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

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

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

1. Filling the Gaps Between Test Outcomes and Usage: An Introduction

Why do we have tests? What useful purposes do they serve? How can test results be used to make decisions? How can a test be proved to provide accurate and usable information? Questions such as these have been posed recently by a concerned public who have become more aware of and concerned about testing, test quality, and appropriate test usage. Their questions are challenging, legitimate queries that can and should be addressed by members of the measurement community . Some of the questions being asked by the public are value laden, providing topics for many thoughtful but heated debates. For example: Would we be better off as a society if we did not have tests? Should testing be banned? Other questions are technical in nature and require accurate answers from the measurement community, which communicates to the public the present state of the art in measurement, assessment, and interpretation. Finally, questions such as How can tests be used to eliminate the errors made in the selection process? can provide an impetus within the measurement field for both theoretical and empirical development and yet are not ones that can, at least so far, be definitely answered . The measurement field should take serious stock of itself and assess, as well as possible, the boundaries of its capabilities. From this assessment, it would be possible to communicate with the public about what testing can do, may be able to do, and is incapable of ever doing. At the present time, however, there appears to be an informational and expectational gap concerning what can be possible with the use of test results. Unless measurement experts and test users obtain a direct line to the angels, for example, error-free measurement will never be a reality! Part of the communication and expectation gap can be assigned to a lack of measurement sophistication on the part of the public. Measurement course work and classes are not readily accessible to the public as a whole and may not be truly meaningful and usable to the public even if they were . A well-meaning but confused public provides fertile ground for test misunderstanding and misrepresentation by both knowledgeable and unknowledgeable test representatives. Tests enter into the lives of the public in so many ways; questionnaires, market surveys, school achievement batteries, classroom exams, and admission screenings are only a few possibilities. Yet the knowledge level of the public is minimal at best with regard to test information and interpretation

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

Synthesis and evaluation of conformationally constrained peptide replacements and studies toward the total synthesis of kidamycin

textA series of conformationally constrained pseudopeptides derivative of the tripeptide pYVN were designed and synthesized. The conformationally restricted compounds contained either trans- or cis-cyclopropanes as replacements to enforce locally extended and reverse turn peptide conformations, respectively. In addition, the proper flexible control molecules were prepared. All compounds were evaluated for the ability to bind to the Grb2-SH2 domain in order to determine the energetic consequences of introducing a conformational constraint into peptide ligands. No difference in the ∆Gbinding between the trans-cyclopropane and its control partner was observed. Surprisingly, there was an entropic disadvantage when comparing the binding energetics of the constrained and flexible pseudopeptides. Therefore, the introduction of the cyclopropane constraint was associated with an entropic disadvantage in the system, which is the opposite of conventional wisdom. An X-ray crystal structure of the trans- cyclopropane containing ligand bound to the Grb2-SH2 domain was obtained and vii discussed. On the other hand, cis-cyclopropane containing pseudopeptides do not seem to enforce the desired turn conformation of the ligand. A method to allow access to unsymmetrical C-aryl glycoside natural products was developed through employing a disposal tether to enforce the desired regioselectivity in a [4+2] cycloaddition between benzyne and glycosyl-substituted furan. Application of this novel strategy toward the synthesis of kidamycin is discussed. Additional synthetic routes, including utilizing Suzuki’s O → C glycoside rearrangement are also provided. Studies toward the synthesis of sugar ring E and F are illustrated.Chemistry and BiochemistryChemistr

Self-Efficacy and Educational Interventions in Heart Failure: A review of the Literature

Purpose: The purpose of this study was to conduct a systematic review of the literature to better understand how to structure educational interventions for heart failure patients to improve their self-efficacy for self-care behaviors. Methods: A computer search of the literature from 1966 through May 2009 was conducted, yielding 84 manuscripts. All manuscripts were reviewed in relation to the search criteria, resulting in 12 articles that were evaluated. Results: Each of the reviewed studies utilized an intervention plus education to improve self-efficacy. Self-efficacy was a primary outcome for seven of the studies, and a secondary outcome for five on the studies in this literature search. Both short and long-term interventions can improve self-efficacy demonstrating that the duration of the intervention can vary and still be successful. Conclusion: Existing evidence suggests that it is not the amount of education (number of sessions/length of sessions) that improves self-efficacy, but some other factor or factors that remain unknown at present. Education delivery costs, flexibility, and the ability to more easily integrate new discoveries need to be explored. Interventions that include components specifically geared toward increasing self-efficacy for self-care in patients with heart failure are needed. Learning activities need to be incorporated into patient education programs in order to provide practice time that may result in behavior changes. The opportunity to practice self-care behaviors within the context of the education provided to those with heart failure, along with ongoing support, needs to be explored in future studies

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

Reading Difficulties of the Third Grade

The problem of what to do with the poor reader and the non-reader of the third grade has disturbed the author for several years. Solutions in the form of preventative measures beginning in the first grade, do not effect the problem immediately. In schools where no such measures have been taken, a class of third grade poor readers and non-readers is always at hand, and something should be done with them before they leave the primary grades