bluuebunny/crossref_metadata_2025_split huggingface dataset:
De-Aliasing of Large-Scale High-Frequency Barotropic Signals from Satellite Altimetry in the Japan/East Sea
Authors: Xu Yongsheng , Watts D. Randolph , Park Jae-Hun 
Published: February 2008

Abstract
In the Japan/East Sea, energetic high-frequency large-scale barotropic motions are shown to lead to large aliasing errors in satellite altimetry observations. The combined aliasing from several neighboring and crossing tracks produces artificial mesoscale signals in altimeter-mapped products, significantly changing the map interpretation. The alias can be well suppressed by subtracting the large-scale barotropic motions observed by bottom pressure sensors. By using coastal tide gauge data in the Japan/East Sea, about 78% of the alias source variance can be removed, which offers an alternative way to suppress the alias for other time intervals without bottom pressure measurements.
Some Remarks on the Reliability of Categorical Probability Forecasts
Authors: Bröcker Jochen 
Published: February 2008

Abstract
Studies on forecast evaluation often rely on estimating limiting observed frequencies conditioned on specific forecast probabilities (the reliability diagram or calibration function). Obviously, statistical estimates of the calibration function are based on only limited amounts of data and therefore contain residual errors. Although errors and variations of calibration function estimates have been studied previously, either they are often assumed to be small or unimportant, or they are ignored altogether. It is demonstrated how these errors can be described in terms of bias and variance, two concepts well known in the statistics literature. Bias and variance adversely affect estimates of the reliability and sharpness terms of the Brier score, recalibration of forecasts, and the assessment of forecast reliability through reliability diagram plots. Ways to communicate and appreciate these errors are presented. It is argued that these errors can become quite substantial if individual sample points have too large influence on the estimate, which can be avoided by using regularization techniques. As an illustration, it is discussed how to choose an appropriate bin size in the binning and counting method, and an appropriate bandwidth parameter for kernel estimates.
An Observational Study of Environmental Dynamical Control of Tropical Cyclone Intensity in the Atlantic
Authors: Zeng Zhihua , Chen Lianshou , Wang Yuqing 
Published: February 2008

Abstract
An attempt has been made to extend the analysis of environmental dynamical control of tropical cyclone (TC) intensity recently performed for the western North Pacific to the North Atlantic. The results show that both the vertical shear and translational speed have negative effects on TC intensity, which is consistent with previous findings for other basins. It shows that few TCs intensified when they moved faster than 15 m s−1. The threshold vertical shear of 20 m s−1—defined as the difference of total winds between 200 and 850 hPa averaged within 5° latitude around the TC center—is found above which few TCs intensified and below which most TCs could reach their lifetime peak intensity. The average intensity of total TCs in the Atlantic is a bit smaller than that in the western North Pacific. The SST-determined empirical maximum potential intensity (EMPI) for a TC for 1981–2003 in this study is slightly higher than that found for 1962–92 by DeMaria and Kaplan in the Atlantic, however.
To be consistent with the theoretical TC MPI, a new EMPI has been constructed, which includes the effect of thermodynamic efficiency. This new EMPI marginally improves the estimation of real TC maximum intensity because the thermodynamic efficiency is largely determined by SST. To include the environmental dynamical control of TC intensity, a dynamical efficiency has been introduced, which is inversely proportional to the combined amplitude of the vertical shear and translational speed. With this dynamical efficiency, an empirical maximum intensity (EMI) for Atlantic TCs has been constructed. This EMI includes not only the positive contribution by SST but also the effects of both thermodynamic and dynamical efficiencies, and it provides more accurate estimations of TC maximum intensity. Furthermore, the formulation of the new EMI explains the observed behavior of TC maximum intensity by thermodynamic and dynamical controls in a transparent and easy-to-interpret manner.
Reproducible and Irreproducible Components in Ensemble Simulations with a Regional Climate Model
Authors: Separovic Leo , de Elía Ramon , Laprise René 
Published: February 2008

Abstract
High-resolution limited-area models (LAMs) have been widely employed to downscale coarse-resolution climate simulations or objective analyses. The growing evidence that LAM climate statistics can be sensitive to initial conditions suggests that a deterministic verification of LAM solutions in terms of finescale atmospheric features might be misguided. In this study a 20-member ensemble of LAM integrations with perturbed initial conditions, driven by NCEP–NCAR reanalyses, is conducted for a summer season over a midlatitude domain. Ensemble simulations allow for the separation of the downscaled information in two parts: a unique, reproducible component associated with lateral-boundary and surface forcing, and an irreproducible component associated with internal variability. The partition in the reproducible and irreproducible components and their seasonal statistics is examined as a function of horizontal length scale, geographical position within the domain, height, and weather episodes during the season. The scale analysis of time-dependent model variables shows that, at scales smaller than a few hundred kilometers, the irreproducible component dominates, on average, the model solution, implying that the downscaled information at these scales is mainly in stochastic form. The constraint exerted by the surface forcing on the internal variability is weak. For seasonal averages, the reproducible component dominates at all scales, although for precipitation the reproducible and irreproducible components are of the same order of magnitude at scales smaller than 150 km. These results imply a need for a probabilistic approach to LAM climate simulations and their verification, especially for shorter integration times, from months to seasons.
Rapid Sampling of Severe Storms by the National Weather Radar Testbed Phased Array Radar
Authors: Heinselman Pamela L. , Priegnitz David L. , Manross Kevin L. , Smith Travis M. , Adams Richard W. 
Published: February 2008

Abstract
A key advantage of the National Weather Radar Testbed Phased Array Radar (PAR) is the capability to adaptively scan storms at higher temporal resolution than is possible with the Weather Surveillance Radar-1988 Doppler (WSR-88D): 1 min or less versus 4.1 min, respectively. High temporal resolution volumetric radar data are a necessity for rapid identification and confirmation of weather phenomena that can develop within minutes. The purpose of this paper is to demonstrate the PAR’s ability to collect rapid-scan volumetric data that provide more detailed depictions of quickly evolving storm structures than the WSR-88D. Scientific advantages of higher temporal resolution PAR data are examined for three convective storms that occurred during the spring and summer of 2006, including a reintensifying supercell, a microburst, and a hailstorm. The analysis of the reintensifying supercell (58-s updates) illustrates the capability to diagnose the detailed evolution of developing and/or intensifying areas of 1) low-altitude divergence and rotation and 2) rotation through the depth of the storm. The fuller sampling of the microburst’s storm life cycle (34-s updates) depicts precursors to the strong surface outflow that are essentially indiscernible in the WSR-88D data. Furthermore, the 34-s scans provide a more precise sampling of peak outflow. The more frequent sampling of the hailstorm (26-s updates) illustrates the opportunity to analyze storm structures indicative of rapid intensification, the development of hail aloft, and the onset of the downdraft near the surface.
Physical limitations and perceived quality of care among family medicine patients
Authors: Rohrer James E , Wilkinson John M , Barnes Darryl E , Adamson Steven C 
Published: February 2008

Objective: To assess how physical limitations relate to patient satisfaction with the quality of medical care among family medicine patients, after adjustment for self-rated overall health and other patient characteristics. Design: A telephone survey of family medicine patients, linked with information extracted from medical records. Setting: A large family medicine department in Rochester, Minnesota. Subjects: Patient ratings of quality were linked to medical records for 674 adult patients. Results: Adjusting for self-rated overall health status and other confounders using multiple logistic regression analysis revealed that having physical limitations was inversely and independently related to excellent perceived quality (adjusted odds ratio = 0.56, P= 0.035). Conclusions: In our sample of family medicine patients, people with physical limitations experience a disparity in perceived quality of care.
Assessing clinically meaningful change following a programme for managing chronic pain
Authors: Fisher Keren 
Published: February 2008

Objectives: (1) To identify criteria for clinically meaningful change scores in commonly used measures of pain and related disability, using Goal Attainment Scaling as an external indicator of success. (2) To investigate the chances of achieving these scores following a pain management programme versus remaining on the waiting list. Design: Participants were assessed on entry to waiting list, on admission and at follow-up from the pain management programme. Three groups of Goal Attainment Scaling scores (-1.0, +1) were created from final Goal Attainment Scaling achievements. Mean scores on other measures were analysed in relation to Goal Attainment Scaling score groups by ANOVA. Differences in numbers achieving clinically meaningful changes when on the pain management programme or waiting list were compared. Subjects: Chronic musculoskeletal pain participants (N = 73) attending a rehabilitation centre, mean age (range) 44.8 (24—70) years, mean age (range) 44.8 (24—70), mean pain duration 7.7 (1—32) years. Intervention: Three-week (15-day) pain management programme based on cognitive behavioural principles. Measures: McGill Pain Questionnaire, 0—10 Pain Intensity Numerical Rating Scale (NRS), Oswestry Disability Questionnaire (ODQ), General Health Questionnaire (GHQ), 5 minute walk, 1 minute sit/stand, 1 minute stair-climbing, and Goal Attainment Scaling (GAS). Results: Mean change scores differed significantly for three GAS groups and were highest in the most successful (+1) group. These scores were used to define clinically meaningful changes on the NRS (-3), ODQ (-12), walk (+87) and stairs (+14). Significantly more participants on the pain management programme achieved these scores than those on the waiting list. Conclusion: Using GAS as a criterion of patient-perceived improvement enabled identification of clinically meaningful changes on some other common measures. These successfully differentiated achievement between patients on the pain management programme and those on the waiting list.
Long-term benefits of exercising on quality of life and fatigue in multiple sclerosis patients with mild disability: a pilot study
Authors: McCullagh Ruth , Fitzgerald Anthony P , Murphy Raymond P , Cooke Grace 
Published: February 2008

Objective: To determine if exercise benefits patients with multiple sclerosis.Design: Randomized controlled trial.Settings: Participants exercised at home and also attended exercise classes held in a hospital physiotherapy gym.Subjects: Thirty patients, diagnosed and independently mobile, were recruited in the Dublin area.Intervention: For three months, classes were held twice-weekly and participants exercised independently once-weekly. The control group was monitored monthly and management remained unchanged.Measurements: Measurements were taken at baseline, three and six months. The Modified Fatigue Impact Scale (MFIS), Multiple Sclerosis Impact Scale-29 (MSIS-29) and Functional Assessment of Multiple Sclerosis (FAMS) were used to measure fatigue and quality of life (QOL). Heart rate (HR) and the Borg's Rating of Perceived Exertion (RPE) were recorded during an incremental exercise test. The change from baseline scores between groups was compared using the Mann—Whitney U-test.Results: Twenty-four participants completed the programme (n = 12 in each group). Based on the change in scores at three months, the exercise group had significantly greater improvements in exercise capacity (HR: —14 [-18.5, -2.5] versus 0.5 [-4, 5.5], P= 0.009), QOL (FAMS: 23 [9.5, 42.5] versus -3.5 [-16, 5], P=0.006) and fatigue (MFIS: -13 [-20, -3] versus 1 [-4, 4.5], P=0.02). At six months, the difference in change scores remained significant for FAMS (19 [14, 31] versus -4.5 [-25, 8], P=0.002) and MFIS (-8.5 [-19.5, -1] versus 0.5 [-2.5, 6.5], P=0.02) only.Conclusions: A three-month exercise programme improved participants' exercise capacity, QOL and fatigue, with the improvements in QOL and fatigue lasting beyond the programme.
An exploratory study of two measures of free-living physical activity for people with multiple sclerosis
Authors: Klassen Laura , Schachter Candice , Scudds Rhonda 
Published: February 2008

Objective: To examine the ability of two measures of physical activity (tri-axial accelerometer and activity diary) to discriminate among groups of inactive, moderately active and active individuals with multiple sclerosis and to explore the relationship between these two measures. Design: Exploratory, descriptive study. Subjects: Thirty individuals with multiple sclerosis and nine controls. Protocol: Individuals with multiple sclerosis were recruited to inactive, moderately active and active groups as defined by Adjusted Activity Scores from the Human Activity Profile. Control participants were recruited to an active group. Free-living physical activity was recorded over four consecutive days. Main measures: A TriTrac RT3 accelerometer and a self-report physical activity diary were used to measure activity. Results: Thirty-six participants completed data collection. For the participants with multiple sclerosis, both the accelerometer (P = 0.004) and the diary (P = 0.006) detected significant differences between inactive and active groups. The accelerometer also detected a significant difference between moderately active and active groups (P = 0.04). In contrast, the diary detected a significant difference between inactive and moderately active groups (P = 0.05). Accelerometer and diary scores were significantly correlated (r = 0.59). Accelerometer scores were significantly correlated with neurological status (rs = -0.64). Conclusions: Both measures readily differentiated least active from most active groups. The accelerometer also differentiated moderately active from active groups, suggesting suitability for use in detecting change in more active client groups, while the diary differentiated inactive from moderately active groups, suggesting suitability for use in detecting change in less active groups.
Surrogate endpoints for overall survival in advanced colorectal cancer: a clinician's perspective
Authors: Piedbois Pascal , Miller Croswell Jennifer 
Published: February 2008

Surrogate endpoints in oncology research and practice have garnered increasing attention over the past two decades. This activity has largely been driven by the promise surrogate endpoints appear to hold: the potential to get new therapies to seriously ill patients more rapidly. However, uncertainties abound. Even agreeing upon a definition of a “valid” surrogate endpoint has not been a straightforward exercise; this article begins by highlighting differences in how this term has been previously captured and applied, as well as laying out the basic criteria essential for its application in advanced colorectal cancer. Ideally, these elements include (but are not limited to) ease of measurement, rapid indication of treatment effect, and, most importantly, reliable and consistent prediction of the true impact of a treatment on the ultimate outcome of interest: overall survival. The strengths and weaknesses of current potential surrogate endpoints in advanced colorectal cancer, including performance status, carcinoembryonic antigen plasma level, overall response rate, time to progression, and disease-free survival, are each considered in turn. Finally, limitations of surrogate endpoints in the clinical setting, including challenges in extrapolation to new therapies, and the incomplete provision of information about potential adverse effects, are discussed. Work remains to be done between physicians and statisticians to bridge the gap between that which is statistically demonstrable and that which will be clinically useful. The term `surrogate endpoint' was virtually unknown by most oncologists 15 years ago. A search in PubMed [http://www.ncbi.nlm.nih.gov] based on the words `surrogate and cancer' shows that more than 2000 papers were published in medical journals in the last 20 years, with a dramatic increase of interest in the last five years. Interestingly, the same trend is observed when the words `surrogate and heart' are entered into PubMed, suggesting that the issue of surrogate endpoints goes beyond the field of oncology, although the frequency of discussion varies (Figure 1; note different y-axis scales for oncology and cardiology). The goal of the present paper is to discuss the main issues surrounding surrogate endpoints from a clinician's point of view, using as an example surrogate endpoints of overall survival (OS) in advanced colorectal cancer (ACC).
PDTD: a web-accessible protein database for drug target identification
Authors: Gao Zhenting , Li Honglin , Zhang Hailei , Liu Xiaofeng , Kang Ling , Luo Xiaomin , Zhu Weiliang , Chen Kaixian , Wang Xicheng , Jiang Hualiang 
Published: February 2008

Abstract

Background
Target identification is important for modern drug discovery. With the advances in the development of molecular docking, potential binding proteins may be discovered by docking a small molecule to a repository of proteins with three-dimensional (3D) structures. To complete this task, a reverse docking program and a drug target database with 3D structures are necessary. To this end, we have developed a web server tool, TarFisDock (Tar get Fis hing Dock ing) http://www.dddc.ac.cn/tarfisdock, which has been used widely by others. Recently, we have constructed a protein target database, P otential D rug T arget D atabase (PDTD), and have integrated PDTD with TarFisDock. This combination aims to assist target identification and validation.

Description
PDTD is a web-accessible protein database for in silico target identification. It currently contains >1100 protein entries with 3D structures presented in the Protein Data Bank. The data are extracted from the literatures and several online databases such as TTD, DrugBank and Thomson Pharma. The database covers diverse information of >830 known or potential drug targets, including protein and active sites structures in both PDB and mol2 formats, related diseases, biological functions as well as associated regulating (signaling) pathways. Each target is categorized by both nosology and biochemical function. PDTD supports keyword search function, such as PDB ID, target name, and disease name. Data set generated by PDTD can be viewed with the plug-in of molecular visualization tools and also can be downloaded freely. Remarkably, PDTD is specially designed for target identification. In conjunction with TarFisDock, PDTD can be used to identify binding proteins for small molecules. The results can be downloaded in the form of mol2 file with the binding pose of the probe compound and a list of potential binding targets according to their ranking scores.

Conclusion
PDTD serves as a comprehensive and unique repository of drug targets. Integrated with TarFisDock, PDTD is a useful resource to identify binding proteins for active compounds or existing drugs. Its potential applications include in silico drug target identification, virtual screening, and the discovery of the secondary effects of an old drug (i.e. new pharmacological usage) or an existing target (i.e. new pharmacological or toxic relevance), thus it may be a valuable platform for the pharmaceutical researchers. PDTD is available online at http://www.dddc.ac.cn/pdtd/.
Evolutionary Pareto-optimization of stably folding peptides
Authors: Gronwald Wolfram , Hohm Tim , Hoffmann Daniel 
Published: February 2008

Abstract

Background
As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the question whether there may be more such peptides that are unknown as yet. These molecules could be helpful in basic research and medicine.

Results
As a method to explore the space of conformationally stable peptides, we have developed an evolutionary algorithm that allows optimization of sequences with respect to several criteria simultaneously, for instance stability, accessibility of arbitrary parts of the peptide, etc. In a proof-of-concept experiment we have perturbed the sequence of the peptide Villin Headpiece, known to be stable in vitro. Starting from the perturbed sequence we applied our algorithm to optimize peptide stability and accessibility of a loop. Unexpectedly, two clusters of sequences were generated in this way that, according to our criteria, should form structures with higher stability than the wild-type. The structures in one of the clusters possess a fold that markedly differs from the native fold of Villin Headpiece. One of the mutants predicted to be stable was selected for synthesis, its molecular 3D-structure was characterized by nuclear magnetic resonance spectroscopy, and its stability was measured by circular dichroism. Predicted structure and stability were in good agreement with experiment. Eight other sequences and structures, including five with a non-native fold are provided as bona fide predictions.

Conclusion
The results suggest that much more conformationally stable peptides may exist than are known so far, and that small fold classes could comprise well-separated sub-folds.