Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Reanalysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,135 records · Page 63Linked to original sources
PubMed2006

Auditory hallucinations in schizophrenia: intrusive thoughts and forgotten memories.

INTRODUCTION: This paper presents a new cognitive model of auditory hallucinations in schizophrenia. We suggest that auditory hallucinations are auditory representations derived from the unintentional activation of memories and other irrelevant current mental associations. Our model proposes that a combination of deficits in intentional inhibition and contextual memory is critical to the experience of auditory hallucinations. The failure in intentional inhibition produces unwanted and uncontrollable mental events which are not recognised because they have lost the contextual cues that would normally facilitate recognition. METHODS: This article amalgamates recently published data and presents a reanalysis of the findings on 43 patients with a diagnosis of schizophrenia (Badcock, Waters, Maybery, & Michie, 2005; Waters, Badcock, Maybery, & Michie, 2003a; Waters, Maybery, Badcock, & Michie, 2004a). Relative risk was also estimated to determine whether the combination of deficits increases the risk of having auditory hallucinations. RESULTS: Almost 90% of patients currently experiencing auditory hallucinations showed the predicted combination of deficits on both inhibition and context memory, compared to only a third of patients without hallucinations. In addition, the results showed that those patients with the specified cognitive deficits were at an especially increased risk of having auditory hallucinations relative to patients without the deficits. CONCLUSIONS: The results of our investigations strongly support the role of intentional inhibition and context memory in auditory hallucinations. Critical consideration of the findings also suggests that additional cognitive processes might be important for the expression of this symptom.

Cognition↗
PubMed2002

Left cradling and left ear advantage for emotional speech: listen to the other side too.

In a recent issue of this journal, Turnbull and Bryson (2001) examined a possible relation between left ear (right hemisphere) advantage for perception of emotional speech and the universal preference of mothers to cradle infants on the left side, referring to a hypothesis that we had previously suggested (Sieratzki & Woll, 1996). Although they concluded that their data do not support our theory, reanalysis does suggest a connection between the hemispheric asymmetry for speech prosody and the leftward cradling bias.

Comment↗
PubMed2005

Recurrent event analysis of lapse and recovery in a smoking cessation clinical trial using bupropion.

We report a reanalysis of data from a prior study describing the event history of quitting smoking aided by bupropion, using recurrent-event models to determine the effect of the drug on occurrence of lapses and recoveries from lapse (resumption of abstinence). Data were collected on 1,070 subjects across two similar double-blind randomized clinical trials of bupropion versus placebo and fitted with separate Cox regression models for lapse and recovery. Analyses were split using discrete time-varying covariates between the treatment (weeks 1-10) and follow-up phases (end of treatment to 12 months). Bupropion was associated with slower lapse during treatment for both sexes, and being female was associated with faster lapse across both phases. Drug did not affect time to recovery for males but was associated with faster recovery among females, allowing women to recover as quickly as men. High levels of nicotine dependence did not affect time to lapse but were associated with slower recovery from lapse across treatment and follow-up phases. During the treatment phase, higher levels of baseline depression symptoms had no effect on time to lapse but were associated with slower recovery from lapse. Results highlight the asymmetry in factors preventing lapse versus promoting recovery. Specifically, dependence, depression symptoms, and a sex x drug interaction were found to affect recovery but not lapse. Further research disentangling lapse and recovery events from summary abstinence measures is needed to help us develop interventions that take advantage of bupropion at its best and that compensate where it is weak.

Adult↗
PubMedDate not supplied

Controlling for potential confounding by occupational exposures.

Occupational exposure is an important potential confounder in air pollution studies because it is plausible that individuals who live in highly polluted areas also work in more polluted environments. While the original investigators made some efforts to control for possible confounding by occupational variables, it was felt that these could be improved upon. The reanalysis team attempted to control for occupational confounding by supplementing the original data sets with two new variables, an indicator of the "dirtiness" of a subject's job and an indicator of possible exposure to occupational lung carcinogens. The attribution of these variables was based on the job title recorded by the original investigators and on the judgment of our experts concerning typical exposure patterns in different occupations. We fitted Cox proportional-hazards models identical to those that had been used by the original investigators while also including one or both of the new occupational covariates in the models. In none of the analyses did the inclusion of the occupational variables materially change the results. It would therefore appear that, in general, the results reported by the original investigators were not distorted by inadequate control of occupational variables. We also carried out some analyses using the dirtiness index as a stratification variable to assess effect modification. There was some indication, albeit inconsistent, that the effect of air pollution on mortality was greater among subjects with dirty jobs than among those with clean jobs.

Adult↗
PubMedDate not supplied

Spatial analysis of the air pollution-mortality relationship in the context of ecologic confounders.

Lack of control for confounding by ecological covariates that may relate to sulfate air pollution and mortality was a key criticism of the two studies that were the focus of the Particle Reanalysis Project. To assess the validity of this criticism, we address the question: "Does sulfate air pollution exert health effects when the impact of other individual and ecologic variables thought to influence health is taken into account?" A related question arises from the possibility of autocorrelation in the mortality risks and ecologic covariates. Failure to control for autocorrelation can lead to false positive significance tests and may indicate bias resulting from a missing variable or group of variables. We control for more than 25 individual risk factors and for 20 ecologic variables representing environmental, socioeconomic, demographic, health- care, and lifestyle determinants of health in a two-stage multilevel analysis. Four modeling strategies are used to control for spatial autocorrelation. Of the 20 ecologic variables tested, only sulfate and sulfur dioxide are significant in models that incorporate spatial autocorrelation. Accounting for autocorrelation also reduces the size and certainty of the sulfate effect on mortality when compared to results generated from Cox models where independent observations are assumed. Confidence limits for the sulfate relative risk include unity in models that simultaneously control for sulfur dioxide and autocorrelation.

Air Pollution↗
PubMedDate not supplied

Promiscuous gene expression in the thymus: the root of central tolerance.

The thymus is a complex organ with an epithelium formed by two main cell types, the cortical thymic epithelial (cTECs) and medullary thymic epithelial cells (mTECs), referred to as stroma. Immature thymocytes arising from the bone marrow, macrophages and dendritic cells also populate the thymus. Thymocytes evolve to mature T cells featuring cell differentiation antigens (CDs), which characterize the phenotypically distinct stages, defined as double-negative (DN), double positive (DP) and single positive (SP), based on expression of the coreceptors CD4 and CD8. The thymus is therefore implicated in T cell differentiation and during development into T cells thymocytes are in close association with the stroma. Recent evidence showed that mTECs express a diverse set of genes coding for parenchymal organ specific proteins. This phenomenon has been termed promiscuous gene expression (PGE) and has led to the reconsideration of the role of the thymus in central T cell tolerance to self-antigens, which prevents autoimmunity. The evidence of PGE is causing a reanalysis in the scope of central tolerance understanding. We summarize the evidence of PGE in the thymus, focusing particularly the use of cDNA microarray technology for the broad characterization of gene expression and demarcation of PGE emergence during thymus ontogeny.

Animals↗
PubMedDate not supplied

Can the famous really postpone death?

David P. Phillips has reported evidence that famous people are often able to postpone their deaths until after a birthday. A reexamination of Phillips' data shows some aspects of his analysis to be questionable, including the lumping together of deaths that occur during the birthmonth, which does not distinguish deaths that occurred before the birthday from those that occurred afterward. A reanalysis of his data shows that there were actually a relatively large number of deaths in the month preceding and the months following the birthday. One explanation is that the anxiety associated with this milestone and the excesses associated with its celebration are sometimes fatal. Another explanation is that Phillips' results were a fluke created by a selective use of data.

Anxiety↗
PubMed1998

Voluntary and involuntary access to autobiographical memory.

Involuntary autobiographical memories recorded in a diary study are compared to voluntary autobiographical memories retrieved in response to verbal cues in a laboratory. The verbal cues were generated to be comparable to the cues that were found to elicit the involuntary memories. The findings demonstrate that voluntary and involuntary retrieval may access different samples of autobiographical memories. The voluntary memories were (1) less specific, (2) more frequently rehearsed, and (3) less emotionally positive than the involuntary memories. A reanalysis of the diary study examined conditions of involuntary retrieval. The memories occurred most frequently when attention was diffuse. They were typically triggered by environmental cues matching central features of the remembered event. The findings are discussed in relation to current models of autobiographical memory.

Adult↗
PubMed1999

Risk/protective factors among addicted mothers' offspring: a replication study.

There are few systematic studies of the school-aged offspring of drug-dependent patients, although this information is useful for planning evidence-based prevention programs. We have completed such a study, which we compare to a similar study independently conducted in 1998. In both studies, both the parent and offspring were assessed blindly and independently by direct diagnostic interviews, and parental assessment of offspring was also obtained. The similarity in design and methods between studies provided an opportunity for replication by reanalysis of data. The major findings are a replication in two independently conducted studies of school-aged offspring of opiate- and/or cocaine-addicted mothers of the high rates of any psychiatric disorder (60% in both studies), major depression (20%, 26%), oppositional defiant disorder (ODD) (18%, 23%), conduct disorder (17%, 9%), attention-deficit/hyperactivity disorder (ADHD) (13%, 8%), and substance abuse (5%, 10%) among offspring. Both studies also found high rates of comorbid alcohol abuse, depression, and multiple drugs of abuse in the mothers. We conclude that efforts to replicate findings by analyses of independently conducted studies are an inexpensive way to test the sturdiness of findings that can provide the empirical basis for preventive efforts. Clinically, the data in both studies suggest that both drug dependence and associated psychopathology should be assessed and treated in opiate addicts with young offspring, and the offspring should be monitored for the development of conduct and mood disorders and substance use.

Adolescent↗
PubMed2004

Modeling missingness for time-to-event data: a case study in osteoporosis.

Clinical trials of long duration are often hampered by high dropout rates, making statistical inference and interpretation of results difficult. Statistical inference should be based on models selected according to whether missingness is independent of response [missing completely at random (MCAR)], or depends on response either through observed responses only [missing at random (MAR)] or through unobserved responses [nonignorable missing (NIM)]. If the dropout rate is high and little is known about the dropout mechanism, plausible nonignorable missing scenarios should be investigated as a sensitivity tool, offering the data analyst an understanding of the robustness of conclusions. Modeling missingness is illustrated by an analysis of an interval censored time-to-event outcome from a 5-year clinical trial on fracture response in osteoporosis in which the overall dropout rate was substantial. In this article, we provide an overview of a reanalysis accounting for possible nonignorable missingness, emphasize the importance of modeling the dropout and response mechanisms jointly, and highlight critical points arising in missing data problems.

Aged↗
PubMed2003

Jail-based substance user treatment: an analysis of retention.

Many jail inmates have a history of substance use and "abuse"; few, however, receive comprehensive treatment for substance use disorders while in jail. The authors offer a longitudinal reanalysis of data from five jail-based substance user treatment programs. Survival analysis was used to identify client characteristics associated with length of time in treatment. Survival curves for the five programs were compared, indicating which ones retained inmates the longest. Results from a model stratified by jail site revealed that inmates over 25 years of age and those already sentenced had significantly longer treatment stays. The Substance Abuse Intervention Division (SAID) program, a modified therapeutic community in a New York jail, and the Deciding, Educating, Understanding, Counseling, and Evaluation (DEUCE) program, a curriculum-based intervention, had the longest survival curves and were, therefore, most effective at retaining inmates in treatment.

Adult↗
PubMed2000

Absence of significant linkage between phonological coding dyslexia and chromosome 6p23-21.3, as determined by use of quantitative-trait methods: confirmation of qualitative analyses.

We recently reported the absence of significant linkage of phonological coding dyslexia (PCD) to chromosome 6p23-p21.3 in 79 families with at least two affected siblings, even though linkage of dyslexia to this region has been found in four other independent studies. Whereas, in our previous analyses, we used a qualitative (affected, unaffected, or uncertain) PCD phenotype, here we report a reanalysis of linkage to the chromosome 6p region, by use of four quantitative measures of reading disability: phonological awareness, phonological coding, spelling, and rapid-automatized-naming (RAN) speed. The phonological-coding and spelling measures were highly correlated with each other and with the qualitative PCD phenotype, whereas the phonological-awareness and RAN-speed measures were only moderately correlated with the other measures. Using two-point and multipoint quantitative-trait sib-pair linkage analyses and variance-components analyses, we were unable to detect significant evidence for a locus in the 6p23-p21.3 region influencing any of the quantitative reading measures, supporting our previous qualitative linkage results. The most likely explanation for our inability to detect linkage between dyslexia and this region is that families with subtypes of dyslexia linked to this region are underrepresented in our sample, because of either chance or varying ascertainment criteria.

Adolescent↗
PubMed2000

Identification and analysis of error types in high-throughput genotyping.

Although it is clear that errors in genotyping data can lead to severe errors in linkage analysis, there is as yet no consensus strategy for identification of genotyping errors. Strategies include comparison of duplicate samples, independent calling of alleles, and Mendelian-inheritance-error checking. This study aimed to develop a better understanding of error types associated with microsatellite genotyping, as a first step toward development of a rational error-detection strategy. Two microsatellite marker sets (a commercial genomewide set and a custom-designed fine-resolution mapping set) were used to generate 118,420 and 22,500 initial genotypes and 10,088 and 8,328 duplicates, respectively. Mendelian-inheritance errors were identified by PedManager software, and concordance was determined for the duplicate samples. Concordance checking identifies only human errors, whereas Mendelian-inheritance-error checking is capable of detection of additional errors, such as mutations and null alleles. Neither strategy is able to detect all errors. Inheritance checking of the commercial marker data identified that the results contained 0.13% human errors and 0.12% other errors (0.25% total error), whereas concordance checking found 0.16% human errors. Similarly, Mendelian-inheritance-error checking of the custom-set data identified 1.37% errors, compared with 2.38% human errors identified by concordance checking. A greater variety of error types were detected by Mendelian-inheritance-error checking than by duplication of samples or by independent reanalysis of gels. These data suggest that Mendelian-inheritance-error checking is a worthwhile strategy for both types of genotyping data, whereas fine-mapping studies benefit more from concordance checking than do studies using commercial marker data. Maximization of error identification increases the likelihood of linkage when complex diseases are analyzed.

Alleles↗
PubMed1998

Envelope structure on 700 AU scales and the molecular outflows of low-mass young stellar objects.

Aperture synthesis observations of HCO+ J = 1-0, 13CO 1-0, and C18O 1-0 obtained with the Owens Valley Millimeter Array are used to probe the small-scale (5" approximately 700 AU) structure of the molecular envelopes of a well-defined sample of nine embedded low-mass young stellar objects in Taurus. The interferometer results can be understood in terms of: (1) a core of radius approximately or less than 1000 AU surrounding the central star, possibly flattened and rotating; (2) condensations scattered throughout the envelope that may be left over from the inhomogeneous structure of the original cloud core or that may have grown during collapse; and (3) material within the outflow or along the walls of the outflow cavity. Masses of the central cores are 0.001-0.1 M (solar), and agree well with dust continuum measurements. Averaged over the central 20" (3000 AU) region, an HCO+ abundance of 4 x 10(-8) is inferred, with a spread of a factor of 3 between the different sources. Reanalysis of previously presented single-dish data yields an HCO+ abundance of (5.0 +/- 1.7) x 10(-9), which may indicate an average increase by a factor of a few on the smaller scales sampled by the interferometer. Part of this apparent abundance variation could be explained by contributions from extended cloud emission to the single-dish C18O lines, and uncertainties in the assumed excitation temperatures and opacities. The properties of the molecular envelopes and outflows are further investigated through single-dish observations of 12CO J = 6-5, 4-3, and 3-2, 13CO 6-5 and 3-2, and C18O 3-2 and 2-1, obtained with the James Clerk Maxwell and IRAM 30 m telescopes, along with the Caltech Submillimeter Observatory. Ratios of the mid-J CO lines are used to estimate the excitation temperature, with values of 25-80 K derived for the gas near line centre. The outflow wings show a similar range, although Tex is enhanced by a factor of 2-3 in at least two sources. In contrast to the well-studied L1551 IRS 5 outflow, which extends over 10' (0.4 pc), seven of the remaining eight sources are found to drive 12CO 3-2 outflows over < or = 1' (0.04 pc); only L1527 IRS has a well-developed outflow of some 3'(0.12 pc). Estimates are obtained for the outflow kinetic luminosity, Lkin, and the flow momentum rate, FCO, applying corrections for line opacity and source inclination. The flow force FCO correlates with the envelope mass and with the 2.7 mm flux of the circumstellar disk. Only a weak correlation is seen with Lbol, while none is found with the relative age of the object as measured by integral Tmb(HCO+ 3-2)dV/Lbol. These trends support the hypothesis that outflows are driven by accretion through a disk, with a global mass infall rate determined by the mass and density of the envelope. The association of compact HCO+ emission with the walls of the outflow cavities indicates that outflows in turn influence the appearance of the envelopes. It is not yet clear, however, whether they are actively involved in sweeping up envelope material, or merely provide a low-opacity pathway for heating radiation to reach into the envelope.

Astronomy↗
PubMed2001

Quantitative-trait-locus analysis of body-mass index and of stature, by combined analysis of genome scans of five Finnish study groups.

In recent years, many genomewide screens have been performed, to identify novel loci predisposing to various complex diseases. Often, only a portion of the collected clinical data from the study subjects is used in the actual analysis of the trait, and much of the phenotypic data is ignored. With proper consent, these data could subsequently be used in studies of common quantitative traits influencing human biology, and such a reanalysis method would be further justified by the nonbiased ascertainment of study individuals. To make our point, we report here a quantitative-trait-locus (QTL) analysis of body-mass index (BMI) and stature (i.e., height), with genotypic data from genome scans of five Finnish study groups. The combined study group was composed of 614 individuals from 247 families. Five study groups were originally ascertained in genetic studies on hypertension, obesity, osteoarthritis, migraine, and familial combined hyperlipidemia. Most of the families are from the Finnish Twin Cohort, which represents a population-wide sample. In each of the five genome scans, approximately 350 evenly spaced markers were genotyped on 22 autosomes. In analyzing the genotype data by a variance-component method, we found, on chromosome 7pter (maximum multipoint LOD score of 2.91), evidence for QTLs affecting stature, and a second locus, with suggestive evidence for linkage to stature, was detected on chromosome 9q (maximum multipoint LOD score of 2.61). Encouragingly, the locus on chromosome 7 is supported by the data reported by Hirschhorn et al. (in this issue), who used a similar method. We found no evidence for QTLs affecting BMI.

Body Height↗
PubMed2001

The Ising model in physics and statistical genetics.

Interdisciplinary communication is becoming a crucial component of the present scientific environment. Theoretical models developed in diverse disciplines often may be successfully employed in solving seemingly unrelated problems that can be reduced to similar mathematical formulation. The Ising model has been proposed in statistical physics as a simplified model for analysis of magnetic interactions and structures of ferromagnetic substances. Here, we present an application of the one-dimensional, linear Ising model to affected-sib-pair (ASP) analysis in genetics. By analyzing simulated genetics data, we show that the simplified Ising model with only nearest-neighbor interactions between genetic markers has statistical properties comparable to much more complex algorithms from genetics analysis, such as those implemented in the Allegro and Mapmaker-Sibs programs. We also adapt the model to include epistatic interactions and to demonstrate its usefulness in detecting modifier loci with weak individual genetic contributions. A reanalysis of data on type 1 diabetes detects several susceptibility loci not previously found by other methods of analysis.

Algorithms↗
PubMed2004

Safety, efficacy, and effectiveness of live, attenuated, cold-adapted influenza vaccine in an indicated population aged 5-49 years.

BACKGROUND: Three important studies have supported licensure of live, attenuated, cold-adapted influenza vaccine (CAIV-T [FluMist; MedImmune Vaccines]): (1) a pediatric efficacy trial involving children 15-71 months of age, (2) a large safety study of medically attended events occurring among children 1-17 years of age, and (3) an effectiveness trial involving healthy working adults 18-64 years of age. METHODS: During the United States Food and Drug Administration (FDA) review for the approval of CAIV-T for use in healthy persons, additional subgroup analyses were conducted to evaluate the safety, efficacy, and effectiveness of the vaccine, by use of various age subsets not prespecified by the original protocols. CAIV-T is currently approved by the FDA for use in healthy persons 5-49 years of age. In this article, we present data from some of the aforementioned subanalyses. RESULTS: The efficacy of CAIV-T in children >or=5 years of age (age range of the children in year 1 of the study, 60-71 months; age range of the children in year 2 of the study, 60-83 months) was similar to that reported for the entire cohort in year 1 (90.6%; 95% confidence interval [CI], 70.3%-97.1%). In year 2 of the study, efficacy was 86.9% (95% CI, 70.8%-94.1%), despite the presence of antigenically drifted influenza type A/Sydney/5/97 (H3N2), which caused most illnesses that occurred in year 2. Safety outcomes for children 5-17 years of age revealed no significant difference between vaccine recipients and placebo recipients, with regard to acute respiratory events, acute gastrointestinal events, systemic bacterial infection, or rare events possibly related to influenza. Effectiveness among adults 18-49 years of age was similar to that reported for the entire cohort--for example, for occurrence of severe febrile illness, there was a 19.5% reduction (P=.02) in adults. CONCLUSIONS: The present reanalysis summarizes data on the indicated uses for CAIV-T in the indicated population aged 5-49 years.

Adaptation, Physiological↗
PubMed2004

Guidelines for genotyping in genomewide linkage studies: single-nucleotide-polymorphism maps versus microsatellite maps.

Genomewide linkage scans have traditionally employed panels of microsatellite markers spaced at intervals of approximately 10 cM across the genome. However, there is a growing realization that a map of closely spaced single-nucleotide polymorphisms (SNPs) may offer equal or superior power to detect linkage, compared with low-density microsatellite maps. We performed a series of simulations to calculate the information content associated with microsatellite and SNP maps across a range of different marker densities and heterozygosities for sib pairs (with and without parental genotypes), sib trios, and sib quads. In the case of microsatellite markers, we varied density across 11 levels (1 marker every 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cM) and marker heterozygosity across 6 levels (2, 3, 4, 5, 10, or 20 equally frequent alleles), whereas, in the case of SNPs, we varied marker density across 4 levels (1 marker every 0.1, 0.2, 0.5, or 1 cM) and minor-allele frequency across 7 levels (0.5, 0.4, 0.3, 0.2, 0.1, 0.05, and 0.01). When parental genotypes were available, a map consisting of microsatellites spaced every 2 cM or a relatively sparse map of SNPs (i.e., at least 1 SNP/cM) was sufficient to extract most of the inheritance information from the map (>95% in most cases). However, when parental genotypes were unavailable, it was important to use as dense a map of markers as possible to extract the greatest amount of inheritance information. It is important to note that the information content associated with a traditional map of microsatellite markers (i.e., 1 marker every ~10 cM) was significantly lower than the information content associated with a dense map of SNPs or microsatellites. These results strongly suggest that previous linkage studies that employed sparse microsatellite maps could benefit substantially from reanalysis by use of a denser map of markers.

Chromosome Mapping↗