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PubMed2004

The world from a cat's perspective--statistics of natural videos.

The mammalian visual system is one of the most intensively investigated sensory systems. However, our knowledge of the typical input it is operating on is surprisingly limited. To address this issue, we seek to learn about the natural visual environment and the world as seen by a cat. With a CCD camera attached to their head, cats explore several outdoor environments and videos of natural stimuli are recorded from the animals' perspective. The statistical analysis of these videos reveals several remarkable properties. First, we find an anisotropy of oriented contours with an enhanced occurrence of horizontal orientations, earlier described in the "oblique effect" as a predominance of the two cardinal orientations. Second, contrast is not elevated in the center of the images, suggesting different mechanisms of fixation point selection as compared to humans. Third, analyzing a sequence of images we find that the precise position of contours varies faster than their orientation. Finally, collinear contours prevail over parallel shifted contours, matching recent physiological and anatomical results. These findings demonstrate the rich structure of natural visual stimuli and its direct relation to extensively studied anatomical and physiological issues.

Animals↗
PubMed2000

The perceptual organization of visual objects: a microgenetic analysis.

Primed matching was used to examine the microgenesis of perceptual organization for line configurations that vary in the connectedness between their four line components, and for hierarchical patterns composed of four outline closed figures. The results for the line configurations showed that the configural organization of the disconnected line segments was available for priming very early, and its effect outweighed possible effects of the line components. An early relative dominance of the components was observed for the stimuli whose components were closed figures. These results suggest that uniform connectedness is not necessary for the designation of entry-level units. Disconnected line segments are rapidly organized into configurations, provided the presence of collinearity and/or closure. Closed figural elements are individuated early and are grouped into higher-level units with time.

Adolescent↗
PubMed1994

Validation of the medical expert system RENOIR.

RENOIR is an expert system developed to assist the diagnosis of 37 diseases of connective tissue and inflammatory arthropathies. Precise diagnosis of rheumatic diseases implies great uncertainty and there is no gold standard with which to compare the expert system output. To overcome this problem a set of clinical cases was submitted to RENOIR and its diagnoses were compared with those of clinicians. Medical records of 81 patients with rheumatic diseases were interpreted by RENOIR and by 12 clinicians at three different expertise levels in rheumatology. Distances between the likelihoods of the 37 considered diseases provided by clinicians and RENOIR were computed as a disagreement measure. Mahalanobis distance was used to correct the collinearity between the possibilities of each pair of diseases. Using the resulting matrices of distances between experts, cluster analyses were carried out to classify RENOIR among human experts. Greater differences between RENOIR and clinicians than among clinicians themselves were not found.

Cluster Analysis↗
PubMed2000

A study of the association between daily mortality and ambient air pollutant concentrations in Pittsburgh, Pennsylvania.

We have studied the possible association of daily mortality with ambient pollutant concentrations (PM10, CO, O3, SO2, NO2, and fine [PM2.5] and coarse PM) and weather variables (temperature and dew point) in the Pittsburgh, PA, area for two age groups--less than 75, and 75 and over--for the 3-year period of 1989-1991. Correlation functions among pollutant concentrations show important seasonal dependence, and this fact necessitates the use of seasonal models to better identify the link between ambient pollutant concentrations and daily mortality. An analysis of the seasonal model results for the younger-age group reveals significant multicollinearity problems among the highly correlated concentrations of PM10, CO, and NO2 (and O3 in spring and summer), and calls into question the rather consistent results of the single- and multi-pollutant non-seasonal models that show a significant positive association between PM10 and daily mortality. For the older-age group, dew point consistently shows a significant association with daily mortality in all models. Collinearity problems appear in the multi-pollutant seasonal and non-seasonal models such that a significant, positive PM10 coefficient is accompanied by a significant, negative coefficient of another ambient pollutant, and the identity of this other pollutant changes with season. The PM2.5 data set is half that of PM10. Identical-model runs for both data sets reveal instability in the pollutant coefficients, especially for the younger age group. The concern for the instability of the pollutant coefficients due to a small signal-to-noise ratio makes it impossible to ascertain credibly the relative associations of the fine- and coarse-particle modes with daily mortality. In this connection, we call for caution in the interpretation of model results for causal inference when the models use fully or partially estimated PM values to fill large data gaps.

Adolescent↗
PubMed1975

Structure-activity correlations among rifamycin B amides and hydrazides.

Structure-antibacterial activity correlation equations have been developed for aseries of 44 amides and 25 hydrazides of rifamycin B in five bacterial systems. The best amide equations show that activity is a parabolic function of log P. A wide variation in log Po was found for the various bacterial systems. The most important correlation parameter in the hydrazide equations is omicron*. The significance of this finding is somewhat obscured by the high degree of collinearity among the parameters evaluated (omicron*, E-s, log P). Two rifamycin B amides were prepared and evaluated as a result of this study. The correlation equations quantitatively predicted their activity in five of six tests.

Amides↗
PubMed2003

Bias and error in estimates of mean shape in geometric morphometrics.

Sampling experiments were performed to investigate mean square error and bias in estimates of mean shape produced by different geometric morphometric methods. The experiments use the isotropic error model, which assumes equal and independent variation at each landmark. The case of three landmarks in the plane (i.e., triangles) was emphasized because it could be investigated systematically and the results displayed on the printed page. The amount of error in the estimates was displayed as RMSE surfaces over the space of all possible configurations of three landmarks. Patterns of bias were shown as vector fields over this same space. Experiments were also performed using particular combinations of four or more landmarks in both two and three dimensions. It was found that the generalized Procrustes analysis method produced estimates with the least error and no pattern of bias. Averages of Bookstein shape coordinates performed well if the longest edge was used as the baseline. The method of moments (Stoyan, 1990, Model. Biomet. J. 32, 843) used in EDMA (Lele, 1993, Math. Geol. 25, 573) exhibits larger errors. When variation is not small, it also shows a pattern of bias for isosceles triangles with one side much shorter than the other two and for triangles whose vertices are approximately collinear causing them to resemble their own reflections. Similar problems were found for the log-distance method of Rao and Suryawanshi (1996, Proc. Nat. Acad. Sci. 95, 4121). These results and their implications for the application of different geometric morphometric methods are discussed.

Animals↗
PubMed2004

Biosynthetic pathway and gene cluster analysis of curacin A, an antitubulin natural product from the tropical marine cyanobacterium Lyngbya majuscula.

Curacin A (1) is a potent cancer cell toxin obtained from strains of the tropical marine cyanobacterium Lyngbya majuscula found in Curaçao. Its structure is unique in that it contains the sequential positioning of a thiazoline and cyclopropyl ring, and it exerts its potent cell toxicity through interaction with the colchicine drug binding site on microtubules. A series of stable isotope-labeled precursors were fed to cultures of curacin A-producing strains and, following NMR analysis, allowed determination of the metabolic origin of all atoms in the natural product (one cysteine, 10 acetate units, two S-adenosyl methionine-derived methyl groups) as well as several unique mechanistic insights. Moreover, these incorporation experiments facilitated an effective gene cloning strategy that allowed identification and sequencing of the approximately 64 kb putative curacin A gene cluster. The metabolic system is comprised of a nonribosomal peptide synthetase (NRPS) and multiple polyketide synthases (PKSs) and shows a very high level of collinearity between genes in the cluster and the predicted biochemical steps required for curacin biosynthesis. Unique features of the cluster include (1) all but one of the PKSs are monomodular multifunctional proteins, (2) a unique gene cassette that contains an HMG-CoA synthase likely responsible for formation of the cyclopropyl ring, and (3) a terminating motif that is predicted to function in both product release and terminal dehydrative decarboxylation.

Amino Acid Sequence↗
PubMed2000

Distinguishing illness severity from tic severity in children and adolescents with Tourette's disorder.

OBJECTIVE: To examine whether tic severity, comorbid disorders, or both are associated with illness morbidity in youths with Tourette's disorder (TD). METHOD: Subjects were 156 consecutively referred youths (aged 5-20 years) who met DSM-III-R criteria for Tourette's disorder at a major academic medical center. All subjects were evaluated with a clinical interview by a child and adolescent psychiatrist and an assessment battery that included the Schedule for Affective Disorders and Schizophrenia for School-Age Children-Epidemiologic version. Statistical analysis used chi 2 and multivariate logistic regression. RESULTS: Nineteen (12%) of the 156 youths with TD required psychiatric hospitalization. Current age, TD severity, TD duration, obsessive-compulsive disorder, psychosis, major depression, bipolar disorder, panic disorder, and overanxious disorder were significant univariate predictors of psychiatric hospitalization (p < .01). While tic severity was marginally significant as a predictor of psychiatric hospitalization (p < .05), major depression (p < .016) and bipolar disorder (p < .001) were robust predictors of psychiatric hospitalization, even after statistical adjustment for collinearity and correction for all other variables assessed. CONCLUSION: The findings indicate that comorbid mood disorders are strongly associated with illness morbidity in youths with TD, highlighting the importance of attention to comorbidity in patients with TD.

Adolescent↗
PubMed2001

Transcript and activity levels of different Pleurotus ostreatus peroxidases are differentially affected by Mn2+.

The white-rot fungus Pleurotus ostreatus produces both manganese-dependent peroxidase (MnP) and versatile peroxidase (VP) in non-manganese-amended peptone medium (PM). We studied the effect of Mn2+ supplementation on MnPs and VPs in P. ostreatus by analysing the enzymatic and transcript abundance profiles of the peroxidases, as well as the lignin mineralization rate. The fungus was grown in PM under solid-state conditions using perlite as an inert solid support. Mn2+ amendment resulted in a 1.7-fold increase in [14C]-lignin mineralization relative to unamended medium. Anion-exchange chromatography was used to resolve the fungal peroxidase's enzymatic activity profile. Five peaks (P1-P5) of VP and one peak (P6) of MnP activity were detected in unamended medium. In Mn2+-amended medium, a reduction in the activity of the VPs was observed. On the other hand, a sharp increase in the MnP activity level of peak P6 was detected. The P6 isoenzyme was purified and showed manganese-dependent peroxidation of phenolic substrates. Internal sequence analysis of the purified enzyme revealed 100% identity with the deduced amino acid sequence of P. ostreatus MnP3 (GenBank AB016519). The effect of Mn2+ on the relative abundance of gene transcripts of three VPs and one MnP from P. ostreatus was monitored using reverse transcription-polymerase chain reaction (RT-PCR) with oligonucleotide primer sets synthesized on the basis of non-conserved sequences of the different peroxidases. The reduction in VP gene transcript abundance and the increase in mnp3 transcript level were collinear with the changes observed in the enzyme activity profiles. These results indicate that the activity of peroxidases is regulated at the transcriptional level. We suggest that the expression of MnP and VP may be differentially regulated by the presence of Mn2+.

Agaricales↗
PubMed2006

Real-time measurement of cytosolic free calcium concentration in Jurkat cells during ELF magnetic field exposure and evaluation of the role of cell cycle.

Extremely low frequency magnetic fields (ELF MF) have been reported to alter a number of cell signaling pathways, including those involved in proliferation, differentiation and apoptosis where cytosolic free calcium ([Ca(2+)](c)) plays an important role. To better understand the biological conditions under which ELF MF exposure might alter [Ca(2+)](c), we measured [Ca(2+)](c) by ratiometric fluorescence spectrophotometry during exposure to ELF MF in Jurkat E6.1 cells synchronized to different phases of the cell cycle. Suspensions of cells were exposed either to a near zero MF (Null) or a 60 Hz, 100 microT sinusoidal MF superimposed upon a collinear 78.1 microT static MF (AC + DC). An initial series of experiments indicated that the maximum increase in [Ca(2+)](c) above baseline after stimulation with anti-CD3 was significantly higher in samples exposed to AC + DC (n = 30) compared to Null (n = 30) with the largest difference in G2-M enriched samples. However, in a second study with G2-M enriched cells, samples treated with AC + DC (n = 17) were not statistically different from Null-treated samples (n = 27). Detailed analysis revealed that the dynamics in [Ca(2+)](c) before and after stimulation with anti-CD3 were dissimilar between Null samples from each study. From the results, we concluded (i) that the ELF MF increased [Ca(2+)](c) during an antibody-induced signaling event, (ii) that the ELF MF effect did not depend to a large degree on cell cycle, and (iii) that a field-related change in [Ca(2+)](c) signaling appeared to correlate with features in the [Ca(2+)](c) dynamics. Future work could evaluate [Ca(2+)](c) dynamics in relation to the phase of the cell cycle and inter-study variation, which may reveal factors important for the observation of real-time effects of ELF MF on [Ca(2+)](c).

Calcium↗
PubMed2004

DAGchainer: a tool for mining segmental genome duplications and synteny.

SUMMARY: Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG). These chains of collinear gene pairs can represent segmentally duplicated regions and genes within a single genome or syntenic regions between related genomes. Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer.

Algorithms↗
PubMed2004

Building genomic profiles for uncovering segmental homology in the twilight zone.

The identification of homologous regions within and between genomes is an essential prerequisite for studying genome structure and evolution. Different methods already exist that allow detecting homologous regions in an automated manner. These methods are based either on finding sequence similarities at the DNA level or on identifying chromosomal regions showing conservation of gene order and content. Especially the latter approach has proven useful for detecting homology between highly divergent chromosomal regions. However, until now, such map-based approaches required that candidate homologous regions show significant collinearity with other segments to be considered as being homologous. Here, we present a novel method that creates profiles combining the gene order and content information of multiple mutually homologous genomic segments. These profiles can be used to scan one or more genomes to detect segments that show significant collinearity with the entire profile but not necessarily with individual segments. When applying this new method to the combined genomes of Arabidopsis and rice, we find additional evidence for ancient duplication events in the rice genome.

Algorithms↗
PubMed1995

Determinants of bone mass in 10- to 26-year-old females: a twin study.

This cross-sectional twin study aimed to quantify the roles of constitutional and lifestyle factors on bone mass in adolescent and young adult women. Areal bone density (BMD) at the lumbar spine, femoral neck, Ward's triangle, and total hip, total body bone mineral content (BMC), and lean mass and fat mass were measured using dual energy X-ray absorptiometry (DXA) in 215 female volunteer twin pairs (122 monozygotic [MZ], 93 dizygotic [DZ]) aged 10 to 26 years. Height, weight, menarchial history, dietary calcium intake, physical activity, current tobacco use, and alcohol consumption were determined by questionnaire. Mean BMD increased with age to around 16 years, when it reached a plateau. Within-pair differences in BMD at the lumbar spine (expressed as a percentage of the pair mean BMD) were univariately associated with pair differences in menarchial status (14 +/- 3%), height (0.7 +/- 0.1% per cm), weight (0.4 +/- 0.1% per kg), lean mass (1.0 +/- 0.1% per kg), and fat mass (0.5 +/- 0.1% per kg). Only menarchial status, height, and lean mass, however, were independent predictors. At the proximal femoral sites, within-pair BMD differences were associated with within-pair lean mass differences (1.0 to 1.1 +/- 0.2%/kg), and no other factor was significant. The same conclusions applied to within-pair differences in BMD/height. Total body BMC was independently associated with menarchial status, height, lean mass, and fat mass; the effects of the latter two variables were stronger in pairs both premenarchial. After adjusting for constitutional factors, no lifestyle factor was independently predictive. By reducing collinearity, the cotwin method clearly identified that lean mass, not fat mass, was the major independent determinant of bone mass at the hip, both pre- and postmenarche.

Absorptiometry, Photon↗
PubMed1987

A new type of papillomavirus associated with cancer of the uterine cervix.

A new human papillomavirus (HPV) type was detected by low-stringency Southern blot hybridization analysis of DNA from an endocervical adenocarcinoma. The genomic DNA of the virus, which was obtained as two BamHI fragments of 3.75 and 4.1 kb, was molecularly cloned into lambda L47 and subsequently subcloned into pBR322 for further characterization. Hybridization studies demonstrated that these viral DNA isolates were only distantly related to other HPV and thus represented a new type of HPV, called HPV 35. A restriction enzyme map was prepared which allowed a comparison of the genetic organization of this HPV with that of HPV 6b; the results demonstrated collinearity of the HPV 35 genome with that of HPV 6b. Prevalence studies revealed that HPV 35 was present in 2 of 158 (1%) anogenital intraepithelial neoplasia and in 3 of 69 (4%) anogenital cancers. Thus HPV 35 is a low-prevalence human papillomavirus associated with anogenital intraepithelial neoplasia and cancer.

Adenocarcinoma↗
PubMed2003

Perceptual organization of local elements into global shapes in the human visual cortex.

The question of how local image features on the retina are integrated into perceived global shapes is central to our understanding of human visual perception. Psychophysical investigations have suggested that the emergence of a coherent visual percept, or a "good-Gestalt", is mediated by the perceptual organization of local features based on their similarity. However, the neural mechanisms that mediate unified shape perception in the human brain remain largely unknown. Using human fMRI, we demonstrate that not only higher occipitotemporal but also early retinotopic areas are involved in the perceptual organization and detection of global shapes. Specifically, these areas showed stronger fMRI responses to global contours consisting of collinear elements than to patterns of randomly oriented local elements. More importantly, decreased detection performance and fMRI activations were observed when misalignment of the contour elements disturbed the perceptual coherence of the contours. However, grouping of the misaligned contour elements by disparity resulted in increased performance and fMRI activations, suggesting that similar neural mechanisms may underlie grouping of local elements to global shapes by different visual features (orientation or disparity). Thus, these findings provide novel evidence for the role of both early feature integration processes and higher stages of visual analysis in coherent visual perception.

Humans↗
PubMed1994

Collinearity judgment as a function of induction angle.

The misalignment which is seen in the Poggendorff illusion can be studied with better control by using a configuration which has only two line segments. Two experiments were conducted in which subjects judged collinearity of a test segment, this judgment being subjected to a biasing influence from a second (induction) segment. Exp. 1 held the test segment at one of three orientations relative to the observer (30 degrees, 45 degrees, and 60 degrees) and systematically varied the orientation of the induction segment in 15 degrees increments through the range of possible positions. The orientation of the page relative to the observer was varied as well. Exp. 2 varied the test segment through a greater range of angles and sampled more levels of induction segment orientation. Analysis indicated that projection errors follow orderly rules similar in kind to but different in magnitude from those observed for the Tilt Illusion, most notably, (a) misprojection is greatest when the orientation of the interfering line is similar to that of the line segment being projected and (b) the strength of this influence decreases as the relative angle becomes orthogonal. Also, the orientation of the segment being projected relative to the observer serves to modulate the strength of the basic induction effect. These perceptual interactions are discussed in relation to neural models for orientation selectivity.

Adult↗
PubMed1992

Genomic organization and expression of the 3' end of the canine and feline enteric coronaviruses.

The genomic organization at the 3' end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Comparison of the latter two has previously revealed an extra open reading frame (ORF) at the 3' end of the FIPV genome, lacking in TGEV, which is currently designated ORF 6b. Both CCV and FECV possess 6b-related ORFs at the 3' ends of their genomes. The presence of ORF 6b in three of four viruses in this antigenic cluster strongly suggests that TGEV has lost this ORF by deletion. The CCV ORF 6b is collinear with that of FIPV, but the predicted amino acid sequences are only 58% identical. The FECV ORF 6b contains a large deletion compared to that of FIPV, reducing the collinear part to 60%. The sequence homologies were highest between CCV and TGEV on the one hand and between FECV and FIPV on the other. Previously, we showed that the expression product of the FIPV ORF 6b can be detected in infected cells by immunoprecipitation (Vennema et al., 1992). In the present study we have performed similar experiments with CCV and FECV. In infected cells both viruses produced proteins related to but different from the FIPV 6b protein.

Amino Acid Sequence↗