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Requires RealPlayer to view.The University Archives has determined that this item is of continuing value to OSU's history.Presentation at Technology for the Rest of Us: What Every Librarian Should Understand about the Technologies that Affect Us, May 24-27, 2004.This project is funded in part through an Institute of Museum and Library Services LSTA grant awarded by the State Library of Ohi

Bringing in the Experts: Library Research Guide Usability Testing in a Computer Science Class

Objective – We sought to develop best practices for creating online research guides in an academic library.Methods – We performed usability tests of particular library research guides in order to determine how to improve them. Students in a Human-Computer Interaction (HCI) class (n=20) participated in the studies both as subjects of the tests and as evaluators of the results. The students were each interviewed and then asked to review the interviews recorded of four other classmates. Based on their own experience with the guides and their viewing of their classmates using the guides, the students worked with librarians to develop best practices.Results – Students were generally unfamiliar with the library\u27s research guides prior to the study. They identified bibliographic databases as the most important links on the guides and felt that these should be prominently placed. Opinions about many specific features (e.g., images, length of guide, annotations) varied widely, but students felt strongly that there should be some organizational consistency among the guides.Conclusions – The importance that students placed on consistency led the library to adopt guidelines dictating the inclusion of a table of contents and short list of major databases at the top of each guide, as well as uniform placement of certain other elements

LibQuest: A Web App for Exploring the IC Library

LibQuest is a web app that is designed to help students explore the physical space of the library and can be used in place of a library scavenger hunt or tour. Questions encourage students to interact with service points and physical collections, and are randomized to discourage copying. Text-input questions are included to increase difficulty, as are questions that can only be answered by visiting the building

The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

<p>Abstract</p> <p>Background</p> <p>Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD) test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets.</p> <p>Methods</p> <p>The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5^th, 10^thand 50^thhighest T_CLDvalue from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively.</p> <p>Results</p> <p>In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001), where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001). In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05), i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position.</p> <p>Conclusions</p> <p>The CLD test can provide evidence for a causative SNP, but its power may be low in situations with closely linked markers. In such situations, also functional evidence will be needed to definitely conclude whether the SNP is causative or not.</p

Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle

<p>Abstract</p> <p>Background</p> <p>Our group has previously identified a quantitative trait locus (QTL) affecting fat and protein percentages on bovine chromosome 6, and refined the QTL position to a 420-kb interval containing six genes. Studies performed in other cattle populations have proposed polymorphisms in two different genes (<it>ABCG2 </it>and <it>OPN</it>) as the underlying functional QTL nucleotide. Due to these conflicting results, we have included these QTNs, together with a large collection of new SNPs produced from PCR sequencing, in a dense marker map spanning the QTL region, and reanalyzed the data using a combined linkage and linkage disequilibrium approach.</p> <p>Results</p> <p>Our results clearly exclude the <it>OPN </it>SNP (<it>OPN_3907</it>) as causal site for the QTL. Among 91 SNPs included in the study, the <it>ABCG2 </it>SNP (<it>ABCG2_49</it>) is clearly the best QTN candidate. The analyses revealed the presence of only one QTL for the percentage traits in the tested region. This QTL was completely removed by correcting the analysis for <it>ABCG2_49</it>. Concordance between the sires' marker genotypes and segregation status for the QTL was found for <it>ABCG2_49 </it>only. The C allele of <it>ABCG2_49 </it>is found in a marker haplotype that has an extremely negative effect on fat and protein percentages and positive effect on milk yield. Of the 91 SNPs, <it>ABCG2_49 </it>was the only marker in perfect linkage disequilibrium with the QTL.</p> <p>Conclusion</p> <p>Based on our results, OPN_3907 can be excluded as the polymorphism underlying the QTL. The results of this and other papers strongly suggest the [A/C] mutation in <it>ABCG2_49 </it>as the causal mutation, although the possibility that <it>ABCG2_49 </it>is only a marker in perfect LD with the true mutation can not be completely ruled out.</p

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets

Background. The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way. Methodology/Principal Findings. In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph – or eFP – Browser, available a

The control of sea lice in Atlantic salmon by selective breeding

Sea lice threaten the welfare of farmed Atlantic salmon and the sustainability of fish farming across the world. Chemical treatments are the major method of control but drug resistance means that alternatives are urgently needed. Selective breeding can be a cheap and effective alternative. Here, we combine experimental trials and diagnostics to provide a practical protocol for quantifying resistance to sea lice. We then combined quantitative genetics with epidemiological modelling to make the first prediction of the response to selection, quantified in terms of reduced need for chemical treatments. We infected over 1400 young fish with Lepeophtheirus salmonis, the most important species in the Northern Hemisphere. Mechanisms of resistance were expressed early in infection. Consequently, the number of lice per fish and the ranking of families were very similar at 7 and 17 days post infection, providing a stable window for assessing susceptibility to infection. The heritability of lice numbers within this time window was moderately high at 0.3, confirming that selective breeding is viable. We combined an epidemiological model of sea lice infection and control on a salmon farm with genetic variation in susceptibility among individuals. We simulated 10 generations of selective breeding and examined the frequency of treatments needed to control infection. Our model predicted that substantially fewer chemical treatments are needed to control lice outbreaks in selected populations and chemical treatment could be unnecessary after 10 generations of selection. Selective breeding for sea lice resistance should reduce the impact of sea lice on fish health and thus substantially improve the sustainability of Atlantic salmon production

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs