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Results for “shared variables”

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PubMed2000

Linkage disequilibrium mapping in populations of variable size using the decay of haplotype sharing and a stepwise-mutation model.

Linkage-disequilibrium (LD) mapping is a powerful tool for fine-mapping disease genes. Recently, McPeek and Strahs [(1999) Am J Hum Genet 65:858-875] proposed a multilocus model for LD mapping based on the decay of haplotype sharing. Here we extend their approach in two ways. First, instead of assuming each marker allele has an equal chance to mutate to one of the other marker alleles, we use the stepwise-mutation model to describe the mutation process for microsatellite markers. Second, in addition to the independence model and the constant population size model they considered, we model the dependence among observed haplotypes due to population structure by using a general conditional-coalescent model with variable population size. Through simulation studies, we study the effects of the stepwise-mutation model and variable population size on the estimates of disease gene location, mutation rate, and time to the most recent common ancestor of the sampled haplotypes. We then use this method to analyze progressive myoclonus epilepsy data.

Chromosome Mapping↗

PubMed1991

Sequence analysis of the major outer membrane protein gene of Chlamydia pneumoniae.

Compared with the major outer membrane proteins (MOMPs) of the other chlamydial species, the Chlamydia pneumoniae MOMP appears to be less antigenically complex, and as determined by immunoblot analysis, it does not appear to be the immunodominant antigen recognized during infection. Nucleotide sequence analysis of the C. pneumoniae MOMP gene (ompA) revealed that it consisted of a 1,167-base open reading frame with an inferred 39,344-dalton mature protein of 366 amino acids plus a 23-amino-acid leader sequence. A ribosomal-binding site was located in the 5' upstream region, and two stop codons followed by an 11-base dyad forming a stable stem-loop structure were identified. This sequence shares 68 and 71% DNA sequence homology to the Chlamydia trachomatis serovar L2 and Chlamydia psittaci ovine abortion agent MOMP genes, respectively. Interspecies alignment identified regions, corresponding to the variable domains, which share little sequence similarity with the other chlamydial MOMPs. All seven cysteines conserved in the C. trachomatis and C. psittaci MOMPs, which are involved in the formation of disulfide cross-linkages, are found in the C. pneumoniae MOMP.

Amino Acid Sequence↗

PubMed1993

Genetic factors that predispose the child to develop hypertension.

Familial aggregation, population, and twin studies all point to important genetic influences on the level of blood pressure in childhood and adolescence. Whether a major gene effect operates during childhood has not been determined. The investigation of polygenic paths leads to the study of variables such as ion transport and reactivity paths that appear to be under strong genetic influences. The evidence suggests that abnormalities in these paths might be linked to a prehypertensive state. Univariate genetic analyses of systolic and diastolic blood pressure show that a significant portion of the variability of these variables is under genetic control. Moreover, during early adolescence, boys differ from girls in the regulation of their resting blood pressure. Multivariate genetic analyses show that in these young adolescents, genetic paths shared with body mass index appear to influence systolic but not diastolic blood pressure. The genetic relationship between systolic and diastolic blood pressure appears largely to be independent of body mass index. Genetic studies can partition the genetic and environmental influences on blood pressure and identify shared paths with variables previously believed to be linked epidemiologically. This information may have the capacity to be the framework for public health guidelines developed to lower the incidence of adult hypertension.

Child↗

PubMed1979

Health costs of economic expansion: the case of manufacturing accident injuries.

The hypothesized relationship between economic expansion and accident injuries is tested using archival economic and accident data from the Los Angeles-Long Beach, California metropolitan area. The association is measured using cross-correlation techniques after variation shared with a comparison metropolitan area (Anaheim-Santa Ana-Garden Grove) is removed. Two tests of association are conducted. The first uses the raw accident rate of the comparison metropolitan area as a control variable while the second adjusts the control variable to reflect shared industrial sectors. Findings suggest that the incidence of disabling accidents increases in the month before and during the month that the manufacturing work force expands. The impact appears strongest during the month that new workers are added.

Accident Prevention↗

PubMed1978

Liver-specific and shared cell membrane antigens. Studies by light- and electron microscopy.

Liver-specific and shared saline-insoluble cell surface antigens were localized by immunofluorescence as well as by light- and electron microscopic immunoenzyme techniques. Antisera against purified mouse liver cell membranes were surface membrane but not organ-specific. Variable quantities of shared antigens were present in endoderm- and mesoderm-derived organs but not in ectodermal nerve tissue. Species crossreactivity was observed for the rat. Repeated absorption produced liver-specific antisera that reacted with antigenic sites distributed along the entire hepatocyte and sinusoidal cell surfaces. For the precise localization as well as the detection of low concentrations of both liver-specific and nonspecific antigens, the ultrastructural visualization of reactive sites proved essential.

Animals↗

PubMed2002

Large-scale effects of timber harvesting on stream systems in the Ouachita Mountains, Arkansas, USA.

Using Basin Area Stream Survey (BASS) data from the United States Forest Service, we evaluated how timber harvesting influenced patterns of variation in physical stream features and regional fish and macroinvertebrate assemblages. Data were collected for three years (1990-1992) from six hydrologically variable streams in the Ouachita Mountains, Arkansas, USA that were paired by management regime within three drainage basins. Specifically, we used multivariate techniques to partition variability in assemblage structure (taxonomic and trophic) that could be explained by timber harvesting, drainage basin differences, year-to-year variability, and their shared variance components. Most of the variation in fish assemblages was explained by drainage basin differences, and both basin and year-of-sampling influenced macroinvertebrate assemblages. All three factors modeled, including interactions between drainage basins and timber harvesting, influenced variability in physical stream features. Interactions between timber harvesting and drainage basins indicated that differences in physical stream features were important in determining the effects of logging within a basin. The lack of a logging effect on the biota contradicts predictions for these small, hydrologically variable streams. We believe this pattern is related to the large scale of this study and the high levels of natural variability in the streams. Alternatively, there may be time-specific effects we were unable to detect with our sampling design and analyses.

Animals↗

PubMed1977

Genetic variability of clinical chemical values.

A study of cardiovascular risk factors in middle-aged twin men provided an opportunity to test for genetic variability in the SMA 12/60 (Technicon) battery of clinical chemistry tests. Classical twin methodology was used to analyze the variation of monozygotic and dizygotic twins. In addition, frequency of co-twin contact was used to control for effects of differences in shared environment. Genetic variability played a definite role in controlling four of the 11 reported tests: one-hour serum glucose, serum urea nitrogen, uric acid, and bilirubin. No genetic variation was found for lactate dehydrogenase, phosphorus, and alkaline phosphatase. Significantly higher means for calcium, total protein, albumin, and aspartate aminotransferase in monozygotic twins precluded any statement about heredity and environment for these tests.

Adult↗

PubMedDate not supplied

Person variables and health: personality predispositions and acute psychological states as shared determinants for disease.

This article reviews prospective evidence linking certain classes of person variables to multiple disease end points. Included in the review is a consideration of the effects of hostility and anger, emotional suppression, depression, fatalism, and pessimism on coronary heart disease, cancer, and acquired immunodeficiency syndrome. A model is presented that integrates several of these variables into an overall conceptual scheme. In addition, several variables are identified that appear to moderate the strength of the relationships that are found between person variables and health. The article concludes with some suggested directions for future research.

Acquired Immunodeficiency Syndrome↗

PubMed2003

Combined MR data acquisition of multicontrast images using variable acquisition parameters and K-space data sharing.

A new technique to reduce clinical magnetic resonance imaging (MRI) scan time by varying acquisition parameters and sharing k-space data between images, is proposed. To improve data utilization, acquisition of multiple images of different contrast is combined into a single scan, with variable acquisition parameters including repetition time (TR), echo time (TE), and echo train length (ETL). This approach is thus referred to as a "combo acquisition." As a proof of concept, simulations of MRI experiments using spin echo (SE) and fast SE (FSE) sequences were performed based on Bloch equations. Predicted scan time reductions of 25%-50% were achieved for 2-contrast and 3-contrast combo acquisitions. Artifacts caused by nonuniform k-space data weighting were suppressed through semi-empirical optimization of parameter variation schemes and the phase encoding order. Optimization was assessed by minimizing three quantitative criteria: energy of the "residue point spread function (PSF)," energy of "residue profiles" across sharp tissue boundaries, and energy of "residue images." In addition, results were further evaluated by quantitatively analyzing the preservation of contrast, the PSF, and the signal-to-noise ratio. Finally, conspicuity of lesions was investigated for combo acquisitions in comparison with standard scans. Implications and challenges for the practical use of combo acquisitions are discussed.

Algorithms↗

PubMed1994

Multiple sclerosis.

Differences in the risk of multiple sclerosis depending on racial background, and the high clinical concordance rates in monozygotic compared with dizygotic twins, have stimulated attempts to identify and locate genes that confer susceptibility to the disease. The risk of multiple sclerosis is increased from 1 in 800 in northern European Caucasians to 1 in 3 in the monozygotic co-twins of affected individuals, with intermediate rates for siblings, offspring and more distant relatives. Concordance rates in monozygotic and dizygotic co-twins of affected individuals rise to 35% and 15%, respectively when magnetic resonance imaging is used to supplement clinical evidence for disease status. The increased recurrence risk in relatives of patients with multiple sclerosis is consistent with a model in which more than one gene contributes to susceptibility. Population studies have demonstrated an association with the class 2 major histocompatibility complex (MHC) phenotypes DR15 and DQw6 and their corresponding genotypes DRB1.1501, DRB5.0101 and DQA1.0102, DQB2.0602. An extensive search, using population studies, for other polymorphic alleles involved in restriction of the immune response may have yielded an additional candidate gene in the VH2-5 immunoglobulin heavy-chain variable region. Identity by descent analysis of candidate genes encoded within the alpha-chain of the T-cell receptor and the gene for myelin basic protein has failed to demonstrate linkage; paradoxically, this is also true for the MHC class 2 region, despite the population association. However, studies involving a large number of sibling pairs have reported a bias in the distribution of T-cell receptor beta-chain variable region haplotype sharing, favouring linkage. This becomes more marked when stratification is made for the presence of DR2 in both affected siblings, suggesting an interaction between genetic polymorphisms encoded within the MHC and T-cell receptor genes, as expected from their known functional co-operation in antigen presentation. The same is true for the immunoglobulin heavy chain, providing provisional evidence for linkage to a gene encoded within the immunoglobulin heavy-chain variable region in families reported from the UK. Taken together, these findings demonstrate the importance of family studies in elucidating the genetic basis of multiple sclerosis, and confirm that several genes are involved, one or more of which regulates genetic restriction of the immune response. The contribution made by the susceptibility genes that have provisionally been identified, occurring in isolation or together, can account for only a proportion of the increased risk of multiple sclerosis implicated by family studies.(ABSTRACT TRUNCATED AT 250 WORDS)

Genes↗

PubMed2001

Depression and smoking: examining correlates in a subset of depressed patients.

OBJECTIVE: The objective of this study was to examine for associations between depression and cigarette smoking. METHOD: A sample of 92 depressed smokers was compared with a control sample of depressed non-smokers, matched for age, gender and diagnostic variables. Comparisons were made across a range of demographic, depression, family history, developmental factors, anxiety and personality style variables, as well as use of alcohol and illicit drugs. RESULTS: We failed to find any difference between smokers and non-smokers in history or severity of depression. Cigarette smokers were distinguished principally by greater exposure to aversive experiences in childhood, disordered personality function, greater use of illicit drugs, anxiolytics and alcohol. Logistic regression identified dysfunctional personality 'domains', physical violence in childhood, long-term anxiolytic use and illicit drug use as the most significant predictor set. CONCLUSIONS: Results favour a model of cigarette smoking and depression as linked by shared early deprivational variables, rather than cigarette smoking causing depression or the converse.

Adult↗

PubMed2003

A longitudinal behavioral genetic analysis of the etiology of aggressive and nonaggressive antisocial behavior.

Developmental studies of antisocial behavior (ASB) have found two subgroups of behaviors, roughly described as aggressive and nonaggressive ASB. Theoretical accounts predict that aggressive ASB, which shows greater stability, should have high heritability. In contrast, nonaggressive ASB is very common in adolescence, shows less continuity, and should be influenced both by genes and shared environment. This study explored the genetic and environmental influences on aggressive and nonaggressive ASB in over 1,000 twin pairs aged 8-9 years and again at 13-14 years. Threshold models were fit to the data to incorporate the skew. In childhood, aggressive ASB was highly heritable and showed little influence of shared environment, whereas nonaggressive ASB was significantly influenced both by genes and shared environment. In adolescence, both variables were influenced both by genes and shared envirnmment. The continuity in aggressive antisocial behavior symptoms from childhood to adolescence was largely mediated by genetic influences, whereas continuity in nonaggressive antisocial behavior was mediated both by the shared environment and genetic influences. These data are in agreement with the hypothesis that aggressive ASB is a stable heritable trait as compared to nonaggressive behavior, which is more strongly influenced by the environment and shows less genetic stability over time.

Adolescent↗

PubMed2003

The role of variability and risk on the persistence of shared-enemy, predator-prey assemblages.

The role of indirect effects such as apparent competition in structuring predator-prey assemblages has recently received empirical attention. That one prey species can be excluded by the impact of a shared-enemy contrasts with the known diversity of multispecies predator-prey interactions. Here, the role of predator foraging among patches of two different prey species is examined as a mechanism that can mediate coexistence in multispecies prey-predator assemblages. Specifically, models of host-parasitoid interactions are constructed to analyse how different types of aggregative behaviour (generated by host-dependent and host-independent responses) affect persistence of the assemblage. How the distribution of hosts and the response of the parasitoid to these distributions can influence coexistence is shown. A generic explanation for coexistence suggests that it is the variability rather than the precise functional relationship that is critical for coexistence under shared-enemy interactions.

Animals↗

PubMed1999

The influence of demographic and socioeconomic factors on health-related quality of life in asthma.

BACKGROUND: Although health-related quality of life (HRQL) in asthma is strongly influenced by disease severity, demographic and socioeconomic variables may also be important factors. OBJECTIVE: We related demographics, asthma severity, and socioeconomic factors to HRQL. METHODS: We interviewed 50 patients with moderate or severe asthma recruited from outpatient health center-based clinics to determine demographics, socioeconomic status, asthma severity, medication use, and HRQL. For HRQL, the mean total score of the Asthma Quality of Life Questionnaire (AQLQ) and the Medical Outcomes Study Short-Form 36 questionnaires physical and mental component summary scores (PCS and MCS, respectively) were used. RESULTS: The mean patient age was 46 +/- 14 years, and the FEV1 was 75% +/- 21% of predicted value. Twenty-nine subjects had been hospitalized for asthma, 29 belonged to a minority racial/ethnic group, and 16 had less than 12 years of education. The mean total AQLQ score was 4.12 +/- 1.42, the PCS was 37 +/- 10, and the MCS was 45 +/- 13. In univariate analyses, severity (nighttime awakenings, prednisone use, and a history of emergency department visits), racial/ethnic group (African American, white, or Hispanic), and socioeconomic status (low educational level, unemployed, family income under $20,000, public assistance, or no health insurance) were related to HRQL. These factors explained 67% of the variance of AQLQ and 48% of the variance of the PCS. Much of the quality of life variance was shared among these variables. Explanatory variables were not related to MCS in multivariate analysis. CONCLUSION: Socioeconomic status is an additional important independent factor influencing HRQL in asthma. In this study it was difficult to separate out the unique effects of socioeconomic status and race/ethnicity.

Adult↗

PubMed1990

Incidence and risk factors of HIV infection: a prospective study of seronegative drug users from Milan and northern Italy, 1987-1989.

To assess the incidence of and risk factors for human immunodeficiency virus (HIV) infection among HIV-negative intravenous drug abusers, we studied a cohort of intravenous drug abusers recruited from drug treatment centers in Milan and northern Italy. We enrolled 933 subjects between January 1, 1987 and April 15, 1989 and we followed 460 subjects with one or more visits for a mean follow-up duration of 10.4 months. The incidence rate of HIV infection was 7.4 per 100 person-years, equivalent to a one-year risk of 7.3%. Relative risk was higher in subjects who had been using intravenous drugs for less than 2 years (RR = 2.3). In a case-control analysis, recent frequent syringe sharing was the behavioral variable most strongly associated with HIV infection, with the highest risk in subjects sharing often (OR = 6.1, 90% CI = 2.6-14.7). We found no association with the use of cocaine in addition to heroin nor with sexual habits. Among biologic variables, relative risks were increased in individuals whose T4-lymphocyte count was lower than 1,000 at first visit (RR = 8.5, 90% CI = 2.9-24.3) or who were carrying HBsAg (RR = 1.9, 90% CI = 0.8-4.2).

Acquired Immunodeficiency Syndrome↗

PubMed2026

Clinical and Functional Characterization of Gain-of-Function ABL1 Variants Expands the Phenotypic Spectrum of CHDSKM.

Germline gain-of-function (GOF) variants in ABL1 cause congenital heart defects and skeletal malformations syndrome (CHDSKM), a multisystem developmental disorder characterized by congenital heart disease, skeletal abnormalities, dysmorphic features, and variable developmental delay. More recently, biallelic loss-of-function variants and ABL haploinsufficiency have been associated with distinct phenotypes, expanding the allelic spectrum of ABL1-related disorders. We report three individuals with ABL1 variants. A female infant with tetralogy of Fallot, critical pulmonary stenosis, covered omphalocele, and a lethal outcome was found by rapid trio genome sequencing to harbor a de novo likely pathogenic ABL1 variant, NM_007313.2:c.354G>T p.(Trp118Cys). We also provide updated clinical follow-up of a previously reported individual and describe a third individual, both carrying the recurrent p.(Tyr245Cys) variant. Functional studies were performed and support a GOF mechanism. Similar activation was observed for Tyr245Cys despite the differences in clinical severity. Our findings expand the phenotypic spectrum of ABL1-related CHDSKM to include severe conotruncal heart disease and covered omphalocele. The comparison of two biochemically activating ABL1 variants demonstrates substantial clinical variability despite a shared molecular mechanism. Furthermore, the overlap between ventral body wall abnormalities in GOF disease and omphalocele associated with ABL1 haploinsufficiency suggests that precise regulation of ABL1 signaling is critical for normal ventral body wall formation.

ABL1↗

PubMedDate not supplied

Pathogenesis of hyperferritinemia cataract syndrome.

Hereditary hyperferritinemia-cataract syndrome (HHCS) is an autosomal dominant disorder characterized by bilateral cataracts and increased serum L-ferritin, in the absence of iron overload. Under physiological conditions, ferritin synthesis is finely regulated at the translational level by iron availability. This regulation is achieved by the high-affinity interaction between cytoplasmic mRNA-binding proteins (iron regulatory proteins, IRPs), and mRNA stem-loop structures, known as iron responsive elements (IREs), located in the untranslated regions (UTRs) of the mRNAs. A single IRE is located on the 5' UTR of a series of genes involved in iron metabolism, like L-ferritin, and the binding IRE-IRPs represses these genes translation. The deregulation of ferritin production responsible of HHCS is caused by heterogeneous mutations in the iron regulatory element (IRE) of L-ferritin that interfere with the binding of iron regulatory proteins, disrupting the negative control of L-ferritin synthesis and causing the constitutive up-regulation of ferritin L-chains. The HHCS families originate from different countries of Europe and North America, suggesting that HHCS may be distributed widely throughout the world and not sporadic, whereas its prevalence remains to be established. The lens seems to be particularly sensitive to the increased amount of L-ferritin and the alteration of the proteic equilibrium in this tissue can be responsible of the cataract. In spite of the elucidation of the genetic basis, the genotype phenotype correlation is not clear. Recently, a study based on the thermo-denaturation profile and dissociation constant of the IRE-IRP complex performed for several mutated IREs has provided evidence for a possible correlation between heterogeneous IRE mutations and serum ferritin levels. On the other hand, the in vivo relevance of these conclusions has not been determined completely. A clinical variability among subjects sharing the same mutation, whether they belonged to the same family or not, has also been demonstrated. These findings suggest that, besides the L-ferritin IRE genotype, additional factors are likely to modulate the lens involvement and the rate of progression to severe cataract in HHCS patients.

Cataract↗

PubMed1998

The structural gene module in Streptococcus thermophilus bacteriophage phi Sfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts.

The structural gene cluster and the lysis module from lytic group II Streptococcus thermophilus bacteriophage phi Sfi11 was compared to the corresponding region from other Siphoviridae. The analysis revealed a hierarchy of relatedness. phi Sfi11 differed from the temperate S. thermophilus bacteriophage phi O1205 by about 10% at the nucleotide level. The majority of the changes were point mutations, mainly at the third base position. Only a single gene (orf 695) differed substantially between the two phages. Over the putative minor tail and lysis genes, phi Sfi11 and the lytic group 1 S. thermophilus phi Sfi19 shared regions with variable degrees of similarity. Orf 1291 from phi Sfi19 was replaced by four genes in phi Sfi11, two of which (orf 1000 and orf 695) showed a complicated pattern of similarity and nonsimilarity compared with phi Sfi19. The predicted orf 695 gp resembles the receptor-recognizing protein of T-even coliphages in its organization, but not its sequence. No sequence similarity was detected between phi Sfi11 and phi Sfi19 in the region covering the major head and tail genes. Comparison of the structural gene map of phi Sfi11 with that of Siphoviridae from gram-positive and -negative bacterial hosts revealed a common genomic organization. Sequence similarity was only found between phi Sfi11 and Siphoviridae from gram-positive hosts and correlated with the evolutionary distance between the bacterial hosts. Our data are compatible with the hypothesis that the structural gene operon from Siphoviridae of the low G + C group of gram-positive bacteria is derived from a common ancestor.

Biological Evolution↗