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PubMed2005

Orientations of axially coordinated imidazoles and pyridines in crystal structures of model systems of cytochromes.

Many properties of cytochromes and model systems depend on orientations of axial ligands. In this work, we elucidated the role of porphyrin substituents on orientation of axial ligands in model systems of cytochromes. The orientations of axially coordinated imidazoles and pyridines in crystal structures of model systems of cytochromes were analyzed and data were compared with previous quantum-chemical calculations. The results show that eight ethyl groups on porphyrin ring strongly favor parallel orientation, hence, in all these complexes axial ligands, pyridines or imidazoles, are mutually parallel. Four phenyl or mesityl groups at meso-carbons also favor parallel orientation but less strongly. Hence, in most of the bis-imidazole complexes the orientation is parallel, while in bis-pyridine complexes the orientation of pyridines depends on oxidation state of Fe. In bis-pyridine Fe(II) complexes orientation is parallel, in Fe(III) it is orthogonal. This analysis is in agreement with previous quantum-chemical calculations.

Crystallography, X-Ray↗
PubMed2004

Validation of the relative 3D orientation of vertebrae reconstructed by bi-planar radiography.

The three dimensional (3D) reconstruction of the spine can be obtained by stereoradiographic techniques. To be safely used on a routine clinics basis, stereoradiography must provide both accurate vertebral shape and coherent position. Although the accuracy of the reconstructed morphology of the vertebrae is well documented, only few authors studied the accuracy of the vertebral orientation. Therefore, this paper focuses on the evaluation of the orientation accuracy of the reconstructed vertebrae (obtained by non-stereo corresponding point technique) considering either a 178 point vertebral model or a 6 point vertebral model (previously proposed in the literature). Five dried vertebrae were fixed on holders containing four markers each. The 3D reconstruction of both vertebrae and markers were obtained by stereoradiographic techniques. Using least square method matching from one position to another, the relative orientation was computed for the vertebral models (6 or 178 points) and the four markers. These vertebral and holder orientations were compared (considering the holder's one as reference). The repeatability of these relative orientations (vertebrae and holders) was also evaluated. The mean (RMS) orientation error of 178 point vertebral model was 0.6 degrees (0.8 degrees ), for lateral rotation, 0.7 degrees (1.0 degrees ) for sagittal rotation and 1.4 degrees (1.9 degrees ) for axial rotation. The intra-observer repeatability was 0.5 degrees (0.7 degrees ) for lateral rotation, 0.7 degrees (0.8 degrees ) for sagittal rotation and 0.9 degrees (1.2 degrees ) for axial rotation. The orientation was found more accurate and precise when using the 178 point vertebral model than when using the basic 6 point vertebral model. The relative orientation (in post-operative follow-up with respect to the pre-operative examination) of the vertebrae of one scoliotic patient was performed as an example of clinical application. The stereoradiographic method is a reliable 3D quantitative tool to assess the spine deformity, that can be used in clinics for the follow-up of scoliotic patients.

Adult↗
PubMed2006

Orienting attention to semantic categories.

We investigated the ability to orient attention to a complex, non-perceptual attribute of stimuli-semantic category. Behavioral consequences and neural correlates of semantic orienting were revealed and compared with those of spatial orienting, using event-related functional magnetic-resonance imaging. Semantic orienting significantly shortened response times to identify word stimuli, showing that it is possible to focus attention on non-perceptual attributes of stimuli to enhance behavioral performance. Semantic-orienting cues engaged parietal and frontal areas that were also involved in spatial orienting, but in addition engaged brain areas associated with semantic analysis of words, such as the left anterior inferior frontal cortex. These findings show that attentional orienting selectively engages brain areas with functional specialization for the predicted attributes. They also support the existence of a core frontoparietal network, which controls attentional orienting in speeded response tasks independently of the type of expectations, interacting with task-relevant functionally specialized areas to optimize perception and action.

Adult↗
PubMed1980

Surface-induced lamellar orientation of multilayer membrane arrays. Theoretical analysis and a new method with application to purple membrane fragments.

The orientation of membrane fragments into a lamellar array by a flat surface is analyzed. This analysis includes processes such as centrifugation and drying and physical effects due to membrane fragment steric interactions, finite size, elasticity, and thermal fluctuations. Several model calculations of optimal orientational order in multilayer membrane arrays are presented. The predictions of a smectic A model agree quantitatively with the measured spatial dependence of the fluctuations in layer orientation in a multilamellar arrays. A new technique, based in part on this analysis, for the preparation of well-oriented multilamellar arrays of natural and artificial membranes, isopotential spin-dry centrifugation, is described. The method involves the use of specially designed inserts for the buckets of a standard vacuum ultracentrifuge. The membrane fragments to be oriented are sedimented from solution or suspension onto a substrate of a convenient material which forms a gravitational isopotential surface at high g. Sedimentation is accompanied by removal of the suspending medium at high g to produce oriented films with a selected degree of solvation. In addition, a method is described whereby small solute molecules can be maintained in constant concentration with the membrane fragments during this process. Initial application of the method to the orientation of purple membrane fragments is described. The degree of orientation obtained in this system is evaluated using freeze-fracture and scanning electron microscopy, optical birefringence, linear dichroism, and microscopy.

Bacteriorhodopsins↗
PubMed1995

Small angle x-ray scattering studies of magnetically oriented lipid bilayers.

Magnetically oriented lipid/detergent bilayers are potentially useful for studies of membrane-associated molecules and complexes using x-ray scattering and nuclear magnetic resonance (NMR). To establish whether the system is a reasonable model of a phospholipid bilayer, we have studied the system using x-ray solution scattering to determine the bilayer thickness, interparticle spacing, and orientational parameters for magnetically oriented lipid bilayers. The magnetically orientable samples contain the phospholipid L-alpha-dilauroylphosphatidylcholine (DLPC) and the bile salt analog 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) in a 3:1 molar ratio in 70% water (w/v) and are similar to magnetically orientable samples used as NMR media for structural studies of membrane-associated molecules. A bilayer thickness of 30 A was determined for the DLPC/CHAPSO particles, which is the same as the bilayer thickness of pure DLPC vesicles, suggesting that the CHAPSO is not greatly perturbing the lipid bilayer. These data, as well as NMR data on molecules incorporated in the oriented lipid particles, are consistent with the sample consisting of reasonably homogeneous and well dispersed lipid particles. Finally, the orientational energy of the sample suggests that the size of the cooperatively orienting unit in the samples is 2 x 10(7) phospholipid molecules.

Biophysical Phenomena↗
PubMed1998

Effect of the length and effective diameter of F-actin on the filament orientation in liquid crystalline sols measured by x-ray fiber diffraction.

We examined factors that affect the filament orientation in F-actin sols to prepare highly well-oriented liquid crystalline sols suitable for x-ray fiber diffraction structure analysis. Filamentous particles such as F-actin spontaneously align with one another when concentrated above a certain threshold concentration. This alignment is attributed to the excluded volume effect of the particles. In trying to improve the orientation of F-actin sols, we focused on the excluded volume to see how it affects the alignment. The achievable orientation was sensitive to the ionic strength of the solvent; the filaments were better oriented at lower ionic strengths, where the effective diameter of the filament is relatively large. Sols of longer filaments were better oriented than those of shorter filaments at the same concentration, but the best achievable orientation was limited, probably because of the filament flexibility. The best strategy for making well-oriented F-actin sols is therefore to concentrate F-actin filaments of relatively short length (<1 micrometer) by slow centrifugation in a low-ionic-strength solvent (<30 mM).

Actins↗
PubMed1978

Effects of the volume conductor on the apparent orientation of a known cardiac dipole.

The surface electrocardiogram (EKG) is dependent on two major factors: the cardiac generator and the volume conductor. This investigation assessed the effects of the volume conductor in man on the apparent orientation of a simulated cardiac dipole. The apparent orientation of the dipole was calculated from measured surface potentials from about 60 locations on the body of five patients with implanted cardiac pacemakers. The real orientation of the dipole (an implanted pacemaker) was determined radiographically. The effects of both inhomogeneity and boundary characteristics of the volume conductor on the apparent orientation of the dipole were assessed using a new inverse algorithm. The difference between the orientation of the real and the calculated dipoles averaged 30 degrees (range 15 degrees--40 degrees) when the torso was assumed to be an infinite-homogeneous volume conductor. When the configuration of the torso was accounted for, however, the difference between the orientation of the real and calculated dipoles was reduced to 9 degrees (range 5 degrees--13 degrees). Thus, by taking into account the geometry of the torso and neglecting the inhomogeneities in the volume conductor, it is possible to calculate the orientation of a dipole in the cardiac region with an accuracy of about 9 degrees. It is reasonable to assume that the orientation of real activation wave fronts from localized areas of the heart could be calculated with a similar degree of accuracy.

Aged↗
PubMed2000

Surface composition and orientation interact to affect subtidal epibiota.

Settlement panels were used to evaluate the effects of composition of the substratum (sandstone, concrete, wood) and orientation (vertical, horizontal undersides) on subtidal epibiota. It was predicted that both factors would influence the development of epibiotic assemblages, but that differences due to composition would be less marked on horizontal undersides compared to vertical panels. Differences in assemblages among sandstone, concrete and wooden panels orientated vertically were predicted to be similar to those described previously among vertical surfaces of sandstone rocky reefs and concrete and wooden urban structures (pilings and pontoons). Multivariate analyses indicated that assemblages were influenced greatly by orientation, whereas the effects of surface composition differed for the two orientations and among sites. Assemblages on wood were always significantly different from those on sandstone or concrete - patterns between the latter two surfaces depended on the orientation of the panels. The taxa that dominated these surfaces were not similar in identity nor abundance to those on urban structures of the same composition. The covers of most taxa were influenced by orientation alone or by surface composition for just one orientation. This study demonstrates the need for caution in generalizing about effects of orientation and surface composition because they may interact with each other and/or with other factors and they are certainly quite different for different taxa and among sites.

Journal Article↗
PubMed1999

Orientation discrimination and tilt aftereffects with luminance and illusory contours.

Orientation discrimination and tilt aftereffects (TAEs) were measured to determine if the orientation of luminance and illusory contours are processed by separate mechanisms. The assumption was made that if a single mechanism supports the perception of both types of contours, then illusory and luminance contours that support the same level of orientation discrimination will be equally effective adapting patterns. Experiment I found that orientation discrimination psychometric functions for illusory and luminance contours are similar, confirming that performance could be matched. Experiment II measured orientation discrimination for a range of intensities for both contours. Experiment III measured TAEs following adaptation to illusory and luminance contours that supported a similar range of orientation discrimination. Similar TAEs were not observed, thus rejecting the single mechanism hypothesis. Experiments IV and V sought to validate the assumption that equivalent orientation discrimination predicts equivalent TAEs by using stimuli that seemed likely to be represented by the same visual mechanism. Luminance contours masked by randomly placed dots and unmasked luminance contours were used with the same procedures as experiments II and III. Equal TAEs were not observed for masked and unmasked contours matched on orientation discrimination, suggesting the assumption relating discriminability to adaptation was incorrect.

Humans↗
PubMed1999

The Poggendorff illusion: a bias in the estimation of the orientation of virtual lines by second-stage filters.

The veridical perception of collinearity between two separated lines is distorted by two parallel lines in the space between them (the Poggendorff illusion). This paper tests the conjecture that the perception of collinearity of separated lines is based on a two-stage mechanism. The first stage encodes the orientation of the virtual line between the proximal terminators of the target lines. The second stage compares this virtual orientation with the orientation of the target lines themselves. Errors can and do arise from either process. Two parallel lines, abutting against the target lines, cause the classical Poggendorff misalignment bias. The magnitude of the bias is increased by Gaussian blur, as is a version of the Poggendorff figure containing only acute angles. In the obtuse-angle figure, on the other hand, blur decreases the misalignment bias. We argue that the acute- and obtuse-angle biases depend upon different mechanisms, and that the obtuse-angle effect is more related to the obtuse-angle version of the Muller-Lyer illusion, which is also decreased by blur. If observers attempt to match the orientation of the virtual line between the two line intersections in the Poggendorff figure they make an error in the same direction as the Poggendorff bias. The orientation of the target lines in the figure, however, is veridically matched to a Gabor-patch probe, unless the target lines are very short, in which case the error is in the same direction as the Poggendorff bias. A small bend in the target lines where they abut the parallels increases the Poggendorff bias if it makes the line more orthogonal to the parallel, but has little effect in the opposite direction. The Poggendorff bias is unlikely to depend upon biases in first-stage linear filters because (a) it still exists in figures composed of short, luminance-balanced lines which are defined by contrast only; and (b) it also exists if the parallels are replaced by grating patches with the same mean luminance as the background. The orientation of the grating in the latter case affects the magnitude of the bias, but even an orientation which should reverse the Poggendorff bias by the mechanism of cross-orientation inhibition fails to do so. The Poggendorff bias is a complex effect arising from several sources. Blurring in second-stage filters with large receptive fields can explain many aspects of the phenomenon.

Contrast Sensitivity↗
PubMed2003

Polycrystal orientation maps from TEM.

Determination of topography of crystallite orientations is an important technique of investigation of polycrystalline materials. A system for creating orientation maps using transmission electron microscope (TEM) Kikuchi patterns and Convergent beam electron diffraction patterns is presented. The orientation maps are obtained using a step-by-step beam scan on a computer-controlled TEM equipped with a CCD camera. At each step, acquired diffraction patterns are indexed and orientations are determined. Although, the approach used is similar to that applied in SEM/electron back scattered diffraction (EBSD) orientation imaging setups, the TEM-based system considerably differs from its SEM counterpart. The main differences appear due to specific features of TEM and SEM diffraction patterns. Also, the resulting maps are not equivalent. On these generated by TEM, the accuracy of orientation determination can be better than 0.1 degrees. The spatial resolution is estimated to be about 10nm. The latter feature makes the TEM orientation mapping system an important tool for studies at fine scale unreachable by SEM/EBSD systems. The automatic orientation mapping is expected to be a useful complement of the conventional TEM contrast images. The new technique will be essential for characterization of fine structure materials. To illustrate that, example maps of an aluminum sample produced by severe plastic deformation are included.

Journal Article↗
PubMed2001

Role of beam orientation optimization in intensity-modulated radiation therapy.

PURPOSE: To investigate the role of beam orientation optimization in intensity-modulated radiation therapy (IMRT) and to examine the potential benefits of noncoplanar intensity-modulated beams. METHODS AND MATERIALS: A beam orientation optimization algorithm was implemented. For this purpose, system variables were divided into two groups: beam position (gantry and table angles) and beam profile (beamlet weights). Simulated annealing was used for beam orientation optimization and the simultaneous iterative inverse treatment planning algorithm (SIITP) for beam intensity profile optimization. Three clinical cases were studied: a localized prostate cancer, a nasopharyngeal cancer, and a paraspinal tumor. Nine fields were used for all treatments. For each case, 3 types of treatment plan optimization were performed: (1) beam intensity profiles were optimized for 9 equiangular spaced coplanar beams; (2) orientations and intensity profiles were optimized for 9 coplanar beams; (3) orientations and intensity profiles were optimized for 9 noncoplanar beams. RESULTS: For the localized prostate case, all 3 types of optimization described above resulted in dose distributions of a similar quality. For the nasopharynx case, optimized noncoplanar beams provided a significant gain in the gross tumor volume coverage. For the paraspinal case, orientation optimization using noncoplanar beams resulted in better kidney sparing and improved gross tumor volume coverage. CONCLUSION: The sensitivity of an IMRT treatment plan with respect to the selection of beam orientations varies from site to site. For some cases, the choice of beam orientations is important even when the number of beams is as large as 9. Noncoplanar beams provide an additional degree of freedom for IMRT treatment optimization and may allow for notable improvement in the quality of some complicated plans.

Algorithms↗
PubMed2002

Incorporating prior knowledge into beam orientation optimization in IMRT.

PURPOSE: Selection of beam configuration in currently available intensity-modulated radiotherapy (IMRT) treatment planning systems is still based on trial-and-error search. Computer beam orientation optimization has the potential to improve the situation, but its practical implementation is hindered by the excessive computing time associated with the calculation. The purpose of this work is to provide an effective means to speed up the beam orientation optimization by incorporating a priori geometric and dosimetric knowledge of the system and to demonstrate the utility of the new algorithm for beam placement in IMRT. METHODS AND MATERIALS: Beam orientation optimization was performed in two steps. First, the quality of each possible beam orientation was evaluated using beam's-eye-view dosimetrics (BEVD) developed in our previous study. A simulated annealing algorithm was then employed to search for the optimal set of beam orientations, taking into account the BEVD scores of different incident beam directions. During the calculation, sampling of gantry angles was weighted according to the BEVD score computed before the optimization. A beam direction with a higher BEVD score had a higher probability of being included in the trial configuration, and vice versa. The inclusion of the BEVD weighting in the stochastic beam angle sampling process made it possible to avoid spending valuable computing time unnecessarily at "bad" beam angles. An iterative inverse treatment planning algorithm was used for beam intensity profile optimization during the optimization process. The BEVD-guided beam orientation optimization was applied to an IMRT treatment of paraspinal tumor. The advantage of the new optimization algorithm was demonstrated by comparing the calculation with the conventional scheme without the BEVD weighting in the beam sampling. RESULTS: The BEVD tool provided useful guidance for the selection of the potentially good directions for the beams to incident and was used to guide the search for the optimal beam configuration. The BEVD-guided sampling improved both optimization speed and convergence of the calculation. A comparison of several five-field IMRT treatment plans obtained with and without BEVD guidance indicated that the computational efficiency was increased by a factor of approximately 10. CONCLUSION: Incorporation of BEVD information allows for development of a more robust tool for beam orientation optimization in IMRT planning. It enables us to more effectively use the angular degree of freedom in IMRT without paying the excessive computing overhead and brings us one step closer to the goal of automated selection of beam orientations in a clinical environment.

Algorithms↗
PubMed1991

Supine and prone head orientation preference in term infants.

Head orientation preference in the supine and prone positions was studied in 62 healthy term born infants at three different times within 24 hours after delivery. Head orientation preference was related to: the foetal position, the initial head position when the newborn was lying prone on the abdomen of the mother, the handedness of the parents and the state of the infant (according to Prechtl). Although for the whole group a head orientation preference for the right side was observed, an individual significant head orientation preference was observed in less than 50% of the infants studied. Neither the occurrence nor the direction of head orientation per individual was constant during the observation period. No relationship was found between an infant's head orientation and foetal position, initial head position, handedness of the parents, or the state of the infant. Our data suggest that persistent head orientation preference to one side in a healthy term born infant within 24 hours after delivery is a sign of abnormality. Head orientation to the right should not be considered as a sign of normality.

Choice Behavior↗
PubMed2002

Synaptic integration by V1 neurons depends on location within the orientation map.

Neurons in the primary visual cortex (V1) are organized into an orientation map consisting of orientation domains arranged radially around "pinwheel centers" at which the representations of all orientations converge. We have combined optical imaging of intrinsic signals with intracellular recordings to estimate the subthreshold inputs and spike outputs of neurons located near pinwheel centers or in orientation domains. We find that neurons near pinwheel centers have subthreshold responses to all stimulus orientations but spike responses to only a narrow range of orientations. Across the map, the selectivity of inputs covaries with the selectivity of orientations in the local cortical network, while the selectivity of spike outputs does not. Thus, the input-output transformation performed by V1 neurons is powerfully influenced by the local structure of the orientation map.

Action Potentials↗
PubMed1995

Only one of the two DNA-bound orientations of AP-1 found in solution cooperates with NFATp.

BACKGROUND: The transcription factor AP-1 activates the expression of numerous genes in response to mitogenic stimuli. AP-1 regulates gene expression both through solitary binding to independent recognition sites and, in cooperation with various heterologous transcription factors, through targeting to composite response elements. The two subunits that make up the AP-1 heterodimer, Fos and Jun, possess identical residues at positions that make sequence-specific contacts to DNA. This degeneracy leaves the protein with no apparent way of orienting itself uniquely on DNA by differentially recognizing its two non-identical half-sites. Here, we have analyzed the orientation of the AP-1 basic-leucine-zipper (bZip) domain on a cognate site, both alone and in the cooperative complex formed together with the 'nuclear factor of activated T cells' (NFATp). RESULTS: The results of affinity cleaving experiments demonstrate that, in solution, the AP-1 bZip binds DNA as a mixture of two orientational isomers. However, in the cooperative complex formed with NFATp on a composite response element, the AP-1 bZip adopts a single orientation, with Jun and Fos bound to the NFATp-proximal and NFATp-distal half-sites, respectively. Protein cross-linking experiments demonstrate that protein-protein contacts are responsible for this 'orientational locking'. CONCLUSIONS: Our results demonstrate that, through protein-protein interactions, one protein can force another to adopt a single DNA-bound orientation. Thus, cooperative interactions between adjacent regulatory proteins can influence not only the energetics of their interactions with DNA, but also their precise geometric and stereochemical arrangement. Because orientational isomers present markedly different structures to the transcriptional apparatus, it seems likely that orientation will exert an effect on the ability to activate transcription.

Amino Acid Sequence↗
PubMed1998

Sexual orientation, sexual behaviors, and pregnancy among American Indian adolescents.

PURPOSE: A recent study found a disproportionate number of pregnancies among Euro-American lesbian and bisexual adolescents compared to heterosexual peers. American Indian adolescents have reported higher prevalence of gay/lesbian/bisexual orientations than Euro-Americans; do they also report higher prevalence of pregnancy? METHODS: The study assessed prevalence of teen pregnancy and related factors by sexual orientation among sexually experienced, reservation-based American Indian adolescent males (n = 2056) and females (n = 1693) who participated in a national school-based survey in 1991. Self-reported orientation was classified as heterosexual, gay/lesbian/bisexual, and "unsure" of orientation. RESULTS: Gay/bisexual males were more likely than other males to report early heterosexual intercourse (<14 years), more consistent contraception, and a higher prevalence of abuse and running away (p < 0.05 to p < 0.0001). Likewise, lesbian/bisexual females were more likely to report early onset of heterosexual intercourse, more frequent intercourse, and running away. Sexual or physical abuse did not vary by orientation for females. Prevalence of pregnancy also did not vary by orientation (males, 18.6% gay/bisexual vs. 10.4% "unsure" vs. 11.8% heterosexual; females, 25.0% lesbian/bisexual vs. 22.1% "unsure" vs. 21.9% heterosexual). For lesbian/bisexual females, no variables were significantly associated with pregnancy history; for "unsure" females, pregnancy was associated with contraceptive frequency and early onset of heterosexual activity. For heterosexual females, age, intercourse frequency, and physical abuse were associated. For gay/bisexual males, intercourse frequency, ineffective contraception, and physical abuse were associated with involvement in a pregnancy; for "unsure" and heterosexual males, most items except ineffective contraception were related to pregnancy involvement history. CONCLUSIONS: Although prevalence of pregnancy is similar, findings show group differences in associated risk factors by sexual orientation. Interventions to reduce pregnancy among American Indian adolescents should include assessment of sexual orientation and behavioral risk factors.

Adolescent↗
PubMedDate not supplied

Distinguishing direction selectivity from orientation selectivity in the rabbit retina.

Direction selectivity and orientation selectivity were examined in the direction-selective (DS) and orientation-selective (OS) ganglion cells in the rabbit retina. Spike activities were recorded in vivo using tungsten-in-glass electrodes. Three types of visual stimuli (flashing slit, moving edges behind a slit, and whole-field drifting gratings) were used to distinguish these attributes. Fourier analysis was performed on data obtained using drifting gratings as proposed by Worgotter and Eysel (1987). Results from both angular and Fourier (polar angle frequency) domains were consistent. DS cells had strong directional components and varying strength of orientational components; they also had intact inhibitory surrounds. The phase of the biased orientation did not have a consistent relationship with the preferred direction. OS cells had predominant orientational components and very weak directional components. We conclude that the orientation bias does not contribute to the generation of direction selectivity, and that the mechanism of this bias of DS cells is rather different from the mechanism that generates orientation selectivity in rabbit OS cells. There are indications that it is similar to the mechanism shown to cause orientation bias in cat concentric cells.

Action Potentials↗