Home About us Contact
|
Home About us Contact | ||
|
|
||
Large-scale Assessment (large-scale + assessment)
Selected AbstractsInvestigating the Effectiveness of Equating Designs for Constructed-Response Tests in Large-Scale AssessmentsJOURNAL OF EDUCATIONAL MEASUREMENT, Issue 2 2010Sooyeon Kim Using data from a large-scale exam, in this study we compared various designs for equating constructed-response (CR) tests to determine which design was most effective in producing equivalent scores across the two tests to be equated. In the context of classical equating methods, four linking designs were examined: (a) an anchor set containing common CR items, (b) an anchor set incorporating common CR items rescored, (c) an external multiple-choice (MC) anchor test, and (d) an equivalent groups design incorporating rescored CR items (no anchor test). The use of CR items without rescoring resulted in much larger bias than the other designs. The use of an external MC anchor resulted in the next largest bias. The use of a rescored CR anchor and the equivalent groups design led to similar levels of equating error. [source] Comparisons among Designs for Equating Mixed-Format Tests in Large-Scale AssessmentsJOURNAL OF EDUCATIONAL MEASUREMENT, Issue 1 2010Sooyeon Kim In this study we examined variations of the nonequivalent groups equating design for tests containing both multiple-choice (MC) and constructed-response (CR) items to determine which design was most effective in producing equivalent scores across the two tests to be equated. Using data from a large-scale exam, this study investigated the use of anchor CR item rescoring (known as trend scoring) in the context of classical equating methods. Four linking designs were examined: an anchor with only MC items, a mixed-format anchor test containing both MC and CR items; a mixed-format anchor test incorporating common CR item rescoring; and an equivalent groups (EG) design with CR item rescoring, thereby avoiding the need for an anchor test. Designs using either MC items alone or a mixed anchor without CR item rescoring resulted in much larger bias than the other two designs. The EG design with trend scoring resulted in the smallest bias, leading to the smallest root mean squared error value. [source] Dynameomics: Large-scale assessment of native protein flexibilityPROTEIN SCIENCE, Issue 12 2008Noah C. Benson Abstract Structure is only the first step in understanding the interactions and functions of proteins. In this paper, we explore the flexibility of proteins across a broad database of over 250 solvated protein molecular dynamics simulations in water for an aggregate simulation time of ,6 ,s. These simulations are from our Dynameomics project, and these proteins represent approximately 75% of all known protein structures. We employ principal component analysis of the atomic coordinates over time to determine the primary axis and magnitude of the flexibility of each atom in a simulation. This technique gives us both a database of flexibility for many protein fold families and a compact visual representation of a particular protein's native-state conformational space, neither of which are available using experimental methods alone. These tools allow us to better understand the nature of protein motion and to describe its relationship to other structural and dynamical characteristics. In addition to reporting general properties of protein flexibility and detailing many dynamic motifs, we characterize the relationship between protein native-state flexibility and early events in thermal unfolding and show that flexibility predicts how a protein will begin to unfold. We provide evidence that fold families have conserved flexibility patterns, and family members who deviate from the conserved patterns have very low sequence identity. Finally, we examine novel aspects of highly inflexible loops that are as important to structural integrity as conventional secondary structure. These loops, which are difficult if not impossible to locate without dynamic data, may constitute new structural motifs. [source] Microsatellite variation and population structure in a declining Australian Hylid Litoria aureaMOLECULAR ECOLOGY, Issue 7 2004Emma L. Burns Abstract The green and golden bell frog (Litoria aurea) was once a common Australian Hylid. Today, many populations are small and fragmented as a result of dramatic declines in distribution and abundance. We undertook a large-scale assessment of genetic structure and diversity in L. aurea using four species-specific microsatellite markers. Twenty-one locations were sampled from throughout the species range covering 1000 km of the east coast of Australia. Levels of allelic diversity and heterozygosity were high (uncorrected mean alleles/locus and HE were 4.8,8.8 and 0.43,0.8, respectively) compared to other amphibian species and significant differences among sampled sites were recorded. Despite recent population declines, no sites displayed a genetic signature indicative of a population bottleneck. Significant genetic structuring (overall FST 0.172) was detected throughout the species range, but was relatively low compared to previous amphibian studies employing microsatellites. In addition we found that some areas sampled within continuous habitat showed evidence of weak genetic structuring (data subset FST 0.034). We conclude that maintaining areas of continuous habitat is critical to the conservation of the species and argue that population recovery and/or persistence in all areas sampled is possible if appropriate protection and management are afforded. [source] LiveBench-1: Continuous benchmarking of protein structure prediction serversPROTEIN SCIENCE, Issue 2 2001Janusz M. Bujnicki Abstract We present a novel, continuous approach aimed at the large-scale assessment of the performance of available fold-recognition servers. Six popular servers were investigated: PDB-Blast, FFAS, T98-lib, GenTHREADER, 3D-PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one-half of the targets, but significantly accurate sequence-structure alignments were produced for only one-third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets,where standard methods such as PSI-BLAST fail,the most sensitive fold-recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence-structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An "ideally combined consensus" prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join. [source] Single nucleotide polymorphism (SNP) discovery in porcine expressed genesANIMAL GENETICS, Issue 3 2002S. C. Fahrenkrug High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs. [source] | ||||||||||