Use Of Datasets Research Articles

New Spectral Templates of Galaxies for Multi Color Classification

AbstractObservations in the Chandra Deep Field South (CDFS) have provided us with a useful set of data in the optical (COMBO-17), near-infrared (GOODS JHK), and mid-infrared (GOODS IRAC bands 1,2) wavelength regimes to test and improve a new spectral galaxy template library, designed to operate in the rest-frame wavelength range between 0.1 and 5 microns. In this range the stellar continuum and emission lines from HII regions dominate the Spectral Energy Distribution (SED) of galaxies. The new library is based on a self-consistent two-burst model, that has been developed in order to reproduce the star formation histories of different types of galaxies more accurately than single-burst histories and thus provides a better match to real galaxy spectra, as well as more reliable mass-to-light ratios. The spectral library is built by using a population synthesis code (PEGASE) assuming a Kroupa (2003) initial mass function. An old burst of exponentially decaying star formation with an initial metallicity of 0.1 solar is followed by a very recent (60 Myr old) second burst in order to reproduce the spectra of actively star forming blue galaxies. In addition, the templates include dust extinction of various strengths. For the multi-color classification the spectral library is red-shifted between z + 0 and z + 2.5 and converted into the 21 colors which have been observed by COMBO-17 plus its near- and mid-infrared extensions provided by the public GOODS data.

A high level interface to SCOP and ASTRAL implemented in Python

BackgroundBenchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources.ResultsWe have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL.ConclusionThe modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

Prediction of Small‐Molecule Binding to Cytochrome P450 3A4: Flexible Docking Combined with Multidimensional QSAR

The inhibition of cytochrome P450 3A4 (CYP3A4) by small molecules is a major mechanism associated with undesired drug-drug interactions, which are responsible for a substantial number of late-stage failures in the pharmaceutical drug-development process. For a quantitative prediction of associated pharmacokinetic parameters, a computational model was developed that allows prediction of the inhibitory potential of 48 structurally diverse molecules. Based on the experimental structure of CYP3A4, possible binding modes were first sampled by using automated docking (Yeti software) taking protein flexibility into account. The results are consistent with both X-ray crystallographic data and data from metabolic studies. Next, an ensemble of energetically favorable orientations was composed into a 4D dataset for use as input for a multidimensional QSAR technique (Raptor software). A dual-shell binding-site model that allows an explicit induced fit was then generated by using hydrophobicity scoring and hydrogen-bond propensity. The simulation reached a cross-validated r2 value of 0.825 and a predictive r2 value of 0.659. On average, the predicted binding affinity of the training ligands deviates by a factor of 2.7 from the experiment; those of the test set deviate by a factor of 3.8 in Ki.

Outcome assessment: recommendations for daily practice.

The choice of instruments for the assessment of outcome in spinal surgery is bewildering. For day-to-day practice, however, consideration of the purpose for which information is required allows construction of simple strategies for data collection. Recommendations are made for short and convenient data sets for use in personal audit, clinical governance, benchmarking, patient selection and business planning. No simple data set can measure in detail every aspect of practice, but use of these recommendations will provide information that will be of great value to the spinal surgeon and ultimately to his patients.

THE NATIONAL BASIN DELINEATION PROJECT

The National Basin Delineation Project (NBDP) was undertaken by the National Severe Storms Laboratory to define flash-flood-scale basin boundaries for the country in support of the National Weather Service (NWS) Flash Flood Monitoring and Prediction (FFMP) system. FFMP-averaged basin rainfall calculations allow NWS forecasters to monitor precipitation in flash-flood-scale basins, improving their ability to make accurate and timely flash-flood-warning decisions. The NBDP was accomplished through a partnership with the U.S. Geological Survey Earth Resources Observation Systems (EROS) Data Center (EDC). The one-arc-second (approximately 30 m)-resolution digital terrain data in the EDC's National Elevation Dataset provided the basis for derivation of the following digital maps using a geographic information system: 1) a grid of hydrologically conditioned elevation values (all grid cells have a defined flow direction), 2) a grid of flow direction indicating which of eight directions water will travel based on slope, 3) a grid of flow accumulation containing a count of the number of upstream grid cells contributing flow to each grid cell, 4) synthetic streamlines derived from the flow accumulation grid, and 5) flash-flood-scale basin boundaries. Special techniques were applied in coastal areas and closed basins (basins with no outflow) to ensure the accuracy of derived basins and streams. Codifying each basin with a unique identifier and including hydrologic connectivity information produced a versatile, seamless dataset for use in FFMP and other national applications.

The Labor Market Experience of Persons With Disabilities

In the context of legislation to promote employment of persons with disabilities (Americans With Disabilities Act), trend data analysis results are showing employment rates that are moving in a downward rather than an upward direction. This review of two recent books on the labor market involvement and experience of persons with disability demonstrates this puzzle and points out some of the problems that may be contributing to those findings. The definition and measurement of disability in the data sets in use seem to be a key factor in the confusion, and both books contribute interesting material to address this aspect. Although The Labor Market Experience of Workers With Disability is well written with impressive analyses, it is in the traditional economics perspective, and while it introduces useful state policy information, it does not provide an answer to the puzzle. The Decline in Employment of People With a Disability uses an edited format to good effect, providing the reader with many creative approaches to the issues even if the puzzle pieces are not ultimately forced to fit.

Mechanical and fracture properties for predicting cracking in semi‐sweet biscuits

SummaryMechanical and fracture properties required for predicting crack development in semi‐sweet (‘rich tea’) biscuits have been experimentally determined. Pilot‐scale biscuits of different fat concentrations were prepared and studied with commercial biscuits at different moisture contents. Bending modulus, fracture stress and strain were measured using three‐point bending tests. All biscuit types showed considerable dependence on moisture content over a range of 4–12%. Young's modulus and failure stress showed a uniform decrease and failure strain showed an increase with increasing moisture content. For pilot‐scale biscuits of different fat concentrations, an increase in fat level caused a decrease in modulus and failure stress values; however, the failure strains were very similar for all the fat types. The testing of the samples with top surface up and top surface down revealed that the sample orientation does not affect the measured parameters. The measured parameters also did not show any directional dependence within the plane, thus assuring that the assumption of an isotropic material would be valid for modelling. The mechanical and fracture properties measured in this study will serve as a very useful set of data to predict the stress state and cracking of the checked biscuits.

PVT Properties and Viscosity Correlations for Gulf of Mexico Oils

Summary New empirical pressure/volume/temperature (PVT) correlations for Gulf of Mexico (GOM) oils have been developed as a function of commonly available field data. Correlations have been developed for the following: Bubblepoint pressure. Solution gas/oil ratio (GOR) at bubblepoint pressure. Oil formation volume factor (FVF) at bubblepoint pressure. Undersaturated isothermal oil compressibility. Dead-oil viscosity. Saturated-oil viscosity. Undersaturated-oil viscosity. For the development of correlations, we have covered a wide range of data. More than 100 PVT reports from the GOM have been used in the development of correlations. Two of the published correlations (those of Standing1 and Petrosky and Farshad2) were tested with our GOM data set. Proposed correlations of this study predicted the PVT properties of GOM oils better than the correlations published in the literature, even when the coefficients of the published correlations are tuned. Using the correlations of this study, we have written a simple program that can generate PVT data sets for use in reservoir simulation. Laboratory-measured differential-liberation data for two different oil samples were also compared against our empirically generated differential-liberation data.

Croplands in West Africa: A Geographically Explicit Dataset for Use in Models

West Africa has experienced increases in cultivated lands over the last 50 yr, as well as increasing rates of deforestation. Croplands have expanded to meet the food demands of a rapidly increasing population. Nevertheless, this region remains one of the most food-deprived places on the planet. While the food demands of an increasing population have to be met through cropland expansion or intensification on existing lands, it is important to evaluate the long-term environmental consequences of the ensuing land-use change. Spatially explicit datasets of land use/land cover for the region would be valuable for assessing the environmental consequences of land-cover change, as well as the implications for food security. A review of the currently available moderate-resolution satellite-derived land-cover datasets for the region finds them to be of poor quality. A high-resolution satellite-derived cropland dataset for the Sahel is available; however, extending this to the entire West African region is an expensive proposition and will require a massive undertaking. Therefore, in this study, a new regional dataset of the spatial distribution of croplands for West Africa was created by synthesizing subnational cropland area statistics, a spatial map of population density, and

Sensitivity- and Uncertainty-Based Criticality Safety Validation Techniques

The theoretical basis for the application of sensitivity and uncertainty (S/U) analysis methods to the validation of benchmark data sets for use in criticality safety applications is developed. Sensitivity analyses produce energy-dependent sensitivity coefficients that give the relative change in the system multiplication factor keff value as a function of relative changes in the cross-section data by isotope, reaction, and energy. Integral indices are then developed that utilize the sensitivity information to quantify similarities between pairs of systems, typically a benchmark experiment and design system. Uncertainty analyses provide an estimate of the uncertainties in the calculated values of the system keff due to cross-section uncertainties, as well as correlation in the keff uncertainties between systems. These uncertainty correlations provide an additional measure of system similarity. The use of the similarity measures from both S/U analyses in the formal determination of areas of applicability for benchmark experiments is developed. Furthermore, the use of these similarity measures as a trending parameter for the estimation of the computational bias and uncertainty is explored. The S/U analysis results, along with the calculated and measured keff values and estimates of uncertainties in the measurements, were used in this work to demonstrate application of the generalized linear-least-squares methodology (GLLSM) to data validation for criticality safety studies.An illustrative example is used to demonstrate the application of these S/U analysis procedures to actual criticality safety problems. Computational biases, uncertainties, and the upper subcritical limit for the example applications are determined with the new methods and compared to those obtained through traditional criticality safety analysis validation techniques.The GLLSM procedure is also applied to determine cutoff values for the similarity indices such that applicability of a benchmark experiment to a criticality safety design system can be assured. Additionally, the GLLSM procedure is used to determine how many applicable benchmark experiments exceeding a certain degree of similarity are necessary for an accurate assessment of the computational bias.

Review of Tropospheric Bomb 14C Data for Carbon Cycle Modeling and Age Calibration Purposes

Comprehensive published radiocarbon data from selected atmospheric records, tree rings, and recent organic matter were analyzed and grouped into 4 different zones (three for the Northern Hemisphere and one for the whole Southern Hemisphere). These 14C data for the summer season of each hemisphere were employed to construct zonal, hemispheric, and global data sets for use in regional and global carbon model calculations including calibrating and comparing carbon cycle models. In addition, extended monthly atmospheric 14C data sets for 4 different zones were compiled for age calibration purposes. This is the first time these data sets were constructed to facilitate the dating of recent organic material using the bomb 14C curves. The distribution of bomb 14C reflects the major zones of atmospheric circulation.

A pseudo-state sensitivity study on hydrogenic ions

An electron-impact excitation study of light hydrogenic ions has been carried outto quantify the effects of coupling to high bound/continuum states utilizing theR-matrixwith pseudo-states method. As the ionization stage increases, the neglect of loss offlux into high-lying excitation/ionization channels impacts less upon excitationbetween the bound terms explicitly included within our close coupling expansion.C5+is used as our benchmark study. The differences in Maxwell averaged collision strengths betweena standard R-matrixcalculation and those of a similar pseudo-state model across a range oftemperatures shall be our criteria for judging differences.We carried out calculations for He+, Li2+, Be3+, B4+, C5+, O7+ andNe9+so as to provide excitation data amongst terms up ton = 5.Pseudo-state calculations were carried out for the first five ions, following a similarmodel to earlier neutral hydrogen work, whilst non-pseudo-state calculationssufficed for the remaining two ions. The results of these seven calculations willenhance existing excitation data sets for use in the modelling of controlled nuclearfusion plasma experiments.

Phosphorus characterization and correlation with properties of selected benchmark soils of the United States

Twenty-one benchmark soils of the United States, including surface and subsurface horizons and satellites, from the Water Erosion Prediction Project (WEPP) were analyzed for phosphorus (P), using methods that include total (TP), water-soluble (WP), Bray 1 (BP), Mehlich No. 3 (MP), Olsen (OLP), New Zealand P Retention (NZP), organic (OP), anion exchange resin (AEP), and acid oxalate (Po). Objectives of this study were to determine relationships among soil P test values and other soil properties. Knowledge and understanding of these relationships are important to researchers when evaluating soil P data sets for use in predictive models for agronomic, soil genesis, or environmental purposes. Important relationships that were developed, using simple or multiple linear regression models, among P methods and other soil properties, e.g., organic carbon (OC), total N (TN), dithionite-citrate extractable iron and aluminum (Fed, Ald), and clay are as follows:

The Internet, Images and Archaeology: ideas for interactive tutorials

This article reports on a small-scale study into how the Internet might be used for tutorial teaching in archaeology, which was undertaken by the authors as part of their project work for a Teaching Diploma at Oxford University. A workshop was developed to explore how the Internet and image-rich resources online could be exploited within the curriculum, and in turn what changes might need to be made to that curriculum in order to embed a critical, reflective approach to student learning. The practicalities of using the computer in the classroom were also investigated, in terms of available facilities, staff and student training, and the impact of computers on staff-student dynamics. Condron was also involved in a more extensive study of the use of C&IT (communication and information technologies) in small-group teaching across a range of subjects (the ASTER project), to which the Oxford case studies have contributed. There is concern that students are not making the best use of all available evidence, including fieldwork reports in libraries, excavations, and visits to local museums and heritage centres. New undergraduates may have little experience of archaeological practice and its interdisciplinary nature, and often find the sheer volume of data overwhelming. Yet archaeology is a highly visual subject, and images are essential to the reconstructions arising from the complex interpretation of what is a partial record of past activities. The range of this imagery is vast, for example, 'objective' site photography, schematic plans and diagrams, and interpretative illustrations. Digital media provide new opportunities for 3D and interactive imagery. These offer many interpretative possibilities for debate, and discussions over the authenticity of reconstructions can often be fierce. In addition, it may be difficult to find the original data on which these reconstructions were based. This, together with the many assumptions and methods that underlie these reconstructions, create a complex maze through which students need to be guided, in order to evaluate and critique archaeological literature. Students also need the essential skills of object recognition and the ability to visualise landscapes, settlements and more. But students may not be encouraged to develop these skills in their everyday reading, and may have problems linking what they learn in practicals (including fieldwork) to the rest of their course. The Internet offers access to a vast range of multimedia material that can be incorporated into teaching, supplementing local resources in the library and museum. Online resources duplicate those available in print: fieldwork reports; monument and landscape surveys; artefact and ecofact collections; museum guides and more. They can also be interactive: searchable catalogues; dynamic maps; images that allow the user to zoom in and pan around; models of buildings one can fly through, over, under; objects that can be virtually picked up and moved around. This flexibility enables users to engage with and explore material in ways not available in printed works. The diversity of online resources and their visual wealth offer great opportunities for education: 1.Students can be exposed to points of view and evidence from around the world that may not be accessible in any other way. These can be useful in initiating debates on evidence and reconstruction. 2.Tutors and students can quickly find and compile datasets for use in their work. 3.As the Web is not a refereed collection, users need to develop their critical faculties to make the best use of this material. 4.Online resources can be used to develop problem-based and student-centred approaches to learning, by offering students the flexibility to choose the topics and formats of assessed coursework. However, there are potential hazards in shifting to virtual as opposed to real worlds: 1.Students may assume that the virtual is an adequate substitute to practical experiences in the lab, field and museum. 2.Including IT into teaching invariably adds to staff workload, and any changes need to be embedded into the curriculum if they are to have a lasting impact on students' approaches to archaeology.

Psychotherapy quality control: the statistical generation of expected recovery curves for integration into an early warning system

AbstractThe results of the development of expected recovery curves for an empirically driven patient profiling system are presented. Patients undergoing a course of psychotherapy (N = 11 492) repeatedly took the Outcome Questionnaire‐45 (OQ‐45). Scores across all patients were combined into an aggregate dataset for use in generating expected recovery curves based on severity of symptoms at intake. SAS PROC MIXED was used to create a mixed linear model of recovery curves based on OQ‐45 scores across sessions and the log transformation of session number. Mean estimates were established for each session from one to 20. Tolerance intervals were then created around each estimated mean score. Expected recovery curves were combined with tolerance intervals to create an early warning system capable of identifying patients whose slow progress suggests that they might be expected to have a negative therapy outcome (terminate treatment prior to obtaining a clinically significant benefit). Current efforts to establish a systematic quality improvement procedure using these curves are discussed. Charts of expected recovery values are plotted, and a straightforward system of patient profiling, early identification of treatment failures, and feedback to clinicians is described. Copyright © 2001 John Wiley & Sons, Ltd.

Determining Urban Storm Water BMP Effectiveness

The goal of this U.S. EPA-funded cooperative research program with the ASCE is to develop a more useful set of data on the effectiveness of storm water best management practices (BMPs) used to reduce pollutant discharges from urban development. BMP monitoring data gathered at a particular site should not only be useful for that site, but also need to be useful for comparing the effectiveness of similar and different types of BMPs at other locations. Most BMP effectiveness studies in the past have provided data that is difficult, if not impossible, to use in comparing BMP design effectiveness and in the selection among individual BMP types to meet desired goals. This paper describes some of the comparability problems encountered between different BMP effectiveness studies. Also discussed are considerations that affect data transferability, such as methods used for determining efficiency and statistical significance. It outlines the efforts used to establish and analyze the currently available data and prop...

A Cooperative Atmosphere–Surface Exchange Study (CASES) Dataset for Analyzing and Parameterizing the Effects of Land Surface Heterogeneity on Area-Averaged Surface Heat Fluxes

Abstract A multiscale dataset that includes atmospheric, surface, and subsurface observations obtained from an observation network covering a region that has a scale order comparable to mesoscale and general circulation models is described and analyzed. The dataset is half-hourly time series of forcing and flux response data developed from the one-month Cooperative Atmosphere–Surface Exchange Study (CASES-97) experiment, located in the Walnut Watershed near Wichita, Kansas. The horizontal complexity of this dataset was analyzed by looking at the sensible and latent heat flux response of station data from the three main land surface types of winter wheat, grass/pastureland, and bare soil/sparse vegetation. The variability in the heat flux response at and among the different sites points to the need for a spatially distributed, time-varying atmospheric-forcing dataset for use in land surface modeling experiments. Such a dataset at horizontal spacings of 1, 5, and 10 km was developed from the station data an...

TECHNICAL NOTE: A SIMPLIFIED TECHNIQUE FOR ESTIMATING LAKE EVAPORATION FOR LONG?TERM STOCHASTIC WATER BALANCE MODELS

A model has been developed to estimate lake evaporation in Oklahoma based on a modified version of theBlaneyCriddle method for computing monthly evapotranspiration. It was developed as a result of the need for a simpletechnique to estimate lake evaporation in a longterm stochastic water balance model. Through this technique, the averagemonthly evaporation was accurately estimated to 4% for all months in each county in Oklahoma. This equation is not meantto replace other methods of estimating lake evaporation when more data are available and a precise monthtomonth estimateof evaporation is desired. It does, however, allow for a simplified technique of generating a realistic lake evaporation dataset for use in longterm stochastic water balance models.

The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial of the National Cancer Institute: History, organization, and status

The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is enrolling 148,000 men and women ages 55–74 at ten sreening centers nationwide with balanced randomization to intervention and control arms. For prostate cancer, men receive a digital rectal examination and a blood test for prostate-specific antigen. For lung cancer, men and women receive a posteroanterior view chest X-ray. For colorectal cancer, men and women undergo a 60-cm flexible sigmoidoscopy. For ovarian cancer, women receive a blood test for the CA125 tumor marker and transvaginal ultrasound. Members of the control arm continue with their usual care. Follow-up in both groups will continue for at least 13 years from randomization to assess health status and cause of death. The primary endpoint is mortality from the four PLCO cancers, which accounts for about 53% of all cancer deaths in men and 41% of cancer deaths in women in the United States each year. Blood specimens are collected from screened participants, buccal cell DNA from controls, and histology slides from cases; these are maintained in a biorepository. Participants complete a baseline questionnaire (covering health status and risk factors) and a dietary questionnaire. More than 12,000 participants were enrolled in the pilot phase (concluded in September 1994). Changes in the eligibility criteria followed. As of April 2000, enrollment exceeded 144,500. Data are scanned into designated on-site computers for uploading by participant identification number to the coordinating center for quality checks, archival storage, and preparation of analysis datasets for use by the National Cancer Institute (NCI). Scientific direction is provided by NCI scientists, trial investigators, external consultants, and an independent data safety and monitoring board. Performance and data quality are monitored via data edits, site visits, random record audits, and teleconferences. The PLCO trial is formally endorsed by the American Cancer Society and has been ranked by the American Urological Association as one of the most important prostate cancer studies being conducted. Special efforts to enroll black participants are cosponsored by the U.S. Centers for Disease Control and Prevention.

The Development of Standard Economic Datasets for use in the Economic Evaluation of Medicines

Regulatory imperatives and competitive forces have led pharmaceutical companies to focus on extending the scope of their randomized controlled trials (RCTs) to collect data to address economic as well as safety and efficacy questions. To guide researchers, a significant literature exists on various methodological aspects of conducting economic evaluations within an RCT framework. Little has been published, however, about data handling issues surrounding the management of the economic data collection effort. Thus, the objective of this paper is to present an overview of a project conducted in order to tackle various aspects of the economic data management process with a view to improving the efficiency of study conduct. The project outputs include case report forms (CRF), guidelines for CRF completion, and templates for producing statistical analysis plans and study protocols. Directions for further research are highlighted.