bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of SNPs in pooled DNA: A decision theoretic model
Authors: König Inke R. , Ziegler Andreas 
Published: December 2003

AbstractSystematic analysis of the genetic background of complex diseases using single nucleotide polymorphisms (SNPs) affords a tremendous amount of genotypings. To reduce the amount of genotypings necessary and hence the overall cost of a case‐control study with SNPs, the genotyping is often performed in two stages: In the first, the DNA of all cases and all controls are mixed into two pools and genotyped for each SNP. The frequency of both alleles is determined in both pooled DNA samples. If different frequencies are observed in the pools of cases and controls, genotyping is performed individually in the second stage and analyzed conventionally. However, so far no well‐founded algorithm is available to guide the decision on whether to genotype a SNP individually. In this report, an approach is introduced for the decision on individual genotyping based on the results from pooled DNA. The analysis is modeled as a decision process with the specific goal to decide on whether to genotype a specific SNP individually. For a given situation, the resulting decision criteria are aimed to be optimal for those conducting the study. Different loss functions and decision rules are presented. Using Monte‐Carlo simulations, we show that for a given situation, the genotyping rates and hence the costs can be reduced remarkably while maintaining acceptable overall error rates. Genet Epidemiol 26:31–43, 2004. © 2003 Wiley‐Liss, Inc.
Principal component analysis for selection of optimal SNP‐sets that capture intragenic genetic variation
Authors: Horne Benjamin D. , Camp Nicola J. 
Published: December 2003

AbstractCandidate gene association studies often utilize one single nucleotide polymorphism (SNP) for analysis, with an initial report typically not being replicated by subsequent studies. The failure to replicate may result from incomplete or poor identification of disease‐related variants or haplotypes, possibly due to naive SNP selection. A method for identification of linkage disequilibrium (LD) groups and selection of SNPs that capture sufficient intra‐genic genetic diversity is described. We assume all SNPs with minor allele frequency above a pre‐determined frequency have been identified. Principal component analysis (PCA) is applied to evaluate multivariate SNP correlations to infer groups of SNPs in LD (LD‐groups) and to establish an optimal set of group‐tagging SNPs (gtSNPs) that provide the most comprehensive coverage of intra‐genic diversity while minimizing the resources necessary to perform an informative association analysis. This PCA method differs from haplotype block (HB) and haplotype‐tagging SNP (htSNP) methods, in that an LD‐group of SNPs need not be a contiguous DNA fragment. Results of the PCA method compared well with existing htSNP methods while also providing advantages over those methods, including an indication of the optimal number of SNPs needed. Further, evaluation of the method over multiple replicates of simulated data indicated PCA to be a robust method for SNP selection. Our findings suggest that PCA may be a powerful tool for establishing an optimal SNP set that maximizes the amount of genetic variation captured for a candidate gene using a minimal number of SNPs. Genet Epidemiol 26:11–21, 2004. © 2003 Wiley‐Liss, Inc.
Power estimation of multiple SNP association test of case‐control study and application
Authors: Hao Ke , Xu Xin , Laird Nan , Wang Xiaobin , Xu Xiping 
Published: December 2003

AbstractAt the current stage, a large number of single nucleotide polymorphisms (SNPs) have been deployed in searching for genes underlying complex diseases. A powerful method is desirable for efficient analysis of SNP data. Recently, a novel method for multiple SNP association test using a combination of allelic association (AA) and Hardy‐Weinberg disequilibrium (HWD) has been proposed. However, the power of this test has not been systematically examined. In this study, we conducted a simulation study to further evaluate the statistical power of the new procedure, as well as of the influence of the HWD on its performance. The simulation examined the scenarios of multiple disease SNPs among a candidate pool, assuming different parameters including allele frequencies and risk ratios, dominant, additive, and recessive genetic models, and the existence of gene‐gene interactions and linkage disequilibrium (LD). We also evaluated the performance of this test in capturing real disease associated SNPs, when a significant global P value is detected. Our results suggest that this new procedure is more powerful than conventional single‐point analyses with correction of multiple testing. However, inclusion of HWD reduces the power under most circumstances. We applied the novel association test procedure to a case‐control study of preterm delivery (PTD), examining the effects of 96 candidate gene SNPs concurrently, and detected a global P value of 0.0250 by using Cochran‐Armitage χ2s as “starting” statistics in the procedure. In the following single point analysis, SNPs on IL1RN, IL1R2, ESR1, Factor 5, and OPRM1 genes were identified as possible risk factors in PTD. Genet Epidemiol 26:22–30, 2004. © 2003 Wiley‐Liss, Inc.
Tests for covariate‐associated heterogeneity in IBD allele sharing of affected relatives
Authors: Mirea Lucia , Briollais Laurent , Bull Shelley 
Published: December 2003

AbstractLinkage studies that aim to map susceptibility genes for complex diseases commonly test for excess allele sharing among affected relatives. Conventional methods based on identical‐by‐descent IBD allele sharing do not allow for possible differences among families, such as arise in the case of locus heterogeneity, and thus have reduced ability to detect linkage in the presence of such heterogeneity. We investigated two approaches to test for heterogeneity in allele sharing, using a family‐level covariate that may be associated with different disease mechanisms leading to differences in allele sharing. Likelihood ratio tests for heterogeneity were formulated based on an extension of the linear and exponential likelihood models developed by Kong and Cox ([1997] Am. J. Hum. Genet. 61:1179–1188). Alternatively, we examined the asymptotic and permutation distributions of T‐tests for differences between mean allele‐sharing linkage scores from two covariate‐defined family subgroups, assuming exchangeability. The size and power of heterogeneity tests were evaluated for Sall and Spairs allele‐sharing scoring functions using data sets of families with affected sibling and cousin pairs, generated under a model of locus heterogeneity. In certain simulation scenarios, the likelihood ratio test statistics did not follow the expected asymptotic distributions. The type I error estimates for the T‐statistics conformed to nominal 5 and 1% levels in all scenarios considered, and corresponding power was comparable to that of the likelihood ratio tests. Application of these tests for heterogeneity detected significant differences in allele sharing between subgroups of families with inflammatory bowel disease. Genet Epidemiol 26:44–60, 2004. © 2003 Wiley‐Liss, Inc.
Family‐based tests for associating haplotypes with general phenotype data: Application to asthma genetics
Authors: Horvath Steve , Xu Xin , Lake Stephen L. , Silverman Edwin K. , Weiss Scott T. , Laird Nan M. 
Published: December 2003

AbstractWe provide a general purpose family‐based testing strategy for associating disease phenotypes with haplotypes when phase may be ambiguous and parental genotype data may be missing. These tests for linkage and association can be used in candidate gene studies with tightly linked markers. Our proposed weighted conditional approach extends the method described in Rabinowitz and Laird [Human Heredity 504:227–233, 2000] to multiple markers. It is attractive because it provides haplotype tests for family‐based studies that are efficient and robust to population admixture, phenotype distribution specification, and ascertainment based on phenotypes. It can handle missing parental genotypes and/or missing phase in both offspring and parents. It yields either haplotype‐specific (univariate) tests or multi‐haplotype (global) tests. This extension has been implemented in the freely available software haplotype FBAT. We used the haplotype FBAT program to test for associations between asthma phenotypes and single nucleotide polymorphisms (SNPs) in the beta‐2 adrenergic receptor gene. Whereas no single SNP showed significant association with asthma diagnosis or bronchodilator responsiveness (quantitative trait), a haplotype‐based global test found a highly significant association with asthma diagnosis (P value <0.00005) and the measure of bronchodilator responsiveness (P value =0.016). Genet Epidemiol 26:61–69, 2004. © 2003 Wiley‐Liss, Inc.
Uncle Sam watches nervously: Foreign investment in U.S. industries
Authors: Rosener James D. , Dorris Gregory C. 
Published: December 2003

AbstractAs the war on terrorism continues, foreign investment in U.S. industries has come under ever closer scrutiny. This has a big impact on M&A
with foreign partners or investors. The authors explain what you need to know to safely navigate this maze. © 2004 Wiley Periodicals,
Inc.
Near zero‐defect accounting with Six Sigma
Authors: Brewer Peter C. , Bagranoff Nancy A. 
Published: December 2003

AbstractMany companies have used the Six Sigma methodology to improve manufacturing processes, but in recent years, companies have started using Six Sigma to
improve the finance function. This article provides an overview of Six Sigma, explains how two companies are using Six Sigma to streamline their
respective finance departments, and offers tips for companies interested in adopting Six Sigma for their finance departments. © 2004 Wiley
Periodicals, Inc.
The relationship of sociotropy and autonomy to posttraumatic cognitions and PTSD symptomatology in trauma survivors
Authors: Kolts Russell L. , Robinson April M. , Tracy Jessica J. 
Published: December 2003

AbstractThe current study examined relationships between sociotropic and autonomous personality styles and posttraumatic stress disorder (PTSD) symptomatology following trauma as well as specific posttraumatic cognitions that have been shown to characterize individuals with PTSD. Self‐report data were collected in a sample of 156 college students indicating a history of traumatic experience. Significant relationships were found between symptoms of PTSD and depression and measures of sociotropy, autonomy, and negative posttraumatic beliefs about self and world. Additionally, measures of autonomy and negative posttraumatic thoughts improved prediction of PTSD symptom level after controlling for depressive symptoms. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
A revised Spanish version of the Beck Depression Inventory: Psychometric properties with a Puerto Rican sample of college students
Authors: Bonilla Janet , Bernal Guillermo , Santos Axel , Santos Douglas 
Published: December 2003

AbstractThe Beck Depression Inventory (BDI) is a widely used self‐report measure for depression. This study has two objectives: (a) to revise, develop, and adapt a Spanish language BDI (BDI‐S) that takes the criteria for the diagnosis of major depression according to the DSM‐IV into consideration; and (b) to evaluate the psychometric properties (internal reliability and construct validity) of the revised version of the BDI (BDI‐S). A sample of 351 undergraduate students at the University of Puerto Rico participated in this study. The participants who agreed to participate in the study and signed the consent form completed self‐report measures related to depression (BDI‐S, CES‐D, and LCSd‐7), dysfunctional cognition (DAS‐A and IBT), stressful life events (LES), and social support (CAS). The coefficient of internal consistency obtained for the 22 BDI‐S items was .88. The correlation coefficients between the BDI‐S and instruments that measured other constructs (not depression) were lower than the correlation coefficients between instruments that measured the same constructs. Factor analysis
revealed that the factor loading for the BDI‐S was congruent with dimensions of depression reported in the literature. These results generally support the internal consistency and the construct validity of the BDI‐S. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Recommendations for applying tests of equivalence
Authors: Cribbie Robert A. , Gruman Jamie A. , Arpin‐Cribbie Chantal A. 
Published: December 2003

AbstractResearchers in psychology reliably select traditional null hypothesis significance tests (e.g., Student's t test), regardless of whether the research hypothesis relates to whether the group means are equivalent or whether the group means are different. Tests of equivalence, which have been popular in biopharmaceutical studies for years, have recently been introduced and recommended to researchers in psychology for demonstrating the equivalence of two group means. However, very few recommendations exist for applying tests of equivalence. A Monte Carlo study was used to compare the test of equivalence proposed by Schuirmann with the traditional Student t test for deciding if two group means are equivalent. It was found that Schuirmann's test of equivalence is more effective than Student's t test at detecting population mean equivalence with large sample sizes; however, Schuirmann's test of equivalence performs poorly relative to Student's t test with small sample sizes and/or inflated variances. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Remembering the 1978 and 1990 task forces on self‐help therapies
Authors: Rosen Gerald M. 
Published: December 2003

AbstractA special series on self‐administered therapies was edited by Forrest R. Scogin for the Journal of Clinical Psychology (Volume 59, Number 3). Articles in the edited series failed to mention two task forces on self‐help therapies that were sponsored by groups within the American Psychological Association in 1978 and 1990. Consideration of the work by these task forces provides an historical perspective for the issues and recommendations provided in Scogin's series. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
A national survey of trainee impairment in clinical, counseling, and school psychology doctoral programs and internships
Authors: Huprich Steven K. , Rudd M. David 
Published: December 2003

AbstractThe purpose of this study was to assess the frequency, type, and management of trainee impairment at a national level across doctoral programs in clinical, counseling, and school psychology and predoctoral internships. A total of 199 surveys were completed, returned, and usable. In general, doctoral programs reported a greater frequency of trainee impairment than internships. However, a greater percentage of internships had a policy and program in place for managing impairments than did doctoral programs. These findings are compared with past studies and reviews of this issue. In light of these findings, specific implications for training programs are discussed, with the recommendation that training programs address more attention to the assessment and management of such problems. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Comparative analysis of methods for determining bite force in the spiny dogfish Squalus acanthias
Authors: Huber Daniel Robert , Motta Philip Jay 
Published: December 2003

AbstractMany studies have identified relationships between the forces generated by the cranial musculature during feeding and cranial design. Particularly important to understanding the diversity of cranial form amongst vertebrates is knowledge of the generated magnitudes of bite force because of its use as a measure of ecological performance. In order to determine an accurate morphological proxy for bite force in elasmobranchs, theoretical force generation by the quadratomandibularis muscle of the spiny dogfish Squalus acanthias was modeled using a variety of morphological techniques, and lever‐ratio analyses were used to determine resultant bite forces. These measures were compared to in vivo bite force measurements obtained with a pressure transducer during tetanic stimulation experiments of the quadratomandibularis. Although no differences were found between the theoretical and in vivo bite forces measured, modeling analyses indicate that the quadratomandibularis muscle should be divided into its constituent divisions and digital images of the cross‐sections of these divisions should be used to estimate cross‐sectional area when calculating theoretical force production. From all analyses the maximum bite force measured was 19.57 N. This relatively low magnitude of bite force is discussed with respect to the ecomorphology of the feeding mechanism of S. acanthias to demonstrate the interdependence of morphology, ecology, and behavior in organismal design. J. Exp. Zool. 301A:26–37, 2004. © 2004 Wiley‐Liss, Inc.
Quantitation of cytomegalovirus DNA in cerebrospinal fluid and serum specimens from AIDS patients using a novel highly sensitive nested competitive PCR and the cobas amplicor CMV monitor™
Authors: Tarragó David , Mateos María‐Luisa , Avellón Ana , Pérez‐Vázquez María‐Dolores , Tenorio Antonio 
Published: December 2003

AbstractA novel nested quantitative‐competitive polymerase chain reaction (nQC‐PCR) assay was developed to quantify as few as ten copies per tube of human cytomegalovirus DNA with an overall dynamic range of 10–105 copies per tube. This nQC‐PCR assay is based on co‐amplification of a mimic DNA and it was evaluated with 26 cerebrospinal fluid (CSF) specimens and 44 serum specimens from 70 CMV‐infected AIDS patients, 35 of them were diagnosed of CMV retinitis. An excellent correlation was found between nQC‐PCR assay and the commercially available Cobas Amplicor CMV Monitor™ (CACM) assay (R = 0.9999; P < 0.001; n = 42). Moreover, 13 serum samples with CMV viral loads undetectable with the CACM were successfully quantified by nQC‐PCR. CMV viral load was significantly higher in patients with CMV retinitis (P = 0.003). The nQC‐PCR assay described below is a very sensitive test for accurate quantitative detection of CMV DNA in different clinical specimens that avoids the need for high‐cost instrumentation. J. Med. Virol. 72:249–256, 2004. © 2004 Wiley‐Liss, Inc.
Hepatitis B virus DNA in liver, serum, and peripheral blood mononuclear cells after the clearance of serum hepatitis B virus surface antigen
Authors: Murakami Yoshiki , Minami Masahito , Daimon Yukiko , Okanoue Takeshi 
Published: December 2003

AbstractThe integration of hepatitis B virus (HBV) DNA in the liver of chronic HBV carriers has been documented extensively. However, the status of the viral genome during acute infection has not been assessed conclusively. While HBV DNA sequences are detected often in serum, liver, and peripheral blood mononuclear cells (PBMCs) after the clearance of serum the hepatitis B virus surface antigen (HBsAg), the precise status of the viral genome, and in particular the possible persistence of integrated genomes in PBMCs, has not been established. A highly sensitive PCR‐derived assay (Alu–PCR) was employed to re‐examine liver and PBMC specimens obtained from patients with acute (n = 19) and chronic (n = 22) hepatitis in whom serum HBsAg was present (n = 12) (HBV‐related chronic active hepatitis) or absent with anti‐HCV (n = 10) (HCV‐related chronic active hepatitis). Viral integration was demonstrated in 3 out of 19 liver specimens from patients with acute hepatitis and 12 out of 12 specimens from patients with chronic hepatitis. Viral integration was also observed in 4 out of 7 PBMC samples from HBV‐related chronic active hepatitis patients and 2 out of 10 liver and PBMC samples from HCV‐related chronic active hepatitis patients. In one liver specimen from an acute hepatitis patient, HBV DNA was found integrated in the intronic sequence of the tumour necrosis factor (TNF)‐induced protein gene; viral integration into cellular sequences was also found in the PBMCs of four HBV‐related chronic active hepatitis and two HCV‐related chronic active hepatitis. The results demonstrate the early integration of HBV genome during acute viral infections and the persistence of the viral genome in an integrated form in PBMCs. J. Med. Virol. 72:203–214, 2004. © 2004 Wiley‐Liss, Inc.
Influence of antigenic drift on the intensity of influenza outbreaks: Upper respiratory tract infections of military conscripts in Finland
Authors: Pyhälä Reijo , Visakorpi Risto , Ikonen Niina , Kleemola Marjaana 
Published: December 2003

AbstractA total of 102,600 upper respiratory infections (URI) were recorded among young military conscripts in the Finnish Defence Forces during the study period from October 1991 to March 1994. This period covered three outbreaks caused by H3N2‐subtype influenza A virus and one outbreak of influenza B. During the 1991/92 outbreak caused by A/Beijing/353/89‐like virus, the calculated influenza A incidence was 2,206/10,000 men. During the 1992/93 outbreak when influenza B was the predominant virus, a new drift variant of influenza A that belonged to the lineage of A/Beijing/32/92‐like and A/Shangdong/9/93‐like viruses circulated but the incidence of influenza A was not more than 1,044/10,000. A higher incidence, 2,810/10,000, was recorded during the 1993/94 outbreak, when the circulating virus was similar to the 1992/93 virus antigenically and with regard to haemagglutinin and neuraminidase (NA) gene sequences. Crossreactive haemagglutination‐inhibition antibodies induced in 1991/92 probably were sufficient to restrict the epidemic activity in 1992/93 but no longer in 1993/94. Furthermore, during the 1991/92 outbreak, some of the A/Beijing/353/89‐like viruses already had shared the NA sequence markers characteristic of the viruses in 1992/93 and 1993/94, which may also have strengthened protection in 1992/93. J. Med. Virol. 72:275–280, 2004. © 2004 Wiley‐Liss, Inc.
Genotyping of the JC virus in urine samples of healthy Korean individuals
Authors: Jeong Byung‐Hoon , Lee Kyung‐Hee , Choi Eun‐Kyoung , Kim Kyunghoon , Kim Yong‐Sun 
Published: December 2003

AbstractA human polyomavirus, JC virus (JCV) is ubiquitous in humans and infects children asymptomatically. It persists in renal tissue and is excreted progeny in urine. DNAs from urine samples of 100 healthy Korean individuals were screened for the presence of JCV by polymerase chain reaction (PCR). Twenty of the samples were positive for JCV. JCV DNA was found in one individual (4%) in the 1–19‐year group, two individuals (9%) in the 20–39‐year group, ten individuals (38%) in the 40–59‐year group, seven individuals (28%) in the over 60‐year group. The prevalence of JC viral DNA was the highest in the 40–59‐year‐old Korean population. To investigate genotypes of JCV in Korea, the genotypes were determined by DNA sequence analysis of the regulatory region (333 bp) and the VT‐intergenic region (656 bp) of DNA from the 20 JCV isolates. We have identified three distinctive JCV strains in the regulatory region and ten distinctive JCV strains in the VT‐intergenic region of DNA from the 20 isolates. Based on restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis of the VT‐intergenic region of JCV, two distinct subtypes, CY and type 2A (MY), were found to be prevalent in this Korean population. CY and type 2A of JCV were identified in 13 individuals (65%) and four individuals (20%), respectively. Interestingly, type 1, which was distributed mostly in Europe, was found in 3 (15%) isolates from healthy Korean individuals. J. Med. Virol. 72:281–289, 2004. © 2004 Wiley‐Liss, Inc.