Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

Background The automated retrieval and integration of information about protein point mutations in combination with structure, domain and interaction data from literature and databases promises to be a valuable approach to study structure-function relationships in biomedical data sets. Results We developed a rule- and regular expression-based protein point mutation retrieval pipeline for PubMed abstracts, which shows an F-measure of 87% for the mutation retrieval task on a benchmark dataset. In order to link mutations to their proteins, we utilize a named entity recognition algorithm for the identification of gene names co-occurring in the abstract, and establish links based on sequence checks. Vice versa, we could show that gene recognition improved from 77% to 91% F-measure when considering mutation information given in the text. To demonstrate practical relevance, we utilize mutation information from text to evaluate a novel solvation energy based model for the prediction of stabilizing regions in membrane proteins. For five G protein-coupled receptors we identified 35 relevant single mutations and associated phenotypes, of which none had been annotated in the UniProt or PDB database. In 71% reported phenotypes were in compliance with the model predictions, supporting a relation between mutations and stability issues in membrane proteins. Conclusion We present a reliable approach for the retrieval of protein mutations from PubMed abstracts for any set of genes or proteins of interest. We further demonstrate how amino acid substitution information from text can be utilized for protein structure stability studies on the basis of a novel energy model

Educating Pharmacy Students to Improve Quality (EPIQ) in Colleges and Schools of Pharmacy

Objective. To assess course instructors’ and students’ perceptions of the Educating Pharmacy Students and Pharmacists to Improve Quality (EPIQ) curriculum. Methods. Seven colleges and schools of pharmacy that were using the EPIQ program in their curricula agreed to participate in the study. Five of the 7 collected student retrospective pre- and post-intervention questionnaires. Changes in students’ perceptions were evaluated to assess their relationships with demographics and course variables. Instructors who implemented the EPIQ program at each of the 7 colleges and schools were also asked to complete a questionnaire. Results. Scores on all questionnaire items indicated improvement in students’ perceived knowledge of quality improvement. The university the students attended, completion of a class project, and length of coverage of material were significantly related to improvement in the students’ scores. Instructors at all colleges and schools felt the EPIQ curriculum was a strong program that fulfilled the criteria for quality improvement and medication error reduction education. Conclusion. The EPIQ program is a viable, turnkey option for colleges and schools of pharmacy to use in teaching students about quality improvement

Ontology-based Assisted Curation of Biomedical Data

Manual curation of biomedical data is highly accurate but time consuming, and does not scale with the ever increasing growth of biomedical literature. Text mining as a high-throughput computational technique scales well but requires human expertise to produce highly accurate results. Ontologies can help organizing large quantities of unstructured information. Here we present three systems, namely GoGene, GoPubMed and GoWeb, employing biomedical ontologies and show how they can assist manual curation of biomedical data.

GoGene associates all genes from different model organisms to concepts of the Gene Ontology (GO) and the Medical Subject Headings (MeSH). The hierarchical structures of both terminologies support clustering and summarizing long lists of genes. Through the integration of known gene annotations from UniProt and EntrezGene with text-mined annotations from all abstracts in PubMed, GoGene currently contains up to 4,000,000 associations between genes and concepts from GO and MeSH for ten model organisms. The quality of all associations can be verified by following the links to their origin, that is, literature or database entries.

GoPubMed aims at reducing the limitations of classical keyword search. It handles inconsistent vocabulary such as synonyms and specialized terminology. It shows the most relevant concepts in GO and MeSH for a search and thus reveals information which otherwise remains buried in the masses of text. This feature as well as the entire bibliography of all authors in PubMed facilitate comprehensive literature search. GoWeb translates these ideas to the World Wide Web and is thus not only limited to PubMed abstracts. GoWeb uses a standard web-search service and organizes search results based on GO, MeSH, and other concepts such as companies and institutions

Assessment Instruction Advice: An Interview with W. James Popham

Non

9. Differential Item Functioning In Licensure Tests

When test scores are used to make important decisions, as is typically the case with licensure tests, the validity of test score interpretations is extremely critical. The validity of the decision (e.g., pass or fail the licensure examination) relies heavily on the validity of the test score that is used in making the licensure decision. So, although validity is always a critical component in test score interpretation, it has increased importance when the score is used in high-stakes decision situations such as licensure testing. Issues in validity for licensure tests have been addressed in Chapter 4 of this volume. The focus of this chapter is on techniques that have been developed for identifying one source of test interpretation invalidity: differential item functioning (DIF) by identifiable groups. The chapter begins with a discussion of what constitutes differential item functioning and under what circumstances differential item functioning poses a source of test interpretation invalidity. Next, various methods for identifying test items that function differentially are highlighted. This section focuses principally on multiple-choice test items although a separate subsection on applications of DIF methods with constructed-response type items is presented. The chapter ends with a conclusion section that makes recommendations for future developments in the area of identification of test items that function inappropriately for different sub-populations. This chapter concentrates on the individual items that comprise the test, not on administrative or other aspects of testing that also might influence examinee test performance. Specifically, this chapter considers ways to identify items that function differentially for identifiable sub-populations. Other reasons for score performance differences (e.g., speeded conditions, administration medium, test anxiety/wiseness) are extremely important. However, these issues are beyond the scope of this chapter. The focus of this chapter is on discussing different approaches that have promise for identifying items that function differentially in licensure tests. It is not the intent of this chapter to present step-by-step details on calculating these various methods. The reader should reference other books that present formulas for such calculations, particularly Berk (1982), Camilli and Shepard (1994), and Holland and Wainer (1993). Further, this chapter is not designed to be a comprehensive resource for DIF methods; instead, the chapter samples from these methods those techniques that are relevant or dominant in use for DIF analysis with licensure test applications

9. Differential Item Functioning In Licensure Tests

When test scores are used to make important decisions, as is typically the case with licensure tests, the validity of test score interpretations is extremely critical. The validity of the decision (e.g., pass or fail the licensure examination) relies heavily on the validity of the test score that is used in making the licensure decision. So, although validity is always a critical component in test score interpretation, it has increased importance when the score is used in high-stakes decision situations such as licensure testing. Issues in validity for licensure tests have been addressed in Chapter 4 of this volume. The focus of this chapter is on techniques that have been developed for identifying one source of test interpretation invalidity: differential item functioning (DIF) by identifiable groups. The chapter begins with a discussion of what constitutes differential item functioning and under what circumstances differential item functioning poses a source of test interpretation invalidity. Next, various methods for identifying test items that function differentially are highlighted. This section focuses principally on multiple-choice test items although a separate subsection on applications of DIF methods with constructed-response type items is presented. The chapter ends with a conclusion section that makes recommendations for future developments in the area of identification of test items that function inappropriately for different sub-populations. This chapter concentrates on the individual items that comprise the test, not on administrative or other aspects of testing that also might influence examinee test performance. Specifically, this chapter considers ways to identify items that function differentially for identifiable sub-populations. Other reasons for score performance differences (e.g., speeded conditions, administration medium, test anxiety/wiseness) are extremely important. However, these issues are beyond the scope of this chapter. The focus of this chapter is on discussing different approaches that have promise for identifying items that function differentially in licensure tests. It is not the intent of this chapter to present step-by-step details on calculating these various methods. The reader should reference other books that present formulas for such calculations, particularly Berk (1982), Camilli and Shepard (1994), and Holland and Wainer (1993). Further, this chapter is not designed to be a comprehensive resource for DIF methods; instead, the chapter samples from these methods those techniques that are relevant or dominant in use for DIF analysis with licensure test applications

Literature-based discovery of diabetes- and ROS-related targets

Abstract Background Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS. Methods We present ROS- and diabetes-related targets (genes/proteins) collected from the biomedical literature through a text mining technology. A web-based literature mining tool, SciMiner, was applied to 1,154 biomedical papers indexed with diabetes and ROS by PubMed to identify relevant targets. Over-represented targets in the ROS-diabetes literature were obtained through comparisons against randomly selected literature. The expression levels of nine genes, selected from the top ranked ROS-diabetes set, were measured in the dorsal root ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in order to evaluate the biological relevance of literature-derived targets in the pathogenesis of diabetic neuropathy. Results SciMiner identified 1,026 ROS- and diabetes-related targets from the 1,154 biomedical papers (http://jdrf.neurology.med.umich.edu/ROSDiabetes/). Fifty-three targets were significantly over-represented in the ROS-diabetes literature compared to randomly selected literature. These over-represented targets included well-known members of the oxidative stress response including catalase, the NADPH oxidase family, and the superoxide dismutase family of proteins. Eight of the nine selected genes exhibited significant differential expression between diabetic and non-diabetic mice. For six genes, the direction of expression change in diabetes paralleled enhanced oxidative stress in the DRG. Conclusions Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy.http://deepblue.lib.umich.edu/bitstream/2027.42/78315/1/1755-8794-3-49.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/2/1755-8794-3-49-S7.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/3/1755-8794-3-49-S10.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/4/1755-8794-3-49-S8.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/5/1755-8794-3-49-S3.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/6/1755-8794-3-49-S1.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/7/1755-8794-3-49-S4.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/8/1755-8794-3-49-S2.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/9/1755-8794-3-49-S12.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/10/1755-8794-3-49-S11.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/11/1755-8794-3-49-S9.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/12/1755-8794-3-49-S5.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/13/1755-8794-3-49-S6.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/14/1755-8794-3-49.pdfPeer Reviewe

Teacher Assessment Literacy: Teachers\u27 Competencies in the Educational Assessment of Students

It has been estimated that teachers are involved in assessment-related activities up to 50 percent of the time. However, teacher training programs frequently do not contain specific training in educational assessment or testing. In order to identify assessment competencies for development of training materials in educational assessment for inservice teachers, a national survey was undertaken to measure teacher knowledge in assessment and testing. The instrument was designed to assess the competencies identified in 1990 by a joint committee of the National Educational Association, the American Federation of Teachers, and the National Council on Measurement in Education, Standards for Teacher Competence in the Educational Assessment of Students. Of the seven competency areas articulated in these Standards, teachers showed their best performance in the area of administering, scoring and interpreting test results and poorest performance in communicating test results. Based on the survey results, a joint committee of NEA, AFT, and NCME is planning the development of a training prototype for delivering inservice programs to increase teacher competency in educational assessment

Preface

The Buros-Nebraska annual Symposia on Measurement and Testing are aimed at providing a forum for discussing important issues in the field of measurement and testing. The topic for the 1987 Symposium was Assessment of Teaching: Purposes, Practices, and Implications for the Profession. This topic was selected because of the current interest in developing, designing, and implementing accountability programs for teaching that are present in many states and education programs. The complex nature of teaching, combined with the unique measurement issues for assessing outcomes in the teaching context, provided the basis for identifying the topic of teacher assessment for the 1987 symposium. As is the tradition for the Institute, after each annual symposium a volume is prepared that contains written versions of the presentations from the symposium as well as additional chapters, invited by the editors, to complement the collection of chapters representing the symposium presentations. During the editorial process, each chapter for the current volume has external review by one or two professionals in the field in order to provide comments and suggestions for improvement of the chapter. We are very grateful to the dedicated efforts of the following persons who served as external reviewers for this volume: Peter Airasian, Jerrilyn Andrews, David Berliner, Carol Dwyer, Stephen Dunbar, Kim Hoogeveen, Ronald Joekel, Michael T. Kane, Steven Murray, Michael Rebell, Carol Robinson, Robert Stalcup, Charol Shakeshaft, Kenneth Strike, James Sweeney, Gary Sykes and Herbert Walberg. We also extend our gratitude to Jane Close Conoley, who as series editor provided the advice, oversight, and continuity necessary for an enterprise of this kind. This volume provides a comprehensive look at the assessment of teaching, covering dimensions of assessment techniques, validity concerns, legal issues, application and implementation considerations, utility of assessment information, and views of the process of teacher assessment from the perspective of both an administrator and a teacher advocate. Therefore, this volume will focus on many related and vital facets of assessment of teaching. The first chapter in the volume is authored by W. James Popham and is titled Face Validity: Siren Song of Teacher-Testers. As the keynote speaker of the Buros-Nebraska Symposium on Measurement and Testing, Dr. Popham sets the stage for concern for validity in teacher assessment programs. The concerns raised by Dr. Popham are echoed by many authors in subsequent chapters in the volume. Dr. Edward Haertel is the author of the second chapter, Teacher Performance Assessments: A New Kind of Teacher Examination. As a member of the team involved in developing an instrument to credential teachers, Dr. Haertel is in a unique position to provide insights into the assessment methods for teaching. The methods identified give an overview for upcoming chapters in the volume on paper-and-pencil assessment instruments (Mehrens) and performance assessment techniques (Stiggins). Improving Teaching Through the Assessment Process is the title of the next chapter authored by Dr. Donald Medley. Most practitioners agree that improvement of teaching should be the primary goal of teacher assessment programs. This chapter provides examples of teacher assessment programs that attempt to realize this critical goal for teacher assessment programs. Dr. William Mehrens\u27 chapter, Assessing the Quality of Teacher Assessment Tests, provides an important continuation of the discussion on assessment methods identified by Dr. Haertel in Chapter 2. Focusing on paper-and-pencil assessment instruments, Dr. Mehrens addresses many critical psychometric issues related to the development and use of instruments for assessing teaching