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PubMed1996

Cloning, restriction endonuclease mapping and partial sequence analysis of the genome of human herpesvirus 7 strain JI.

Human herpesvirus 7 (HHV-7) is a recently isolated herpesvirus that has been shown to be related to human cytomegalovirus and human herpesvirus 6 and to be a member of the betaherpesvirus subgroup. Here we report the cloning, restriction endonuclease mapping and partial sequence analysis of HHV-7 strain JI DNA. Virus particles were obtained from the supernatant of infected SupT1 cells, the DNA isolated by proteinase K treatment-phenol extraction, and full-length viral DNA was purified and isolated on a pulsed-field gel. Aliquots of this highly purified material were treated in the following ways: (i) sonicated and end-repaired to create short randomly sheared fragments for cloning into M13mp 18-Smal vector DNA; (ii) cut with EcoRI for cloning into EcoRI-cut lambda ZAPII or lambda DASHII vectors; (iii) cut with BamHI for cloning into BamHI-cut lambda ZAP-Express or lambda DASHII vectors. Partial nucleotide sequencing of the M13 clones followed by detection of open reading frames and their translation allowed the identification of homologues through FASTA searches of the database. Relevant M13 clones were used as probes to isolate corresponding lambda phage clones, which could tentatively be mapped to the genome on the basis of presumed genetic collinearity between HHV-7 and HHV-6. Genomic "walking' between EcoRI and BamHI lambda genomic libraries enabled overlapping neighbouring clones to be identified and mapped. Each of these clones was analysed to map BamHI, EcoRI, Sa/l, Smal and Xhol restriction endonuclease sites to provide complete endonuclease maps for the entire genome.

Amino Acid Sequence↗

PubMed1997

Some methods to address collinearity among pollutants in epidemiological time series.

The aim of this paper is to provide accurate estimation methods for regression models used in epidemiological time series to deduce quantitative morbidity relationships. Such models often include highly correlated variables (pollutant levels and climatic conditions) as well as lagged and unlagged values of the same variables (which also show a high collinearity due to the stochastic dependency of consecutive measurements). We first describe some methods to detect and assess multicollinearity. We recall the drawbacks of usual methods of estimation, and then after briefly mentioning traditional solutions, we explore three alternative methods accounting for multicollinearity: Sclove's estimation; Almon's method; and a combination of Almon's method and principal components procedure. We compare these methods in obtaining efficient estimators on environmental epidemiological data (children's hospital admissions as dependent variable and unlagged and lagged values of outdoor temperature, SO2, NO and CO as explanatory variables.

Bias↗

PubMedDate not supplied

Preliminary comparison of landscape pattern-normalized difference vegetation index (NDVI) relationships to Central Plains stream conditions.

We explored relationships of water quality parameters with landscape pattern metrics (LPMs), land use-land cover (LULC) proportions, and the advanced very high resolution radiometer (AVHRR) normalized difference vegetation index (NDVI) or NDVI-derived metrics. Stream sites (271) in Nebraska, Kansas, and Missouri were sampled for water quality parameters, the index of biotic integrity, and a habitat index in either 1994 or 1995. Although a combination of LPMs (interspersion and juxtaposition index, patch density, and percent forest) within Ozark Highlands watersheds explained >60% of the variation in levels of nitrite-nitrate nitrogen and conductivity, in most cases the LPMs were not significantly correlated with the stream data. Several problems using landscape pattern metrics were noted: small watersheds having only one or two patches, collinearity with LULC data, and counterintuitive or inconsistent results that resulted from basic differences in land use-land cover patterns among ecoregions or from other factors determining water quality. The amount of variation explained in water quality parameters using multiple regression models that combined LULC and LPMs was generally lower than that from NDVI or vegetation phenology metrics derived from time-series NDVI data. A comparison of LPMs and NDVI indicated that NDVI had greater promise for monitoring landscapes for stream conditions within the study area.

Agriculture↗

PubMed2003

The effects of chronic arsenic exposure from drinking water on the neurobehavioral development in adolescence.

This cross-sectional study examined the possible influence on the development of cognitive function among adolescents due to long-term arsenic exposure. Forty-nine junior school students drinking arsenic-containing well water and 60 controls matched with age, sex, education, body height, body weight, body mass index, and socioeconomic status were compared. The former was divided into two groups: high and low exposure, with mean cumulative arsenic levels of 520629.0+/-605824.2 and 13782.2+/-12886.0 ppm, respectively. Four neurobehavioral tests including continuous performance test (CPT), symbol digit (SD), pattern memory (PM) and switching attention (SA) were applied. A strong correlation between age and education caused collinearity in the multiple regression model (r=0.84, P<0.0001). Only education and sex, excluding age, were entered into the model as covariates. Pattern memory and switching attention were significantly affected by long-term cumulative exposure to arsenic after adjusting for education and sex. It is suggested that the arsenic levels in the well water may be monitored extensively, but if there is no intervention, then neurobehavioral function will not be protected. Limitations of the current study require replication of this effect in other studies to confirm this conclusion.

Adolescent↗

PubMed2005

Trajectory design for space missions to libration point L2.

This work is focused on the detection and computation of "free" transfer trajectories from parking orbits around the Earth to quasiperiodic orbits around the collinear libration point L(2), in the Sun-Earth system; no correction or insertion maneuvers into the final orbits have been considered. The circular restricted three-body problem is the mathematical model used to describe the motion of a spacecraft, in the gravitational field of the two primaries, computed by integrating the nonlinearized equations of motion. A shooting method has been designed and developed to determine the increment of velocity required for the perigee maneuver, which injects a spacecraft into its transfer trajectory: first the velocity boundary for the Earth escape/capture condition is detected and then an iterative bisection method is applied until the burnout velocity, tangential to the parking orbit, leads the spacecraft to its final Lissajous orbit. For a launch from Kourou at local noon, Ariane5 GTO and Soyuz GTO "equivalent" have been studied and compared, considering fuel minimization for the transfer maneuver and general mission constraints, as maximum excursion of the final Lissajous orbit from the ecliptic plane and eclipses avoidance during the mission. This analysis highlights advantages and drawbacks of various parking orbits. Mission goals are the key factor for the tradeoff among orbit selection, launch options, and the other constraints, fixed by mission requirements.

Journal Article↗

PubMed2002

Linking gene expression data with patient survival times using partial least squares.

There is an increasing need to link the large amount of genotypic data, gathered using microarrays for example, with various phenotypic data from patients. The classification problem in which gene expression data serve as predictors and a class label phenotype as the binary outcome variable has been examined extensively, but there has been less emphasis in dealing with other types of phenotypic data. In particular, patient survival times with censoring are often not used directly as a response variable due to the complications that arise from censoring. We show that the issues involving censored data can be circumvented by reformulating the problem as a standard Poisson regression problem. The procedure for solving the transformed problem is a combination of two approaches: partial least squares, a regression technique that is especially effective when there is severe collinearity due to a large number of predictors, and generalized linear regression, which extends standard linear regression to deal with various types of response variables. The linear combinations of the original variables identified by the method are highly correlated with the patient survival times and at the same time account for the variability in the covariates. The algorithm is fast, as it does not involve any matrix decompositions in the iterations. We apply our method to data sets from lung carcinoma and diffuse large B-cell lymphoma studies to verify its effectiveness.

Algorithms↗

PubMed2001

The spatial profile of visual attention in mental curve tracing.

In a curve-tracing task, subjects have to judge whether items are located on a single, continuous curve. Spatially separate segments of such a curve are related to each other through grouping criteria, like collinearity and connectedness. These grouping cues need to be exploited during curve tracing, but it is still an open issue how grouping of contour segments is achieved by the visual system. Many contemporary theories of visual perception assume that grouping operations are carried out pre-attentively, with unlimited capacity. The present study examines this assumption by investigating the involvement of attention in curve tracing. The results show that attention is directed to contour segments that need to be grouped together. The distribution of attention is guided by grouping criteria, such as connectedness. Apparently, attention is required to group spatially separate contour segments into a coherent representation of a curve.

Adolescent↗

PubMedDate not supplied

Simple device for the direct visualization of oral-cavity tissue fluorescence.

Early identification of high-risk disease could greatly reduce both mortality and morbidity due to oral cancer. We describe a simple handheld device that facilitates the direct visualization of oral-cavity fluorescence for the detection of high-risk precancerous and early cancerous lesions. Blue excitation light (400 to 460 nm) is employed to excite green-red fluorescence from fluorophores in the oral tissues. Tissue fluorescence is viewed directly along an optical axis collinear with the axis of excitation to reduce inter- and intraoperator variability. This robust, field-of-view device enables the direct visualization of fluorescence in the context of surrounding normal tissue. Results from a pilot study of 44 patients are presented. Using histology as the gold standard, the device achieves a sensitivity of 98% and specificity of 100% when discriminating normal mucosa from severe dysplasia/carcinoma in situ (CIS) or invasive carcinoma. We envisage this device as a suitable adjunct for oral cancer screening, biopsy guidance, and margin delineation.

Carcinoma, Squamous Cell↗

PubMed2004

Designing optically tracked instruments for image-guided surgery.

Most image-guided surgery (IGS) systems track the positions of surgical instruments in the physical space occupied by the patient. This task is commonly performed using an optical tracking system that determines the positions of fiducial markers such as infrared-emitting diodes or retroreflective spheres that are attached to the instrument. Instrument tracking error is an important component of the overall IGS system error. This paper is concerned with the effect of fiducial marker configuration (number and spatial distribution) on tip position tracking error. Statistically expected tip position tracking error is calculated by applying results from the point-based registration error theory developed by Fitzpatrick et al. Tracking error depends not only on the error in localizing the fiducials, which is the error value generally provided by manufacturers of optical tracking systems, but also on the number and spatial distribution of the tracking fiducials and the position of the instrument tip relative to the fiducials. The theory is extended in two ways. First, a formula is derived for the special case in which the fiducials and the tip are collinear. Second, the theory is extended for the case in which there is a composition of transformations, as is the situation for tracking an instrument relative to a coordinate reference frame (i.e., a set of fiducials attached to the patient). The derivation reveals that the previous theory may be applied independently to the two transformations; the resulting independent components of tracking error add in quadrature to give the overall tracking error. The theoretical results are verified with numerical simulations and experimental measurements. The results in this paper may be useful for the design of optically tracked instruments for image-guided surgery; this is illustrated with several examples.

Computer-Aided Design↗

PubMed1999

The effect of noncollinearity of 15N-1H dipolar and 15N CSA tensors and rotational anisotropy on 15N relaxation, CSA/dipolar cross correlation, and TROSY.

Current approaches to 15N relaxation in proteins assume that the 15N-1H dipolar and 15N CSA tensors are collinear. We show theoretically that, when there is significant anisotropy of molecular rotation, different orientations of the two tensors, experimentally observed in proteins, nucleic acids, and small peptides, will result in differences in site-specific correlation functions and spectral densities. The standard treatments of the rates of longitudinal and transverse relaxation of amide 15N nuclei, of the 15N CSA/15N-1H dipolar cross correlation, and of the TROSY experiment are extended to account for the effect of noncollinearity of the 15N-1H dipolar and 15N CSA (chemical shift anisotropy) tensors. This effect, proportional to the degree of anisotropy of the overall motion, (D parallel/D perpendicular - 1), is sensitive to the relative orientation of the two tensors and to the orientation of the peptide plane with respect to the diffusion coordinate frame. The effect is negligible at small degrees of anisotropy, but is predicted to become significant for D parallel/D perpendicular > or = 1.5, and at high magnetic fields. The effect of noncollinearity of 15N CSA and 15N-1H dipolar interaction is sensitive to both gross (hydrodynamic) properties and atomic-level details of protein structure. Incorporation of this effect into relaxation data analysis is likely to improve both precision and accuracy of the derived characteristics of protein dynamics, especially at high magnetic fields and for molecules with a high degree of anisotropy of the overall motion. The effect will also make TROSY efficiency dependent on local orientation in moderately anisotropic systems.

Hydrogen↗

PubMed2002

Characterization and effects of the replicated flowering time gene FLC in Brassica rapa.

Functional genetic redundancy is widespread in plants and could have an important impact on phenotypic diversity if the multiple gene copies act in an additive or dosage-dependent manner. We have cloned four Brassica rapa homologs (BrFLC) of the MADS-box flowering-time regulator FLC, located at the top of chromosome 5 of Arabidopsis thaliana. Relative rate tests revealed no evidence for differential rates of evolution and the ratios of nonsynonymous-to-synonymous substitutions suggest BrFLC loci are not under strong purifying selection. BrFLC1, BrFLC2, and BrFLC3 map to genomic regions that are collinear with the top of At5, consistent with a polyploid origin. BrFLC5 maps near a junction of two collinear regions to Arabidopsis, one of which includes an FLC-like gene (AGL31). However, all BrFLC sequences are more closely related to FLC than to AGL31. BrFLC1, BrFLC2, and BrFLC5 cosegregate with flowering-time loci evaluated in populations derived by backcrossing late-flowering alleles from a biennial parent into an annual parent. Two loci segregating in a single backcross population affected flowering in a completely additive manner. Thus, replicated BrFLC genes appear to have a similar function and interact in an additive manner to modulate flowering time.

Base Sequence↗

PubMed2003

The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome.

The gene complement of wild-type human cytomegalovirus (HCMV) is incompletely understood, on account of the size and complexity of the viral genome and because laboratory strains have undergone deletions and rearrangements during adaptation to growth in culture. We have determined the sequence (241 087 bp) of chimpanzee cytomegalovirus (CCMV) and have compared it with published HCMV sequences from the laboratory strains AD169 and Toledo, with the aim of clarifying the gene content of wild-type HCMV. The HCMV and CCMV genomes are moderately diverged and essentially collinear. On the basis of conservation of potential protein-coding regions and other sequence features, we have discounted 51 previously proposed HCMV ORFs, modified the interpretations for 24 (including assignments of multiple exons) and proposed ten novel genes. Several errors were detected in the published HCMV sequences. We presently recognize 165 genes in CCMV and 145 in AD169; this compares with an estimate of 189 unique genes for AD169 made in 1990. Our best estimate for the complement of wild-type HCMV is 164 to 167 genes.

Amino Acid Sequence↗

PubMed1992

Protective factors and social risk factors for hospitalization and mortality among young men.

The association between presumed protective factors and social risk factors for hospitalization and mortality was studied during a 14-year follow-up period in a cohort of 8,168 Swedish men aged 18-20 years at baseline. Using Cox regression analysis, the authors found that five protective factors (high social class, home well-being, school well-being, good emotional control, and self-perceived good health) were associated with lower risks of hospitalization and death. Four social risk factors (contact with police or child welfare authorities, running away from home, having divorced parents, and ever using narcotics) were significantly associated with increased risk of hospitalization and mortality. The relative hazard decreased with the number of protective factors and increased with the number of social risk factors, almost linearly. The relative hazard was 0.24 for hospitalization among those with six protective factors and 0.24 for mortality for those with five or six protective factors. The relative hazard for hospitalization was 3.09 among those with five social risk factors compared with those with none, while for mortality the relative hazard among those with four or five social risk factors was 5.74 compared with those with none. While these results indicate strong cumulative effects for both the social risk factors and the protective factors, the associations of individual factors with the two outcome measures were generally reduced in models which simultaneously adjusted for all factors, which presumably indicates collinearity among the factors. There was only limited support for a buffering, or interacting, effect between the risk factors and the protective factors.

Adolescent↗

PubMed2003

Penalized estimating equations.

Penalty models--such as the ridge estimator, the Stein estimator, the bridge estimator, and the Lasso-have been proposed to deal with collinearity in regressions. The Lasso, for instance, has been applied to linear models, logistic regressions, Cox proportional hazard models, and neural networks. This article considers the bridge penalty model with penalty sigma(j)/beta(j)/gamma for estimating equations in general and applies this penalty model to the generalized estimating equations (GEE) in longitudinal studies. The lack of joint likelihood in the GEE is overcome by the penalized estimating equations, in which no joint likelihood is required. The asymptotic results for the penalty estimator are provided. It is demonstrated, with a simulation and an application, that the penalized GEE potentially improves the performance of the GEE estimator, and enjoys the same properties as linear penalty models.

Air Pollution↗

PubMed2001

Detection of a gabor patch superimposed on an illusory contour.

Interactions between visual stimuli have been found to be specific to the spatial frequency, orientation and phase of the interacting stimuli. We asked if there are any interactions between luminance-defined Gabor patches and Kanizsa-type illusory contours. In psychophysical experiments we studied whether induction of a vertical illusory line affects detection thresholds for a Gabor patch superimposed on this line and whether these effects depend on the orientation, spatial frequency and phase of the Gabor elements. Employing a 2AFC method with a staircase procedure we measured contrast detection thresholds and varied the orientation, spatial frequency and phase of the test Gabor patch and the separation between the two pacmen in four experimental series. The results show that in a situation where the two inducers generate perception of an illusory line, the contrast detection of the Gabor patch is facilitated relative to a control condition where the rotated pacmen do not induce illusory contours. This facilitation was more pronounced for test Gabor signals that were collinear to the illusory line, but the observer's performance was not altered by changes in the spatial frequency or phase of the Gabor stimuli. With increasing spatial separation of the two pacmen (and, consequently, with a decreasing support ratio), the difference between performance in the test and control conditions diminished. From the data obtained we cannot infer that we have measured some neural interactions between Gabor patches and Kanizsa-type illusory contours, and nor can we draw a unique conclusion about what causes the facilitation of detection of the test Gabor patch in the experimental situation that allows induction of the illusory line. We discuss possible mechanisms of the facilitation, such as contextual influences or a reduction of uncertainty about spatial location of the test Gabor patch.

Adult↗

PubMed2006

Observations in collinear femtosecond-nanosecond dual-pulse laser-induced breakdown spectroscopy.

In the work reported herein, we have combined a short-lived femtosecond laser-induced plasma (LIP) and a longer-lived nanosecond LIP in a collinear pulse configuration to examine the source(s) of atomic emission and signal-to-noise enhancement in dual-pulse laser-induced breakdown spectroscopy (LIBS). Initial studies indicate that the primary source of dual-pulse LIBS enhancement in the collinear configuration may in large part be a matter of pulse focus; focusing on the sample surface, for example, yields atomic emission enhancements whose lifetime correlates reasonably well with the femtosecond LIP emissive lifetime, suggesting that plasma-plasma coupling may play an important role at that pulse focus. At a second "optimal" focal position above the sample surface, alternatively, atomic emission and signal-to-noise enhancements correlate quite well with the nitrogen and oxygen atomic emission reductions previously seen following use of a femtosecond air spark and a nanosecond ablative pulse in the orthogonal dual-pulse configuration, suggesting that pressure or number density reductions due to femtosecond LIP formation in air may be significant at that pulse focus.

Equipment Design↗

PubMed2001

Evaluating models of collinearity judgment for reliability and scale.

In prior work from this laboratory, we have examined how accurately subjects can judge collinearity, i.e. alignment, as a function of the angular position of stimulus elements. In those experiments, subjects were presented with a line segment (or a pair of dots) which varied across the 360 degrees range of angular positions, and were required to select and mark a point which was perceived as being collinear. We found that the models of error for each subject consisted of a complex set of peaks and valleys which are herein described as delta excursions. The error tendencies appeared to be idiosyncratic, in that each subject manifested a different profile of these excursions. Here we report the results of three experiments. In the first, we tested subjects across five sessions, and found that the five models of error were fairly comparable for a given subject. In the second and third experiments, we tested at close intervals of angular position, and found evidence for localized sources of error. We continue to find that the error model for each subject is idiosyncratic, and argue that the excursions may be due to defects in a system which combines responses from position-encoding fields that vary in size.

Analysis of Variance↗

PubMed1998

Molecular cloning of the chicken melanocortin 2 (ACTH)-receptor gene.

The chicken melanocortin 2-receptor (MC2-R) gene was isolated. It is found to be a single copy gene encoding a 357 amino acid protein, sharing 65.8-68.7% identity with mammalian counterparts. The chicken MC2-R mRNA is expressed in the adrenal and spleen, suggesting that the receptor mediates both endocrine and immunoregulatory functions of ACTH in the chicken. The amino acid sequence of the chicken MC2-R is collinear with those of other subtypes of MC-R, whereas all cloned mammalian MC2-Rs contain a gap in the third intracellular loop, suggesting that mammalian MC2-R molecules have evolved by lacking a part of the domain which determines the specificity of signal transduction in G-protein coupled receptors. Interestingly, the codon usage differs dramatically between MC1-R and MC2-R in the chicken; the GC-contents at the third codon position in MC1-R and MC2-R are 94.6 and 50.6%, respectively. It may reflect selective constraints on the usage of synonymous codons.

Adrenal Glands↗