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Results for “collinearity analysis”

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PubMed1997

Relationship between body condition scores and conception at first artificial insemination in a large dairy herd of high yielding Holstein cows.

This study investigated the relationship between changes in body condition during the dry period and early lactation and conception to first postpartum AI. Holstein cows (n = 720) on a commercial dairy farm were scored weekly for body condition beginning at dry-off and continuing until first AI. Occurrence of postpartum diseases was recorded. A multiple logistic regression model was a significant predictor of the success or failure of conception for multiparous cows, but not for primiparous cows. Principal component analysis reduced collinearity among independent variables and allowed the variables to be ranked based on their contribution to the interval from first AI to conception. The top three ranking variables were lactation number, milk yield at 120 d of lactation, and change in body condition score between parturition and wk 4 of lactation. Increased milk yield at 120 d of lactation was associated with an increased likelihood of conception, and decreased body condition during the 1st mo of lactation was associated with a decreased likelihood of conception. Health problems were less associated with conception than were body condition or milk yield in this herd. Body condition during the dry period and during the first 30 d of lactation is an important tool to identify cows at risk for failure to conceive at first AI.

Adipose Tissue↗

PubMed1992

Collinearity diagnosis for a relative risk regression analysis: an application to assessment of diet-cancer relationship in epidemiological studies.

In epidemiologic studies, two forms of collinear relationships between the intake of major nutrients, high correlations, and the relative homogeneity of the diet, can yield unstable and not easily interpreted regression estimates for the effect of diet on disease risk. This paper presents tools for assessing the magnitude and source of the corresponding collinear relationships among the estimated coefficients for relative risk regression models. I show how to extend three tools (condition indices, variance decomposition proportions, and standard inflation factors) for diagnosing collinearity in standard regression models to likelihood and partial likelihood estimation for logistic and proportional hazards models. This extension is based on the analogue role of the information matrix in such analyses and the cross-product matrix in the standard linear model. I apply the methodology to relative risk models that relate crude intakes (on the log scale) and nutrient densities to breast cancer cases in the NHANES-I follow-up study. The three diagnostic tools provide complementary evidence of the existence of a strong collinearity in all models that is due largely to homogeneity of the population with respect to our risk scale for the crude intakes. The analysis suggests that the non-significant relative risks for the crude intakes in these models may be due to their involvement in collinear relationships, while the nonsignificant relative risks for the nutrient densities are far less affected by multicollinearity.

Adult↗

PubMed1999

Steroid analysis in single cells by capillary electrophoresis with collinear laser-induced fluorescence detection.

Capillary electrophoresis with collinear laser-induced fluorescence detection was used for the analysis of steroids in single R2C cells. Progesterone secretion was monitored from cultured cells and subsequently detected in single cells. Mass detection limit of 10(-18) mol for dansylated steroids was achieved with the 325-nm line of a helium-cadmium laser. Dansylhydrazine proved to be an effective fluorescent tag for derivatization of steroids outside and inside the biological cell. Fluorescence microscopy indicates that a dimethyl sulfoxide-containing physiological buffer was sufficient to incorporate the tag inside the cell for subsequent steroid derivatization.

Animals↗

PubMed2006

Statistical issues of regression analysis on development of an age-predictive equation.

Several statistical information criteria and other statistical issues such as residual examinations and multi-collinearity in regression analysis were argued to establish the predictive equation of age from physical fitness measurements. These independent variables of physical fitness, body composition, two blood pressures, and bone strength were taken from 31 Japanese males (48 +/- 11.9 years old) living in rural areas. The following equation was selected as the optimal one according to Akaike's information criterion: ŷ = 90.0 -1.294 * SITUP - 0.467 * MAP - 0.094 * BALANCE (R = 0.837). When all ten variables were included in the initial equation, R was 0.864, and the highest R* (R adjusted for d.f.) was observed at the fifth step.

Adult↗

PubMed2006

Detection and resolution of genetic loci affecting circadian period in Brassica oleracea.

Circadian rhythms regulate many aspects of plant growth, fitness and vigour. The components and detailed mechanism of circadian regulation to date have been dissected in the reference species Arabidopsis thaliana. To determine the genetic basis and range of natural allelic variation for intrinsic circadian period in the closest crop relatives, we used an accurate and high throughput data capture system to record rhythmic cotyledon movement in two immortal segregating populations of Brassica oleracea, derived from parent lines representing different crop types. Periods varied between 24.4 and 26.1 h between the parent lines, with transgressive segregation between extreme recombinant lines in both populations of approximately 3.5 h. The additive effect of individual QTL identified in each population varied from 0.17 to 0.36 h. QTL detected in one doubled haploid population were verified and the mapping intervals further resolved by determining circadian period in genomic substitution lines derived from the parental lines. Comparative genomic analysis based on collinearity between Brassica and Arabidopsis also allowed identification of candidate orthologous genes known to regulate period in Arabidopsis, that may account for the additive circadian effects of specific QTL. The distinct QTL positions detected in the two populations, and the extent of transgressive segregation suggest that there is likely to be considerable scope for modulating the range of available circadian periods in natural populations and crop species of Brassica. This may provide adaptive advantage for optimising growth and development in different latitudes, seasons or climate conditions.

Brassica↗

PubMed2026

Genomic and evolutionary basis of parthenogenesis in a disease-vector tick species.

Haemaphysalis longicornis is an important tick species and pathogen vector characterized by the co-circulation of triploid parthenogenetic and diploid bisexual strains. However, the evolutionary basis of parthenogenesis in this species is unclear. Here we report reference-quality, haplotype-resolved genome assemblies of the parthenogenetic strain and two reference-quality genomes of the bisexual strains. Comparative genomic analysis revealed high collinearity between the parthenogenetic and bisexual genomes, with a stable chromosomal architecture maintained among the three haplotypes of the parthenogenetic strain. The parthenogenetic H. longicornis genome exhibited a major expansion in cell cycle-related gene families, including the inhibitor of apoptosis protein (IAP) family, but was characterized by a contraction in other gene families. Population resequencing of 179 individuals revealed two distinct subpopulations, with chromosome 7 harbouring high genetic differentiation and several candidate genes probably associated with parthenogenesis. Functional experiments showed that knockdown of the BIRC5 gene, a member of the IAP family, suppressed oviposition in both strains, with the parthenogenetic strain exhibiting milder adverse effects probably due to a stronger transcriptional response. Overall, our results reveal the genomic and evolutionary features associated with polyploid parthenogenesis in H. longicornis.

Animals↗

PubMed2025

Chromosome-level Genome Assembly of the Halophytic Turfgrass Zoysia macrostachya.

Zoysia macrostachya Franch. & Sav. is a halophytic perennial turfgrass in the Poaceae family, commonly found in the coastal regions of Korea, Japan, and East Asia. Z. macrostachya thrives in high-salinity environments, making it an excellent model for studying abiotic stress resilience. In this study, we present a chromosome-level genome assembly of Z. macrostachya, constructed using Oxford Nanopore long reads, Illumina short reads, and Omni-C sequencing data. The assembly spans 329.78 Mb across 20 chromosomes, with a scaffold N50 of 19.24 Mb, and includes complete telomeric sequences at both ends. The assembly showed 97.8% complete BUSCOs, indicating high genome completeness. Repeat element and gene annotation identified 44.03% of the genome as repetitive elements and 33,474 protein-coding genes. The gene annotation showed 97.1% complete BUSCOs and 86.92% functionally characterized genes. Macrosynteny analysis highlighted highly collinear relationships with related species, providing a foundational understanding of the Z. macrostachya genomic structure. This high-quality genome serves as a valuable resource for advancing salinity tolerance research and improving the genetic diversity of Zoysia species.

Genome, Plant↗

PubMed1994

Covalent catalysis in nucleotidyl transfer reactions: essential motifs in Saccharomyces cerevisiae RNA capping enzyme are conserved in Schizosaccharomyces pombe and viral capping enzymes and among polynucleotide ligases.

Formation of the 5' cap structure of eukaryotic mRNAs occurs via transfer of GMP from GTP to the 5' terminus of the primary transcript. RNA guanylyltransferase, the enzyme that catalyzes this reaction, has been isolated from many viral and cellular sources. Though differing in molecular weight and subunit structure, the various guanylyltransferases employ a common catalytic mechanism involving a covalent enzyme-(Lys-GMP) intermediate. Saccharomyces cerevisiae CEG1 is the sole example of a cellular capping enzyme gene. In this report, we describe the identification and characterization of the PCE1 gene encoding the capping enzyme from Schizosaccharomyces pombe. PCE1 was isolated from a cDNA library by functional complementation in Sa. cerevisiae. Induced expression of PCE1 in bacteria and in yeast confirmed that the 47-kDa Sc. pombe protein was enzymatically active. The amino acid sequence of PCE1 is 38% identical (152 of 402 residues) to the 52-kDa capping enzyme from Sa. cerevisiae. Comparison of the two cellular capping enzymes with guanylyltransferases encoded by DNA viruses revealed local sequence similarity at the enzyme's active site and at four additional collinear motifs. Mutational analysis of yeast CEG1 demonstrated that four of the five conserved motifs are essential for capping enzyme function in vivo. Remarkably, the same motifs are conserved in the polynucleotide ligase family of enzymes that employ an enzyme-(Lys-AMP) intermediate. These findings illuminate a shared structural basis for covalent catalysis in nucleotidyl transfer and suggest a common evolutionary origin for capping enzymes and ligases.

Amino Acid Sequence↗

PubMed1999

Risk factors associated with Salmonella enterica serovar typhimurium infection in Danish broiler flocks.

A retrospective longitudinal study was conducted to identify risk factors associated with Salmonella enterica serovar typhimurium (S. typhimurium) infection in Danish broiler flocks. The data included all broiler flocks slaughtered in 1995, and the epidemiological unit was the individual broiler flock. The S. typhimurium status was determined by microbiological examination of 60 fresh fecal samples. This procedure should detect an infected flock with a probability above 95%, if the prevalence is above 5%, and given that the sensitivity of the test is 100%. Nineteen variables were selected for analysis. Five factors and an interaction term were found significant by multivariate logistic regression analysis. An increased risk for S. typhimurium infection was associated with two parent flocks, one confirmed infected and one suspected of being infected with S. typhimurium, with two of the hatcheries, and with five houses on the farm. An interaction between season and the previously mentioned hatcheries, and a random effect at farm level was also found to be statistically significant. Twelve variables were not found to be associated with S. typhimurium infection: medication, growth promoters, breed of the laying flock, animal density, size of the flock, area of the house, age of the house, geographical location of the farm, observation of beetles, number of days between disinfection and replacement, visual appearance of the bedding, and age of the chickens when they were tested for Salmonella. Three variables (feed mill, slaughterhouse, and Salmonella status of the preceding flock) were not evaluated in the multivariate analysis due to collinearity with other included variables.

Animals↗

PubMed1990

Obscure phenomena in statistical analysis of quantitative structure-activity relationships. Part 1: Multicollinearity of physicochemical descriptors.

Multicollinearity of physicochemical descriptors leads to serious consequences in quantitative structure-activity relationship (QSAR) analysis, such as incorrect estimators and test statistics of regression coefficients of the ordinary least-squares (OLS) model applied usually to QSARs. Beside the diagnosis of the known simple collinearity, principal component regression analysis (PCRA) also allows the diagnosis of various types of multicollinearity. Only if the absolute values of PCRA estimators are order statistics that decrease monotonically, the effects of multicollinearity can be circumvented. Otherwise, obscure phenomena may be observed, such as good data recognition but low predictive model power of a QSAR model.

Chemical Phenomena↗

PubMed1994

Guarding against pitfalls in multivariate analysis. An illustration from fitness testing of the spinally-injured.

Potential pitfalls in the multivariate analysis of data, and methods of overcoming such problems, are illustrated by reference to recent research that has examined relationships between fitness variables and overall productivity in a population of young male paraplegics. Particular attention is directed to the need for residual analysis, tests of multiple collinearity, and a cautious approach to interpreting the theoretical meaning of individual coefficients in multiple regression equations.

Humans↗

PubMed1988

A least-squares algorithm for the equiform transformation from spatial marker co-ordinates.

The present paper describes an algorithm for estimating the translation vector and the rotation matrix of a moving body from noisy measurements on the spatial co-ordinates of at least three non-collinear markers. A sensitivity analysis of the estimated parameters and of the helical axis is presented in terms of characteristics of the marker distribution. The implementation of the proposed algorithm in a FORTRAN-subroutine is appended.

Algorithms↗

PubMed2000

Development of screening systems for drugs against human papillomavirus-associated cervical cancer: based on E6-E6AP binding.

Human papillomavirus (HPV) E6 protein forms a ternary complex with the cell-cycle regulator p53 and the E6-associated protein (E6AP) known as an E3 ubiquitin protein ligase, leading to the degradation of p53 via the ubiquitination pathway. As an attempt to employ interaction between HPV viral oncogene E6 and a cellular protein E6AP for in vitro screening system of drugs against HPV infection, we primarily investigated the E6AP-E6 binding through pull down assay and enzyme-linked immunosorbent assay (ELISA). E6AP immobilized on the resin produced specifically complexes with bacterially expressed E6 in a dose-dependent manner, as determined by immunoblot analysis. This result was collinear with that shown in ELISA, which is a useful system for mass-screening potential drugs with rapidity and cheapness. Screening system based on the interaction between E6AP and E6 may be a promising system in the development of drugs against cervical cancer caused by HPV infection.

Blotting, Western↗

PubMed1998

Yeast and viral RNA 5' triphosphatases comprise a new nucleoside triphosphatase family.

Saccharomyces cerevisiae Cet1p catalyzes the first step of mRNA capping, the hydrolysis of the gamma phosphate of triphosphate-terminated RNA to form a 5' diphosphate end. The RNA triphosphatase activity of Cet1p is magnesium-dependent and has a turnover number of 1 s-1. Here we show that purified recombinant Cet1p possesses a robust ATPase activity (Km = 2.8 microM; Vmax = 25 s-1) in the presence of manganese. Cobalt is also an effective cofactor, but magnesium, calcium, copper, and zinc are not. Cet1p displays broad specificity in converting ribonucleoside triphosphates and deoxynucleoside triphosphates to their respective diphosphates. The manganese- and cobalt-dependent nucleoside triphosphatase of Cet1p resembles the nucleoside triphosphatase activities of the baculovirus LEF-4 and vaccinia virus D1 capping enzymes. Cet1p, LEF-4, and D1 share three collinear sequence motifs. Mutational analysis establishes that conserved glutamate and arginine side chains within these motifs are essential for the RNA triphosphatase and ATPase activities of Cet1p in vitro and for Cet1p function in vivo. These findings are in accord with the effects of single alanine mutations at analogous positions of vaccinia capping enzyme. We suggest that the metal-dependent RNA triphosphatases encoded by yeast and DNA viruses comprise a novel family of phosphohydrolase enzymes with a common active site.

Acid Anhydride Hydrolases↗

PubMed2000

Identification of insertion and deletion genes in Autographa californica nucleopolyhedrovirus variants isolated from Galleria mellonella, Spodoptera exigua, Spodoptera litura and Xestia c-nigrum.

The genomic DNA of four Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) variants isolated from Galleria mellonella, Spodoptera exigua, Spodoptera litura and Xestia c-nigrum was analyzed in comparison with the AcMNPV E2 strain. Restriction endonuclease analysis revealed a deletion and an insertion in collinear regions of the four variants. Polymerase chain reaction analysis indicated that, in the four variants, the deletion occurred in the region corresponding to AcMNPV C6 ORF86 (pnk/pnl). Also the insertion, with a length of approximately 1.1 kb, was commonly identified in the fragments corresponding to the PstI-J fragment (18.5 m.u.-21.2 m.u.) of AcMNPV E2. Sequencing analysis of the variant from S. litura showed that the insertion contains an additional open reading frame encoding 322 amino acids between homologues of AcMNPV ORF30 and ORF31 (the superoxide dismutase gene). This ORF has 82.8% amino acid identity to Bombyx mori NPV T3 ORF 22 (bro-a, one of the baculovirus repeated ORFs) and thus, it was named Splt-bro-a. Southern blot hybridization study indicated that the other three variants also contain Splt-bro-a homologue. In addition, the labeled Splt-bro-a gene weakly hybridized to the PstI-D fragment (99.0 m.u.-8.0 m.u.) of AcMNPV E2. This fragment contains AcMNPV ORF2, a member of bro family. The signal was also observed on the corresponding fragment of the four variants. This result suggested that two bro genes are present in the four variants, although AcMNPV E2 and C6 are known to contain a single bro gene.

Amino Acid Sequence↗

PubMed1979

On the interpretability of quantitative structure-activity relationships (QSAR).

QSAR are a powerful tool to obtain information on the molecular mechanism of drug action as well as on properties of receptors. They can be evaluated at different levels of sophistication using different parameters to describe physical chemical properties of the drugs and different mathematical methods. In this presentation only QSAR at the level of extrathermodynamic parameters will be considered. Interpretation of QSAR is always connected with two basic questions: 1) Which requirements must be met in order to get meaningful (interpretable) QSAR and what can be done to satisfy these requirements? 2) What information can be gained (and in which way) from QSAR? Some of the most important aspects of these questions to be discussed in this paper are: 1) Interrelationships between parameters and the separability of hydrophobic, electronic and steric effects. 2) Description of hydrophobic interactions. 3) Separation of hydrophobic effects connected with transport and hydrophobic bonding. 4) Estimation of the biological point of attack. 5) Selection and informational content of biological response data. Factor analysis will be shown to be a useful data preprocessing step allowing one to systematize data and to recognize and to eliminate collinearities. Another multivariate method, principal component analysis, may be used to separate pharmacokinetic and pharmacodynamic effects.

Biological Transport↗

PubMed1999

Joint effects on cancer risk of age at childbirth, time since birth and attained age: circumventing the problem of collinearity.

In previous studies of female cancer risk, we introduced a new method for circumventing the problem of collinearity in age-adjusted analysis of the joint effects of age at birth and time since birth. The basic idea was to estimate the pure age effect considering nulliparous women, assuming that the age effect is common to all women. However, risk estimates for attained age obtained in this manner may suffer from bias, in particular in small data sets, which may in turn influence risk estimates for reproductive factors among parous women. Certain factors possibly affecting cancer risk among nulliparous women only, for instance biological infertility, might also introduce bias. The purpose of this paper is to investigate the accuracy of risk estimates obtained by the joint approach, and to reveal the extent of bias in traditional separate age-adjusted analyses of age at birth or time since birth among parous women. Results are based on analyses of simulated data sets reflecting reproductive and demographic characteristics of a cohort of 1.1 million Norwegian women. Incidence rate ratios are calculated in Poisson regression analyses of person-years at risk. Our simulations show that the joint analysis in general yields unbiased risk estimates, but the number of cases must be rather high to achieve reliable results. Risk estimates from separate analyses can be seriously biased, although the amount of bias depends on the strength and direction of associations with cancer risk. With a total of 5500 cancer cases, the estimators for age at last birth and time since last birth were 13-78 per cent and 5-66 per cent more efficient in the joint than in the separate analysis, respectively. Significance levels were close to the nominal 5 per cent in the joint analysis, but about twice as high in the separate analysis. Adding an effect of biological infertility on cancer risk among nulliparous women, without taking it into account in the analyses, did not seriously affect risk estimates in the joint model.

Adult↗

PubMed2002

Mild to moderate chronic airways disease does not carry an excess risk of cognitive dysfunction.

BACKGROUND AND AIMS: Whether chronic obstructive pulmonary disease (COPD) carries a risk of cognitive dysfunction prior to the onset of arterial hypoxemia is not known. Our objective was to assess both the prevalence and main correlates of subclinical cognitive dysfunction in older patients with non-hypoxemic COPD. METHODS: Home-dwelling non-demented subjects over 64 years of age consecutively attending 24 outpatient Departments of Respiratory Medicine or Geriatrics because of COPD (N = 233), asthma (N = 203), non-obstructive bronchitis (N = 92) or chronic non-respiratory and non-dementing diseases (controls, N = 1080) underwent a multidimensional assessment. Cognitive status was assessed by the Mini-Mental State Examination (MMSE). Independent correlates of MMSE < 24 were identified by logistic regression analysis. In order to limit the confounding effect of collinearity between COPD group membership and the 6' walked distance, a properly designed multivariate analysis was performed. RESULTS: Prevalence of MMSE < 24 ranged from 16.7% (controls) to 21.9% (COPD). Education < 9 years (Odds Ratio = 1.56, Confidence Intervals = 1.22-1.98), a score > 6 on the 15-item Geriatric Depression Scale (OR = 1.37, CI = 1.16-1.62). a 6' walked distance < 242 m (OR = 1.22, CI = 1.02-1.45), a Barthel Index greater than 80 (OR = 1.48, CI = 1.03-2.14) and a Forced Vital Capacity inferior to 80% of the predicted value (OR = 1.17, CI = 1.09-1.38) qualified as independent correlates of MMSE < 24. The multivariate analysis confirmed that groups had comparable MMSE scores. CONCLUSIONS: Non-hypoxemic COPD did not increase the risk of subclinical cognitive dysfunction in an older population.

Aged↗