paradigm to elucidate the cognitive and neural processes that underlie both processes while also examining the relationship between them to understand how the two may work together. Results indicated that encoding-related processes in the left inferior PFC and medial-temporal lobe (MTL) contribute to subsequent memory success, whereas inhibitory processes in the right superior frontal gyrus and right inferior parietal lobe contribute to subsequent forgetting success. Furthermore, connectivity analyses found a negative correlation between activity in the right superior frontal cortex and activity in the left MTL during successful intentional forgetting but not during successful encoding, incidental forgetting, or incidental encoding. Results support the theory that intentional forgetting is mediated by inhibition-related activity in the right frontal cortex and the interaction of this activity with that of encoding-related activity in the MTL. Further support for this inhibitory-related account was found through a clear dissociation between intentional and incidental forgetting, such that intentional forgetting was associated with regions shown to support inhibition, whereas incidental forgetting was associated with regions supporting encoding.
Prediction of September–December Fire in New Caledonia (Southwestern Pacific) Using July Niño-4 Sea Surface Temperature Index
Authors: Moron Vincent , Barbero Renaud , Mangeas Morgan , Borgniet Laurent , Curt Thomas , Berti-Equille Laure 
Published: October 2012

AbstractAn empirical statistical scheme for predicting September–December fires in New Caledonia in the southwestern Pacific Ocean region using a cross-validated generalized linear model has been developed for the 2000–10 period. The predictor employs July sea surface temperatures (SST) recorded over the Niño-4 box (5°S–5°N, 160°–210°E), which are closely related to austral spring (September–November) rainfall anomalies across New Caledonia. The correlation between the logarithm of observed and simulated total burned areas across New Caledonia is 0.87. A decrease in the local-scale skill (median correlation between the log of observed and simulated total burned areas in a 20-km radius around a rain gauge = 0.46) around the main town (Nouméa) and its suburbs in the southwest of Grande Terre, and also in northern New Caledonia, could be associated either with a weaker climatic forcing from the Niño-4 SST index or a small-scale climatic forcing not linearly related to the El Niño–Southern Oscillation (ENSO) phenomenon. It is more likely that the decrease is tied to the influence of human-driven factors that blur the regional-scale climatic signal mostly associated with central Pacific ENSO events.
A Comparison of Tidal Conversion Parameterizations for Tidal Models
Authors: Green J. A. Mattias , Nycander Jonas 
Published: October 2012

Abstract
The conversion of barotropic to baroclinic tidal energy in the global abyssal ocean is calculated using three different formulations. The calculations are done both “offline,” that is, using externally given tidal currents to estimate the energy conversion, and “online,” that is, by using the formulations to parameterize linear wave drag in a prognostic tidal model. All three schemes produce globally integrated offline dissipation rates beneath 500-m depth of ~0.6–0.8 TW for the M2 constituent, but the spatial structures vary significantly between the parameterizations. Detailed investigations of the energy transfer in local areas confirm the global results: there are large differences between the schemes, although the horizontally integrated conversion rates are similar. The online simulations are evaluated by comparing the sea surface elevation with data from the TOPEX/Poseidon database, and the error is then significantly lower when using the parameterization provided by Nycander than with the other two parameterizations examined.
The Operational Generation of Continuous Winds in the Australian Region and Their Assimilation with 4DVAR
Authors: Le Marshall John , Seecamp Rolf , Xiao Yi , Gregory Paul , Jung Jim , Stienle Peter , Skinner Terry , Tingwell Chris , Le Tan 
Published: October 2012

Abstract
Atmospheric motion vectors (AMVs) have been generated continuously from Multifunctional Transport Satellite 1 Replacement (MTSAT-1R) radiance data (imagery) since 2005, and more recently from MTSAT-2, which are operated by the Japan Meteorological Agency (JMA). These are the primary geostationary meteorological satellites observing the western Pacific, Asia, and the Australian region. The vectors are used operationally, for analysis in the Darwin Regional Forecast Office. The near-continuous AMVs have been stringently error characterized and used in near-real-time trials to gauge their impact on operational regional numerical weather prediction (NWP), using four-dimensional variational data assimilation (4DVAR). The use of these locally generated hourly vectors (the only hourly AMV source in the region at the time) and 4DVAR has resulted in both improved temporal and spatial data coverage in the operational regional forecast domain. The beneficial impact of these data on the Bureau of Meteorology’s (Bureau’s) current operational system is described. After these trials, the hourly MTSAT AMVs were introduced into the Bureau’s National Meteorological and Oceanographic Centre’s (NMOC) operational NWP suite for use by the operational Australian Community Climate Earth System Simulator (ACCESS) regional and global models, ACCESS-R and ACCESS-G, respectively. Examples of their positive impact on both midlatitude and tropical cyclone forecasts are presented.
Composite Severity Indices Reflect Sleep Apnea Disease Burden More Comprehensively Than the Apnea‐Hypopnea Index
Authors: Balakrishnan Karthik , James Kathryn T. , Weaver Edward M. 
Published: October 2012

ObjectiveTo compare 2 composite indices of sleep apnea disease burden with the commonly used apnea‐hypopnea index with regard to baseline measurement of subjective and objective disease burden.Study DesignCross‐sectional study.SettingTertiary academic medical center sleep laboratory.Subjects and MethodsPatients with suspected diagnosis of sleep apnea undergoing first diagnostic polysomnography. Subjective data were collected via validated questionnaires; objective data were obtained by standardized physical examination, chart extraction, and polysomnography. Four subjective (patient‐reported) disease burden measures and 3 objective (anatomic and physiologic) disease burden measures were used for validation. Associations between composite indices or apnea‐hypopnea index and these 7 construct validation measures were compared using bootstrapped correlation coefficients.ResultsTwo hundred sixteen subjects were included in the final analysis. Both composite disease burden indices showed clinically important or nearly important associations with 3 of 4 subjective validation measures and all 3 objective validation measures, whereas the apnea‐hypopnea index was associated only with the objective validation measures.ConclusionComposite indices of sleep apnea disease burden may capture the breadth of baseline sleep apnea disease burden, particularly subjective disease burden, better than the apnea‐hypopnea index.
Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data
Authors: Sakellariou Argiris , Sanoudou Despina , Spyrou George 
Published: October 2012

Abstract

Background
A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list, there should be clusters of genes that share similar biological functions related to the investigated disease. Thus, instead of keeping N top ranked genes, it would be more appropriate to define and keep a number of gene cluster exemplars.

Results
We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We applied mAP-KL on real microarray data, as well as on simulated data, and compared its performance against 13 other feature selection approaches. Across a variety of diseases and number of samples, mAP-KL presents competitive classification results, particularly in neuromuscular diseases, where its overall AUC score was 0.91. Furthermore, mAP-KL generates concise yet biologically relevant and informative N-gene expression signatures, which can serve as a valuable tool for diagnostic and prognostic purposes, as well as a source of potential disease biomarkers in a broad range of diseases.

Conclusions
mAP-KL is a data-driven and classifier-independent hybrid feature selection method, which applies to any disease classification problem based on microarray data, regardless of the available samples. Combining multiple hypothesis testing and AP leads to subsets of genes, which classify unknown samples from both, small and large patient cohorts with high accuracy.
Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data
Authors: Sambo Francesco , Trifoglio Emanuele , Di Camillo Barbara , Toffolo Gianna M , Cobelli Claudio 
Published: October 2012

Abstract

Background
Multifactorial diseases arise from complex patterns of interaction between a set of genetic traits and the environment. To fully capture the genetic biomarkers that jointly explain the heritability component of a disease, thus, all SNPs from a genome-wide association study should be analyzed simultaneously.

Results
In this paper, we present Bag of Naïve Bayes (BoNB), an algorithm for genetic biomarker selection and subjects classification from the simultaneous analysis of genome-wide SNP data. BoNB is based on the Naïve Bayes classification framework, enriched by three main features: bootstrap aggregating of an ensemble of Naïve Bayes classifiers, a novel strategy for ranking and selecting the attributes used by each classifier in the ensemble and a permutation-based procedure for selecting significant biomarkers, based on their marginal utility in the classification process. BoNB is tested on the Wellcome Trust Case-Control study on Type 1 Diabetes and its performance is compared with the ones of both a standard Naïve Bayes algorithm and HyperLASSO, a penalized logistic regression algorithm from the state-of-the-art in simultaneous genome-wide data analysis.

Conclusions
The significantly higher classification accuracy obtained by BoNB, together with the significance of the biomarkers identified from the Type 1 Diabetes dataset, prove the effectiveness of BoNB as an algorithm for both classification and biomarker selection from genome-wide SNP data.

Availability
Source code of the BoNB algorithm is released under the GNU General Public Licence and is available at http://www.dei.unipd.it/~sambofra/bonb.html.
Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail
Authors: Frésard Laure , Leroux Sophie , Dehais Patrice , Servin Bertrand , Gilbert Hélène , Bouchez Olivier , Klopp Christophe , Cabau Cédric , Vignoles Florence , Feve Katia , Ricros Amélie , Gourichon David , Diot Christian , Richard Sabine , Leterrier Christine , Beaumont Catherine , Vignal Alain , Minvielle Francis , Pitel Frédérique 
Published: October 2012

Abstract

Background
As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome.

Results
The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene.

Conclusions
These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix.
Electrophysiological correlates of object-repetition effects: sLORETA imaging with 64-channel EEG and individual MRI
Authors: Kim Myung-Sun , Jang Kyoung-Mi , Che Huije , Kim Do-Won , Im Chang-Hwan 
Published: October 2012

AbstractBackgroundWe investigated the electrophysiological correlates of object-repetition effects using an object categorization task, standardized low-resolution electromagnetic tomography (sLORETA), and individual magnetic resonance imaging. Sixteen healthy adults participated, and a total of 396 line drawings of living and non-living objects were used as stimuli. Of these stimuli, 274 were presented only once, and 122 were repeated after one to five intervening pictures. Participants were asked to categorize the objects as living or non-living things by pressing one of two buttons.ResultsThe old/new effect (i.e., a faster response time and more positive potentials in response to repeated stimuli than to stimuli initially presented) was observed at 350-550 ms post-stimulus. The distributions of cortical sources for the old and new stimuli were very similar at 250-650 ms after stimulus-onset. Activation in the right middle occipital gyrus/cuneus, right fusiform gyrus, left superior temporal gyrus, and right inferior frontal gyrus was significantly reduced in response to old compared with new stimuli at 250-350, 350-450, 450-550, and 550-650 ms after stimulus-onset, respectively. Priming in response time was correlated with the electrophysiological priming at left parietal area and repetition suppression at left superior temporal gyrus in 450-550 ms.ConclusionsThese results suggest processing of repeated objects is facilitated by sharpening perceptual representation and by efficient detection or attentional control of repeated objects.
“The balancing act”— Licensed practical nurse experiences of falls and fall prevention: a qualitative study
Authors: Häggqvist Beatrice , Stenvall Michael , Fjellman-Wiklund Anncristine , Westerberg Kristina , Lundin-Olsson Lillemor 
Published: October 2012

Abstract

Background
Falls are common in old age and may have serious consequences. There are many strategies to predict and prevent falls from occurring in long-term care and hospitals. The aim of this study was to describe licensed practical nurse experiences of predicting and preventing further falls when working with patients who had experienced a fall-related fracture. Licensed practical nurses are the main caretakers that work most closely with the patients.

Methods
A qualitative study of focus groups interviews and field observations was done. 15 licensed practical nurses from a rehabilitation ward and an acute ward in a hospital in northern Sweden were interviewed. Content was analyzed using qualitative content analysis.

Results
The result of the licensed practical nurse thoughts and experiences about risk of falling and fall prevention work is represented in one theme, “the balancing act”. The theme includes three categories: “the right to decide”, “the constant watch”, and “the ongoing negotiation” as well as nine subcategories. The analysis showed similarities and differences between rehabilitation and acute wards. At both wards it was a core strategy in the licensed practical nurse work to always be ready and to pay attention to patients’ appearance and behavior. At the rehabilitation ward, it was an explicit working task to judge the patients’ risk of falling and to be active to prevent falls. At the acute ward, the words “risk of falling” were not used and fall prevention were not discussed; instead the licensed practical nurses used for example “dizzy and pale”. The results also indicated differences in components that facilitate workplace learning and knowledge transfer.

Conclusions
Differences between the wards are most probably rooted in organizational differences. When it is expected by the leadership, licensed practical nurses can express patient risk of falling, share their observations with others, and take actions to prevent falls. The climate and the structure of the ward are essential if licensed practical nurses are to be encouraged to routinely consider risk of falling and implement risk reduction strategies.
Associations of sex hormone-binding globulin and testosterone with diabetes among men and women (the Saku Diabetes study): a case control study
Authors: Goto Atsushi , Morita Akemi , Goto Maki , Sasaki Satoshi , Miyachi Motohiko , Aiba Naomi , Terauchi Yasuo , Noda Mitsuhiko , Watanabe Shaw ,   the Saku Cohort Study Group
Published: October 2012

Abstract

Background
Sex hormone-binding globulin (SHBG) levels and sex hormones have been implicated in the pathogenesis of type 2 diabetes and cardiovascular diseases. As fatty liver has been suggested to be a major determinant of SHBG levels, we examined whether the associations of SHBG and testosterone with diabetes were independent of fatty liver.

Methods
We conducted a case–control study that included 300 diabetes cases (215 men and 85 women) and 300 matched controls from the Saku cohort study. Diabetes was defined by either fasting plasma glucose levels ≥126 mg/dL, 2-h post-load glucose levels ≥200 mg/dL after a 75 g oral glucose tolerance test, or diabetes diagnosed by physicians. We fitted conditional logistic regression models to examine the associations between SHBG and total testosterone levels with diabetes by sex. To evaluate the impact of fatty liver, we used the fatty liver index (FLI), a validated measure derived from serum triglyceride levels, body mass index (BMI), waist circumference, and γ-glutamyltransferase levels.

Results
After adjusting for age, family history of diabetes, smoking, physical activity, BMI, and FLI, SHBG levels were inversely associated with diabetes among women (odds ratio [OR] comparing the highest with the lowest quartiles, 0.13 [95% confidence interval {CI}, 0.02–0.96]), but not among men. Similar patterns were observed in a subgroup analysis restricted to postmenopausal women"(OR, 0.12 [95% CI, 0.01–1.17]). In contrast, testosterone levels were inversely associated with diabetes among men (OR, 0.45 [95% CI, 0.23–0.89]), but not among women.

Conclusions
Our findings suggest that SHBG in women and testosterone in men may be inversely associated with diabetes.