Integrated Testlets and the Immediate Feedback Assessment Technique

The increased use of multiple-choice (MC) questions in introductory-level physics final exams is largely hindered by reservations about its ability to test the broad cognitive domain that is routinely accessed with typical constructed-response (CR) questions. Thus, there is a need to explore ways in which MC questions can be utilized pedagogically more like CR questions while maintaining their attendant procedural advantages. we describe how an answer-until-correct MC response format allows for the construction of multiple-choice examinations designed to operate much as a hybrid between standard MC and CR testing. With this tool - the immediate feedback assessment technique (IF-AT) - students gain complete knowledge of the correct answer for each question during the examination, and can use such information for solving subsequent test items. This feature allows for the creation of a new type of context-dependent item sets; the "integrated testlet". In an integrated testlet certain items are purposefully inter-dependent and are thus presented in a particular order. Such integrated testlets represent a proxy of typical CR questions, but with a straightforward and uniform marking scheme that also allows for granting partial credit for proximal knowledge. We present a case study of an IF-AT-scored midterm and final examination for an introductory physics course, and discuss specific testlets with varying degrees of integration. In total, the items are found to allow for excellent discrimination, with a mean item-total correlation measure for the combined 45 items of the two examinations of $\bar{r}'=0.41\pm 0.13$ (mean $\pm$ standard deviation) and a final examination test reliability of $\alpha=0.82$ ($n=25$ items). Furthermore, partial credit is shown to be allocated in a discriminating and valid manner in these examinations.Comment: 13 pages. 7 figures. Accepted to the American Journal of Physics (August 2013

A Construct-Modeling Approach to Develop a Learning Progression of how Students Understand the Structure of Matter

This paper builds on the current literature base about learning progressions in science to address the question, “What is the nature of the learning progression in the content domain of the structure of matter?” We introduce a learning progression in response to that question and illustrate a methodology, the Construct Modeling (Wilson, 2005) approach, for investigating the progression through a developmentally based iterative process. This study puts forth a progression of how students understand the structure of matter by empirically inter-relating constructs of different levels of sophistication using a sample of 1,087 middle grade students from a large diverse public school district in the western part of the United States. The study also shows that student thinking can be more complex than hypothesized as in the case of our discovery of a substructure of understanding in a single construct within the larger progression. Data were analyzed using a multidimensional Rasch model. Implications for teaching and learning are discussed—we suggest that the teacher’s choice of instructional approach needs to be fashioned in terms of a model, grounded in evidence, of the paths through which learning might best proceed, working toward the desired targets by a pedagogy which also cultivates students’ development as effective learners. This research sheds light on the need for assessment methods to be used as guides for formative work and as tools to ensure the learning goals have been achieved at the end of the learning period. The development and investigation of a learning progression of how students understand the structure of matter using the Construct Modeling approach makes an important contribution to the research on learning progressions and serves as a guide to the planning and implementation in the teaching of this topic. # 2017 Wiley Periodicals, Inc. J Res Sci Teach 54: 1024–1048, 201

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Optimizing substitution matrix choice and gap parameters for sequence alignment

<p>Abstract</p> <p>Background</p> <p>While substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or approximately optimal gap penalties. It is also not well understood which substitution matrices are the most effective when alignment accuracy is the goal rather than homolog recognition. Here a new parameter optimization procedure, POP, is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments.</p> <p>Results</p> <p>POP is compared to a recent method due to Kim and Kececioglu and found to achieve from 0.2% to 1.3% higher accuracies on pair-wise benchmarks extracted from BALIBASE. The VTML matrix series is shown to be the most accurate on several global pair-wise alignment benchmarks, with VTML200 giving best or close to the best performance in all tests. BLOSUM matrices are found to be slightly inferior, even with the marginal improvements in the bug-fixed RBLOSUM series. The PAM series is significantly worse, giving accuracies typically 2% less than VTML. Integer rounding is found to cause slight degradations in accuracy. No evidence is found that selecting a matrix based on sequence divergence improves accuracy, suggesting that the use of this heuristic in CLUSTALW may be ineffective. Using VTML200 is found to improve the accuracy of CLUSTALW by 8% on BALIBASE and 5% on PREFAB.</p> <p>Conclusion</p> <p>The hypothesis that more accurate alignments of distantly related sequences may be achieved using low-identity matrices is shown to be false for commonly used matrix types. Source code and test data is freely available from the author's web site at <url>http://www.drive5.com/pop</url>.</p

Parameters for accurate genome alignment

<p>Abstract</p> <p>Background</p> <p>Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed.</p> <p>Results</p> <p>We have assessed 495 combinations of score parameters for alignment of animal, plant, and fungal genomes. As our gold-standard of accuracy, we used genome alignments implied by multiple alignments of proteins and of structural RNAs. We found the HOXD scoring schemes underlying alignments in the UCSC genome database to be far from optimal, and suggest better parameters. Higher values of the X-drop parameter are not always better. E-values accurately indicate the rate of spurious alignment, but only if tandem repeats are masked in a non-standard way. Finally, we show that γ-centroid (probabilistic) alignment can find highly reliable subsets of aligned bases.</p> <p>Conclusions</p> <p>These results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours <url>http://last.cbrc.jp/</url>.</p