bluuebunny/crossref_metadata_2025_split huggingface dataset:
Value of Mendelian Laws of Segregation in Families: Data Quality Control, Imputation, and Beyond
Authors: Blue Elizabeth M. , Sun Lei , Tintle Nathan L. , Wijsman Ellen M. 
Published: August 2014

ABSTRACTWhen analyzing family data, we dream of perfectly informative data, even whole‐genome sequences (WGSs) for all family members. Reality intervenes, and we find that next‐generation sequencing (NGS) data have errors and are often too expensive or impossible to collect on everyone. The Genetic Analysis Workshop 18 working groups on quality control and dropping WGSs through families using a genome‐wide association framework focused on finding, correcting, and using errors within the available sequence and family data, developing methods to infer and analyze missing sequence data among relatives, and testing for linkage and association with simulated blood pressure. We found that single‐nucleotide polymorphisms, NGS data, and imputed data are generally concordant but that errors are particularly likely at rare variants, for homozygous genotypes, within regions with repeated sequences or structural variants, and within sequence data imputed from unrelated individuals. Admixture complicated identification of cryptic relatedness, but information from Mendelian transmission improved error detection and provided an estimate of the de novo mutation rate. Computationally, fast rule‐based imputation was accurate but could not cover as many loci or subjects as more computationally demanding probability‐based methods. Incorporating population‐level data into pedigree‐based imputation methods improved results. Observed data outperformed imputed data in association testing, but imputed data were also useful. We discuss the strengths and weaknesses of existing methods and suggest possible future directions, such as improving communication between data collectors and data analysts, establishing thresholds for and improving imputation quality, and incorporating error into imputation and analytical models.
Complex Pedigrees in the Sequencing Era: To Track Transmissions or Decorrelate?
Authors: Li Dalin , Zhou Jin , Thomas Duncan C. , Fardo David W. 
Published: August 2014

ABSTRACTNext‐generation sequencing (NGS) studies are becoming commonplace, and the NGS field is continuing to develop rapidly. Analytic methods aimed at testing for the various roles that genetic susceptibility plays in disease are also rapidly being developed and optimized. Studies that incorporate large, complex pedigrees are of particular importance because they provide detailed information about inheritance patterns and can be analyzed in a variety of complementary ways. The nine contributions from our Genetic Analysis Workshop 18 working group on family‐based tests of association for rare variants using simulated data examined analytic methods for testing genetic association using whole‐genome sequencing data from 20 large pedigrees with 200 phenotype simulation replicates. What distinguishes the approaches explored is how the complexities of analyzing familial genetic data were handled. Here, we explore the methods that either harness inheritance patterns and transmission information or attempt to adjust for the correlation between family members in order to utilize computationally and conceptually simpler statistical testing procedures. Although directly comparing these two classes of approaches across contributions is difficult, we note that the two classes balance robustness to population stratification and computational complexity (the transmission‐based approaches) with simplicity and increased power, assuming no population stratification or proper adjustment for it (decorrelation approaches).
Genetic Prediction in the Genetic Analysis Workshop 18 Sequencing Data
Authors: Ziegler Andreas , Bohossian Nora , Diego Vincent P. , Yao Chen 
Published: August 2014

ABSTRACTHigh‐throughput sequencing data can be used to predict phenotypes from genotypes, and this corresponds to establishing a prognostic model. In extended pedigrees the relatedness of subjects provides additional information so that genetic values, fixed or random genetic components, and heritability can be estimated. At the Genetic Analysis Workshop 18, the working group on genetic prediction dealt with both establishing a prognostic model and, in one contribution, comparing standard logistic regression with robust logistic regression in a sample of unrelated affected or unaffected individuals. Results of both logistic regression approaches were similar. All other contributions to this group used extended family data, in general using the quantitative trait blood pressure. The individual contributions varied in several important aspects, such as the estimation of the kinship matrix and the estimation method. Contributors chose various approaches for model validation, including different versions of cross‐validation or within‐family validation. Within‐family validation included model building in the upper generations and validation in later generations. The choice of the statistical model and the computational algorithm had substantial effects on computation time. If decorrelation approaches were applied, the computational burden was substantially reduced. Some software packages estimated negative eigenvalues, although eigenvalues of correlation matrices should be non‐negative. Most statistical models and software packages have been developed for experimental crosses and planned breeding programs. With their specialized pedigree structures, they are not sufficiently flexible to accommodate the variability of human pedigrees in general, and improved implementations are required.
Pathway Analysis Approaches for Rare and Common Variants: Insights From Genetic Analysis Workshop 18
Authors: Aslibekyan Stella , Almeida Marcio , Tintle Nathan 
Published: August 2014

ABSTRACTPathway analysis, broadly defined as a group of methods incorporating a priori biological information from public databases, has emerged as a promising approach for analyzing high‐dimensional genomic data. As part of Genetic Analysis Workshop 18, seven research groups applied pathway analysis techniques to whole‐genome sequence data from the San Antonio Family Study. Overall, the groups found that the potential of pathway analysis to improve detection of causal variants by lowering the multiple‐testing burden and incorporating biologic insight remains largely unrealized. Specifically, there is a lack of best practices at each stage of the pathway approach: annotation, analysis, interpretation, and follow‐up. Annotation of genetic variants is inconsistent across databases, incomplete, and biased toward known genes. At the analysis stage insufficient statistical power remains a major challenge. Analyses combining rare and common variants may have an inflated type I error rate and may not improve detection of causal genes. Inclusion of known causal genes may not improve statistical power, although the fraction of explained phenotypic variance may be a more appropriate metric. Interpretation of findings is further complicated by evidence in support of interactions between pathways and by the lack of consensus on how to best incorporate functional information. Finally, all presented approaches warranted follow‐up studies, both to reduce the likelihood of false‐positive findings and to identify specific causal variants within a given pathway. Despite the initial promise of pathway analysis for modeling biological complexity of disease phenotypes, many methodological challenges currently remain to be addressed.
A descriptive qualitative study of the roles of family members in older men's depression treatment from the perspectives of older men and primary care providers
Authors: Hinton Ladson , Apesoa‐Varano Ester Carolina , Unützer Jürgen , Dwight‐Johnson Megan , Park Mijung , Barker Judith C. 
Published: August 2014

ObjectiveThe aim of this study is to describe the roles of family members in older men's depression treatment from the perspectives of older men and primary care physicians (PCPs).MethodsCross‐sectional, descriptive qualitative study conducted from 2008–2011 in primary care clinics in an academic medical center and a safety‐net county teaching hospital in California's Central Valley. Participants in this study were the following: (1) 77 age ≥ 60, noninstitutionalized men with a 1‐year history of clinical depression and/or depression treatment who were identified through screening in primary care clinics and (2) a convenience sample of 15 PCPs from the same recruitment sites. Semi‐structured and in‐depth qualitative interviews were conducted and audiotaped then transcribed and analyzed thematically.ResultsTreatment‐promoting roles of family included providing an emotionally supportive home environment, promoting depression self‐management and facilitating communication about depression during primary care visits. Treatment‐impeding roles of family included triggering or worsening men's depression, hindering depression care during primary care visits, discouraging depression treatment and being unavailable to assist men with their depression care. Overall, more than 90% of the men and the PCPs described one or more treatment‐promoting roles of family and over 75% of men and PCPs described one or more treatment‐impeding roles of family.ConclusionsFamilies play important roles in older men's depression treatment with the potential to promote as well as impede care. Interventions and services need to carefully assess the ongoing roles and attitudes of family members and to tailor treatment approaches to build on the positive aspects and mitigate the negative aspects of family support. Copyright © 2014 John Wiley & Sons, Ltd.
Now you see it, now you don't: Testing environments modulate the association between hippocampal volume and cortisol levels in young and older adults
Authors: Sindi Shireen , Fiocco Alexandra J. , Juster Robert‐Paul , Lord Catherine , Pruessner Jens , Lupien Sonia J. 
Published: August 2014

ABSTRACTThe hypothalamic pituitary adrenal axis production of the stress hormone cortisol interacts with the hippocampal formation and impacts memory function. A growing interest is to determine whether hippocampal volume (HV) predicts basal and/or reactive cortisol levels in young and older adults. Recent evidence shows that contextual features in testing environments might be stressful and inadvertently induce a stress response in young and/or older populations. This latter result suggests that variations in testing environments might influence associations between HV and cortisol levels in young and older adults. To this end, we investigated 28 healthy young adults (ages 18–35) and 32 healthy older adults (ages 60–75) in two different environments constructed to be more or less stressful for each age group (Favoring‐Young versus Favoring‐Old conditions). Cortisol levels were repeatedly assessed in each environment, and young and older participants underwent an anatomical magnetic resonance imaging scan for subsequent assessment of HV. Results in both age groups showed that HV was significantly associated with cortisol levels only in the unfavorable stressful testing conditions specific for each age group. This association was absent when testing environments were designed to decrease stress for each age group. These findings are fundamental in showing that unless the nature of the testing environment is taken into consideration, detected associations between HV and cortisol levels in both young and older populations might be confounded by environmental stress. © 2014 Wiley Periodicals, Inc.
THE RELATIONSHIP BETWEEN THE VALIDITY OF A SINGLE TEST AND ITS CONTRIBUTION TO THE PREDICTIVE EFFICIENCY OF A TEST BATTERY
Authors: Horst Paul 
Published: August 2014

ABSTRACTTypical selection or classification testing programs should provide for improvement of the predictive efficiency of the test battery. Such provision calls for the administration of experimental tests along with the operational battery administration and follow‐up analysis to determine the value of the experimental material. It is possible to determine without waiting for criterion data what the validity of the experimental test must be in order to improve the battery validity. The method together with the proof is presented.
ON THE STANDARD LENGTH OF A TEST*
Authors: Woodbury Max A. 
Published: August 2014

ABSTRACTA new concept, that of the standard length of a test, seems useful in simplifying formulas for reliability and validity coefficients for tests of altered length. The usefulness of the concept is a consequence of the fact that it is possible to define a unit of test information, this being, in fact, the amount of information in a test of standard length. The amount of information in a test is its length L in terms of its standard length as a unit. From this one computes the reliability r of the test by the formula r = L/(L + 1). For small amounts of information, the reliability and the information are approximately equal. It is readily seen that the standard length of a test is that length which would make its reliability one half. The length of a test in terms of its standard length as a unit required to produce a given reliability is given by L = r/(1 ‐ r). Both formulas reduce to (1 + L) (1 ‐ r) = 1.The correlation between two tests of length L1 and L2 in terms of their standard lengths as units is r12 = R12 L1L2/(L1 + 1)(L2 + 1)1/2, where R12 is the correlation corrected for attenuation. For the case of correlation with a criterion this becomes r1c = R1c L1/L1 + 11/2 where R1c is the validity coefficient corrected for attenuation.
OPTIMAL TEST LENGTH FOR MAXIMUM BATTERY VALIDITY
Authors: Horst Paul 
Published: August 2014

ABSTRACTHaving given a fixed amount of total testing time it is important to know how long each test in the battery should be so that the correlation of the battery with the criterion will be a maximum. The precise solution for the test lengths will depend on a particular set of conditions which may be specified. The writer has previously presented solutions for two sets of conditions. This article presents the solution for a third set of conditions. These are: (1) The total number of items or testing time is fixed. (2) The score is the total number of items correctly answered. (3) The test lengths are determined in such a way that the correlation of total score with the criterion is a maximum.The solutions for the two previous sets of conditions, together with the current set are summarized. A set of experimental data is submitted to each solution and the three sets of results are compared.
A GENERAL SOLUTION FOR THE LATENT CLASS MODEL OF LATENT STRUCTURE ANALYSIS*
Authors: Green Bert F. 
Published: August 2014

ABSTRACTFor the point distribution model of Lazarsfeld's latent structure analysis, the general matrix equation is stated which relates the manifest data in the form of joint occurrence matrices to the latent parameters. A general solution of this equation for the latent parameters is presented, which is based on the notion of factoring two joint occurrence matrices. The solution is valid under certain conditions which will usually be fulfilled. The solution assumes that estimates are available for the elements in the joint occurrence matrices with recurring subscripts, analogous to item communality or reliability. Some alternative methods of obtaining these estimates are discussed. Finally, a method is indicated for calculating a certain joint occurrence matrix needed in the solution.
VALIDATION OF THE STUDY OF ARGUMENTS AND VOCABULARY INTEREST TEST EXPERIMENTAL SECTIONS OF ONE FORM OF THE LAW SCHOOL ADMISSION TEST
Authors: French John W. 
Published: August 2014

ABSTRACTA half‐hour, long‐passage reading comprehension test and a half‐hour vocabulary test designed to test interest in debating, current affairs, literature, and hobbies were tried out in the experimental section of the Law School Admission Test in the spring of 1951. The validities of these tests were computed for five law schools and were found to be insufficient for making an appreciable addition to the validity already provided by the present LSAT.
DIFFERENTIAL PREDICTABILITY IN THE USE OF TEST SCORES
Authors: Frederiksen Norman , Melville S. Donald 
Published: August 2014

ABSTRACTThe purpose of this study is to illustrate how a test may be used more effectively for prediction through the identification of subgroups of individuals for whom the test is especially valid as a predictor.It was hypothesized that scores on the Strong Vocational Interest Blank would be more predictive of success in an engineering school for noncompulsive than for compulsive students. Students were classified as compulsive or noncompulsive in two ways: on the basis of (1) scores on the Accountant Scale of the Strong blank, and (2) reading speed in relation to vocabulary. The compulsive subgroups were composed of students who most resembled accountants in one case, and students whose speed of comprehension was low in relation to vocabulary in the other. The value of the Strong scores as predictors of freshman average grade was determined for compulsive and for noncompulsive groups. The results tended to confirm the hypothesis that Strong scores are more valid predictors of academic success for compulsive than for noncompulsive students.It is concluded that this study demonstrates that the use of tests could be improved by discovering subgroups of people for whom a test is expecially appropriate as a predictor.
AN EMPIRICAL COMPARISON OF FIVE METHODS OF SHORTENING A TEST*
Authors: Olsen Marjorie A. , Schrader William B. 
Published: August 2014

ABSTRACTThis study was designed to provide an empirical comparison of the following methods of shortening the Law School Admission Test: (1) Internal consistency item analysis; (2) External criterion item analysis; (3) A method involving the ratio of item‐criterion correlation to item‐subtest correlation, substantially as described by Gulliksen; (4) A method described by Horst for estimating optimal times for subtests; and (5) A linear method for estimating optimal times for subtests. The analysis was carried out separately for two parallel subsamples of 500 first‐year law school students, and trial scoring keys requiring 135 minutes of testing time were assembled from material originally requiring 190 minutes.When the trial scoring keys obtained from one subsample were validated against first‐year law school grades for the opposite subsample, the results were as follows: For one subsample, the validity coefficients for the five trial keys ranged from .568 to .576; the coefficient for total score on the 190 minute test was .586. For the second subsample, the validities of the trial keys were between .483 and .496, as compared with .493 for the 190 minute test.
SELECTION AND CLASSIFICATION TESTS FOE WOMEN: A REVIEW OF THE LITERATURE
Authors: Wand Barbara , Mollenkopf William G. 
Published: August 2014

ABSTRACTThe purpose of this review of the literature was to examine the appropriateness of using with women the same selection and classification procedures that are used with men in situations in which both men and women are selected for the same jobs. Particular attention was paid to reports of the selection of women for jobs similar to billets in the U. S. Navy.Two valuable sources of information on women which included comparable data for men were U. S. Air Force reports of the selection of personnel for Air Force technical schools and British reports of the selection of women for the Auxiliary Territorial Service during World War II.Most industrial studies were based on samples of one sex. It became apparent that in normal times most civilian jobs are held predominantly by members of one sex or the other, and hence the practical problem of the influence of sex differences on predictive measures has not been investigated to any extent by those who are conducting personnel research in industry.The findings tend to support the assumption that tests developed and used for the selection of men must be carefully examined prior to their use in selecting women for the same jobs. This seems particularly true for tests in mechanical and computational areas. In general, findings seem to indicate that a given tests score may not predict the same level of on‐the‐job performance for a woman as for a man, there being evidence that women do better than would be predicted from scores based on tests and procedures developed for men.
THE WEST POINT TRYOUT OF THE GUIDANCE BATTERY, PART 2
Authors: French John W. 
Published: August 2014

ABSTRACTFor the purpose of studying differential and comparative prediction with pure‐factor tests, information was desired on which to base the selection of appropriate factors and of appropriate measures for each factor. In August, 1950 some interest‐information variables and a battery including two, three, or four tests to represent each of thirteen established factors were administered to an entering class of West Point cadets. The tests and five criterion variables were intercorrelated and factored. The tests, the administration, and the intercorrelations of tests are described in RB‐51‐12. The present bulletin describes the correlations with course grades, the factor analysis, and the interpretations of factors. Sixteen factors were extracted and rotated to simple structure. These include twelve of the thirteen factors planted in the battery, two interest factors, the grade factor, and a residual factor. The study served to supply satisfactory information for setting up an experimental battery that could be used in studying the feasibility of making useful differential and comparative predictions of college major‐field success with pure‐factor tests.
THE RELATIONSHIP BETWEEN ITEM DIFFICULTY AND TEST VALIDITY AND RELIABILITY
Authors: Myers Charles T. 
Published: August 2014

ABSTRACTUsing freshman average grades as a criterion, this research compares the validity and reliability of part scores based on sets of items selected from a verbal and mathematical aptitude test for college freshmen, the sets having been selected on the basis of their “difficulty.” Two parallel sets of 24 items each were selected from the items whose difficulty fell within the limits of 40 per cent passing and 74 per cent passing. Two other parallel sets of 24 items were selected from the items outside this range with one half the items in each set easy and one half the items hard.The subjects were 1600 freshmen at 12 liberal arts colleges.For each college a table was prepared of correlations between sets of items and between each set of items and grade averages. The correlations between parallel sets of items were taken as the reliability coefficients. The correlations between average grades and the sums of scores on pairs of parallel sets were taken as the validity coefficients. Thus there were 12 pairs of reliability coefficients and 12 pairs of validity coefficients, one pair of each for each college. The significance of the differences between the two kinds of sets was tested by Wilcoxon's matched pairs signed ranks test.No significant differences were found for the validities. The mean validity coefficient for all sets was .50. The sets of medium “difficulty” items were found to be more reliable at the two per cent level of significance. The mean reliability of these sets of 24 items was .69 while the mean reliability of the other sets was .63.