Symmetric Regions Research Articles

A Symmetric Region of the HIV-1 Integrase Dimerization Interface Is Essential for Viral Replication

HIV-1 integrase (IN) is an important target for contemporary antiretroviral drug design research. Historically, efforts at inactivating the enzyme have focused upon blocking its active site. However, it has become apparent that new classes of allosteric inhibitors will be necessary to advance the antiretroviral field in light of the emergence of viral strains resistant to contemporary clinically used IN drugs. In this study we have characterized the importance of a close network of IN residues, distant from the active site, as important for the obligatory multimerization of the enzyme and viral replication as a whole. Specifically, we have determined that the configuration of six residues within a highly symmetrical region at the IN dimerization interface, composed of a four-tiered aromatic interaction flanked by two salt bridges, significantly contributes to proper HIV-1 replication. Additionally, we have utilized a quantitative luminescence assay to examine IN oligomerization and have determined that there is a very low tolerance for amino acid substitutions along this region. Even conservative residue substitutions negatively impacted IN multimerization, resulting in an inactive viral enzyme and a non-replicative virus. We have shown that there is a very low tolerance for amino acid variation at the symmetrical dimeric interface region characterized in this study, and therefore drugs designed to target the amino acid network detailed here could be expected to yield a significantly reduced number of drug-resistant escape mutations compared to contemporary clinically-evaluated antiretrovirals.

Diagnostic Ability of Retinal Nerve Fiber Layer Thickness Measurements and Neurologic Hemifield Test to Detect Chiasmal Compression

The purpose of the study was to investigate the diagnostic ability of the neurologic hemifield test (NHT) and retinal nerve fiber layer (RNFL) thickness measurements to detect chiasmal compression. Thirty-seven patients with chiasmal compression, 35 patients with glaucoma, and 30 patients with glaucoma suspect were enrolled. The NHT score was established from a 30-2 visual field pattern deviation probability plot. Each test point value was calculated for a number that was inversely proportional to its pattern deviation probability. The NHT score was the absolute value of the difference in the sum of the point scores for two symmetrical regions of 16 points on either side of the vertical meridian. RNFL thickness was scored from 0 to 10 according to the pattern of RNFL loss and probability of abnormality. Solely present nasal or temporal RNFL defects were scored high, and exclusively appearing superior or nasal RNFL defects were scored low. The differences in the NHT and RNFL scores among the three groups were compared. Diagnostic ability was assessed by receiver operating characteristic (ROC) analysis. The NHT and RNFL scores were significantly higher in patients with chiasmal compression than in patients with glaucoma and glaucoma suspect. The area under the ROC curve (AROC) was 0.734 of the NHT score and 0.613 of the RNFL score. When AROC was calculated using the NHT and RNFL scores concurrently, AROC was increased to 0.807. The NHT score and RNFL score have diagnostic ability to detect chiasmal compression, and simultaneous assessment of NHT and RNFL scores improves the diagnostic power.

Confidence and Tolerance Regions for the Signal Process

Iterative schemes play a dominant role in evaluating parameters in statistics. Sequences and iterations are related to the signal process. The first order autoregressive model is discussed. The problem of evaluating confidence intervals for the involved parameter is discussed and a simulation approach is provided. Eventually, within the interval (-1,1) the estimated coverage is very close to the nominal level. Different small sample sizes provide evidence that the method performs well, minimizing uncertainty. The contribution of this paper concerns: (i) The confidence interval for the signal process even in the case of such a small sample that provides coverage (1-α)100% despite the theoretical problems, and (ii) The tolerance region introduced performs well with sample size n = 10 , while it is accepted for applications with sample size n = 5 . Patents related to topic have been discussed. Keywords: Sequential procedure, signal process, autoregressive model, confidence interval, tolerance region, autoregressive error, Hierarchical Networks, Model–Oriented Design and Analysis, symmetric tolerance regions, computation, Mean Square Error, D–optimal design, discrete time system, Fisher’s information matrix

Complementary cloak based on conventional cloak with axial symmetrical cloaked region

Based on the concept of complementary medium, a method which can make the conventional cylindrical cloak with axial symmetrical cloaked region to be not blind by filling the isotropic complementary in inner cloaked region is proposed. Firstly, the perfect electric conductor cylindrical shell was removed. Secondly, the symmetrical cloaked region was separated into two symmetrical regions along the symmetry axis and filled with isotropic complementary medium according to folding transformation. Full wave simulations are performed to confirm the effectiveness of the proposed method. The simulation results show that the converted cloak not only can exchange information with the outside, but also its presence cannot be detected.

Constructing cubature formulae of degree 5 with few points

This paper is devoted to construct a family of fifth degree cubature formulae for n-cube with symmetric measure and n-dimensional spherically symmetrical region. The formula forn-cube contains at most n2+5n+3 points and for n-dimensional spherically symmetrical region contains only n2+3n+3 points. Moreover, the numbers can be reduced to n2+3n+1 and n2+n+1 if n=7 respectively, the latter of which is minimal.

SU-E-T-478: Geometrical Splitting Technique to Improve the Computational Efficiency in Monte Carlo Calculations for Proton Therapy.

To implement a geometry based particle splitting technique in order to reduce the computation time when generating treatment head phase space files for proton therapy dose calculations using Monte Carlo (MC) calculations and to validate the doses generated from these phase spaces with respect to reference simulations. The treatment nozzles at the Francis H Burr Proton Therapy Center (FHBPTC) were modeled with a new MC tool ('TOPAS' based on Geant4). For variance reduction purposes, two particle-splitting planes were implemented, one downstream of the second ionization chamber the other upstream of the aperture of the nozzle and phase spaces in IAEA format were recovered. The symmetry of the proton beam was considered to split the particles by a factor of 4 per plane. Split particles were randomly positioned at different locations rotated around the beam axis. The computational efficiency was calculated and dose profiles compared for a voxelized water phantom for different treatment fields for both the reference and optimized simulations. Depth-dose curves and beam profiles were analyzed. Dose calculation in patients was simulated to compare the performance. Normalized computational efficiency between 10 and 14.5 were reached. Percentage difference between dose profiles in water for simulations done with and without particle splitting is within the statistical precision of 2%, 1 standard deviation. Dose distributions for the realistic patient treatment show differences up to 4% in the regions of interest, within 2 standard deviations. By considering the cylindrically symmetric region of the nozzle and the splitting planes separated at strategic distance, considerable time reduction can be achieved without compromising the precision. This approach will reduce the time for phase space simulations for clinical MC dose calculation at FHBPTC by more than a factor of 10.

Design of digital allpass-based two-channel quincunx QMF banks

This paper presents a novel structure for constructing two-channel quincunx quadrature mirror filter (QQMF) banks. The analysis and synthesis filters of the QQMF bank are composed of two-dimensional (2-D) recursive digital allpass filters with symmetric half-plane support regions. Using the 2-D doubly complementary half-band property possessed by the analysis and synthesis filters, we facilitate the design of the digital allpass-based two-channel QQMF banks. For finding the coefficients of the 2-D recursive symmetric half-plane digital allpass filters, the design problem is appropriately formulated to result in an optimization problem that can be solved by using a weighted least-squares algorithm in the minimax (L∞) optimal sense. The novelty of the proposed design method is that the designed 2-D QQMF bank achieves perfect magnitude response and possesses satisfactory phase response without requiring extra phase equalizer. Simulation results are also provided for illustration and comparison. Copyright © 2012 John Wiley & Sons, Ltd.

Frequency Tuning in Integrated InGaAsP/InP Ring Mode-Locked Lasers

We demonstrate for the first time, continuous frequency tuning >;40 MHz using symmetric phase tuning regions in an InGaAsP/InP 18 GHz passively mode-locked ring laser. Frequency tuning is achieved through current injection into passive waveguides, via the free-carrier plasma effect, which is enhanced by the concurrent increase in cavity losses from free-carrier absorption. Stable mode-locking with ~1 ps pulse-width is realized from -2.5 to -7.5 V bias on the saturable absorber and 170 to 290 mA drive current. The average RF power is 50 dB above the noise level over this regime.

COLLAGEN AS IN VIVO QUANTITATIVE FLUORESCENT BIOMARKERS OF ABNORMAL TISSUE CHANGES

Collagen is an endogenous fluorophore that accounts for about 70% of all proteins of human skin, so it can be an optical marker for structural abnormalities in tissues registered by laser fluorescent diagnostics in vivo. Using the examples of such abnormalities as scars, scleroderma and basal cell carcinoma, this study shows the differences between coefficients of fluorescent contrast kf(λ) of abnormalities from the ones for healthy tissues at fluorescent excitation wavelength 360–380 nm. It is shown that scars and dysplasia are characterized by reduced values of kf(λ) for collagen. Due to high turbidity and phase heterogeneousness as well as variation of parameters of blood microcirculation and concentrations of other related chromophores, there is no mathematical model that precisely calculates the concentration of collagen in tissues only with the use of the value of fluorescent signal intensity. So, probably, the best marker of the pathological process is a comprehensive representation of kf(λ) for all endogenous fluorophores, i.e., for all used visible wavelengths. In this case identification of abnormal tissues is quite possible by detecting some deviations of coefficients kf(λ) for the optically identical and symmetrical regions of the human body.

Finite Element Analysis of Stress for Nozzle Zone at Channel of Pressure Vessel

With the development of petrochemical industry, the status of pressure vessel has become increasingly important, and higher requirements are introduced for the security of nozzle zone at the pressure bearing region of pressure vessel. In order to study the stress status of nozzle zone at the channel of pressure vessel, solid modeling for channel and straight pipe was performed with ANSYS software. Through finite element analysis and calculation, the stress concentration region of channel was determined and the reason was analyzed. In addition, the nozzle zones of the model before and after loading were compared. The result reveals that symmetrical stress concentration region lies at the junction of channel and pipe. The maximum stress is located at the inside of nozzle zone of channel and less than the yield stress of material.

Response and sensitivity of lipid related molecular structure to wet and dry heating in Canola tissue

Heat treatments are used to manipulate nutrient utilization, availability and functional properties. The objective of this study was to characterize any molecular level changes of the functional groups associated with lipid structure in canola (Brassica) seed, as affected during the wet and dry heat treatment processes using molecular spectroscopy. The parameters included lipid CH3 asymmetric (ca. 2970–2946cm−1), CH2 asymmetric (ca. 2945–2880cm−1), CH3 symmetric (ca. 2881–2864cm−1) and CH2 symmetric (ca. 2864–2770cm−1) functional groups, lipid carbonyl CO ester group (ca. 1774–1711cm−1), lipid unsaturation group (CH attached to C–C) (ca. 3007cm−1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Raw canola seeds were used for the control or autoclaved at 120°C for 1h (HT-1: wet heating) or dry roasted at 120°C for 1h (HT-2: dry heating). Molecular spectral analysis of lipid functional group ratios were not significantly changed (P>0.05) in the CH2 asymmetric to CH3 asymmetric stretching band peak intensity ratios for canola seed. Both wet (HT-1) and dry heating method (HT-2) had no significant effect (P>0.05) on lipid carbonyl CO ester group and lipid unsaturation group (CH attached to CC). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH3 and CH2 asymmetric and symmetric region (ca. 2992–2770cm−1), unsaturated lipids band region (ca. 3025–2993cm−1) and lipid carbonyl CO ester band region (ca. 1774–1711cm−1). The results indicated that both dry and wet heating of given intense had no impact to the molecular spectrum in lipid related functional groups of canola seed, and was not strong enough to elicit heat-induced changes in lipid conformation.

Spontaneous symmetry breaking of a Bose—Fermi mixture in a two-dimensional double-well potential

We study the spontaneous symmetry breaking of a superfluid Bose—Fermi mixture in a two-dimensional double-well potential. The mixture is described by a set of coupled Gross—Pitaevskii equations. The symmetry breaking phenomenon is demonstrated in the two-dimensional double-well potential in the mixture. The results are summarized in the phase diagrams of the mixture particle numbers, which are divided into symmetric and asymmetric regions by the asymmetry ratios. The dynamical pictures of the spontaneous symmetry breaking induced by a gradual transformation of the single-well potential into a double-well one are also illustrated. The properties of the quantum degenerate mixture are explored using the realistic parameters for a 40K−87Rb system.

A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome

Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the ‘proto-ribosome’. This ‘proto-ribosome’ could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the ‘pre-proto-ribosome’, which was adapted for producing proteins.

Evaluation of an Algorithm for Detecting Visual Field Defects Due to Chiasmal and Postchiasmal Lesions: The Neurological Hemifield Test

To develop an automated neurologic hemifield test (NHT) to detect visual field loss caused by chiasmal or postchiasmal lesions. Visual field locations from 24-2 pattern automated visual fields were grouped into two symmetric regions with 16 points on either side of the vertical meridian. A scoring system similar to the Glaucoma Hemifield Test (GHT) was used to calculate point scores using the pattern deviation values from the right and left regions. The cross-vertical difference in the sum of these values was the NHT score. The NHT was evaluated using visual fields from subjects with known neurologic disease, subjects with glaucoma, and glaucoma suspects (92 pairs of eyes each). The NHT score was calculated for each eye. Four masked reviewers scored all pairs of visual fields with regard to the likelihood of neurologic and glaucomatous optic neuropathy. Both NHT score and expert field ratings were compared with clinical diagnosis by receiver operating characteristic (ROC) analysis. The NHT effectively discriminated neurologic fields from those of glaucoma patients and glaucoma suspects (area under the ROC curve [AUC] = 0.90; 95% confidence interval [CI], 0.86-0.94). The NHT score correlated well with clinician grading (Pearson correlation estimates, 0.74-0.78). Even when field defects were subtle, the NHT had some ability to discriminate neurologic from nonneurologic fields (AUC 0.68; 95% CI, 0.56-0.79). The NHT distinguished neurologic field defects from those of glaucoma and glaucoma suspects, rivaling the performance of subspecialist clinicians. Its implementation may help identify unsuspected neurologic disease.

On The Relative Effectiveness of Symmetry and Convexity as Figural Cues

The effectiveness of convexity as a figural cue varies with context: subjects are increasingly likely to perceive convex regions as figures as the number of alternating convex and concave regions increases from 2 to 8 (57%–89%). Peterson and Salvagio (2008) observed these context effects only when the concave regions were homogenously colored, regardless of the heterogeneity or homogeneity of convex regions. Goldreich and Peterson (2010) modeled convexity context effects with a Bayesian observer that decided whether the displays were 2-D or 3-D assuming that (1) single objects are likely to be homogeneously colored and unlikely to change color only when occluded; (2) multiple objects can be any color; and (3) in 3-D, objects are more likely to be convex than concave. On Assumption 1 homogeneity of color is a background cue. When convex regions were homogeneously colored, however, the prior for 3-D convex objects was stronger than the background cue. We tested whether similar context effects occur with symmetry. In Exp. 1, symmetry's effectiveness as a figural cue increased as the number of alternating black and white symmetric and asymmetric regions increased from 4 to 6 (56%–68%), p = .001, but didn't increase farther with 8 regions (68%). Thus, the bias toward symmetric 3-D objects overcame the background cue when both symmetric and asymmetric regions were homogeneously colored. In Experiment 2, using 8-region displays, we found that the prior for symmetric 3D objects wasn't large enough to overcome the background cue when symmetric regions were homogeneously colored and asymmetric regions were not: Here, subjects saw symmetric regions as figures on only 40% of trials versus 63% of trials when asymmetric regions were homogeneously colored and symmetric regions were not, p < .0001. Thus, the prior is smaller for 3D symmetric objects than for 3D convex objects.

Effect of Domain Perturbations on the Critical Condition for Steady-State Thermal Explosions

A region heated by a temperature-dependent source is said to be stable if the heat conducted to the surroundings can balance the heat generated in the region. The critical value of the Frank-Kamenetskii number gives the limit of stability, the point at which a steady temperature field is no longer possible. Assuming that the critical Frank-Kamenetskii number can be obtained for a symmetric region where the problem is one-dimensional, we present a method for determining how it changes as the region is displaced into a less-symmetric region. We find that the displacement can be either stabilizing or destabilizing. The case of exponential heat generation is fairly well-predicted by the case of linear heat generation.

Film Excerpts Shown to Specifically Elicit Various Affects Lead to Overlapping Activation Foci in a Large Set of Symmetrical Brain Regions in Males

While the limbic system theory continues to be part of common scientific parlance, its validity has been questioned on multiple grounds. Nonetheless, the issue of whether or not there exists a set of brain areas preferentially dedicated to emotional processing remains central within affective neuroscience. Recently, a widespread neural reference space for emotion which includes limbic as well as other regions was characterized in a large meta-analysis. As methodologically heterogeneous studies go into such meta-analyses, showing in an individual study in which all parameters are kept constant, the involvement of overlapping areas for various emotion conditions in keeping with the neural reference space for emotion, would serve as valuable confirmatory evidence. Here, using fMRI, 20 young adult men were scanned while viewing validated neutral and effective emotion-eliciting short film excerpts shown to quickly and specifically elicit disgust, amusement, or sexual arousal. Each emotion-specific run included, in random order, multiple neutral and emotion condition blocks. A stringent conjunction analysis revealed a large overlap across emotion conditions that fit remarkably well with the neural reference space for emotion. This overlap included symmetrical bilateral activation of the medial prefrontal cortex, the anterior cingulate, the temporo-occipital junction, the basal ganglia, the brainstem, the amygdala, the hippocampus, the thalamus, the subthalamic nucleus, the posterior hypothalamus, the cerebellum, as well as the frontal operculum extending towards the anterior insula. This study clearly confirms for the visual modality, that processing emotional stimuli leads to widespread increases in activation that cluster within relatively confined areas, regardless of valence.

Symmetry-based monocular vehicle detection system

In this paper, we describe the development of a symmetry-based vehicle detection system. The system uses a single forward looking camera to capture the road scene. Vehicles are detected based on their edges and symmetrical characteristics. A method to extract the symmetric regions in the image using a multi-sized window and clustering technique is introduced. We hypothesize the vehicle’s locations in the image from the detected symmetric regions and the regions are then further processed to enhance their symmetrical edges. A bounding box of a vehicle is detected from the projection maps of the enhanced vertical and horizontal edges. The hypothesized vehicles are then verified using a two-class classifier, which consists of an edge oriented histogram (EOH) feature extractor and a support vector machine (SVM). Once a vehicle is verified, a tracking process based on a Kalman filter and a reliability point system is used to track the movement of the vehicle in consecutive video frames. The system was successfully implemented and tested on a standard PC. Experimental results on live video feed and pre-recorded video sequences for various road scenes showed that the system is able to detect multiple vehicles in real time.

IR and FTMW-IR Spectroscopy and Vibrational Relaxation Pathways in the CH Stretch Region of CH3OH and CH3OD

Infrared spectra of jet-cooled CH(3)OD and CH(3)OH in the CH stretch region are observed by coherence-converted population transfer Fourier transform microwave-infrared (CCPT-FTMW-IR) spectroscopy (E torsional species only) and by slit-jet single resonance spectroscopy (both A and E torsional species, CH(3)OH only). Twagirayezu et al. reported the analysis of ν(3) symmetric CH stretch region (2750-2900 cm(-1); Twagirayezu et al. J. Phys. Chem. A 2010, 114, 6818), and the present work addresses the more complicated higher frequency region (2900-3020 cm(-1)) containing the two asymmetric CH stretches (ν(2) and ν(9)). The additional complications include a higher density of coupled states, more extensive mixing, and evidence for Coriolis as well as anharmonic coupling. The overall observed spectra contain 17 interacting vibrational bands for CH(3)OD and 28 for CH(3)OH. The sign and magnitude of the torsional tunneling splittings are deduced for three CH stretch fundamentals (ν(3), ν(2), ν(9)) of both molecules and are compared to a model calculation and to ab initio theory. The number and distribution of observed vibrational bands indicate that the CH stretch bright states couple first to doorway states that are binary combinations of bending modes. In the parts of the spectrum where doorway states are present, the observed density of coupled states is comparable to the total density of vibrational states in the molecule, but where there are no doorway states, only the CH stretch fundamentals are observed. Above 2900 cm(-1), the available doorway states are CH bending states, but below, the doorway states also involve OH bending. A time-dependent interpretation of the present FTMW-IR spectra indicates a fast (∼200 fs) initial decay of the bright state followed by a second, slower redistribution (about 1-3 ps). The qualitative agreement of the present data with the time-dependent experiments of Iwaki and Dlott provides further support for the similarity of the fastest vibrational relaxation processes in the liquid and gas phases.

The transmission of upstream waves to the magnetosphere: An analysis at widely separated ground stations

[1] On 18 February 2003 a long-duration, almost monochromatic, wave event was detected by Cluster at radial distances from the bow shock smaller than ≈10 Re. The interplanetary magnetic field orientation determined a wide and almost symmetric foreshock region around the bow shock nose, providing highly favorable conditions for a direct wave penetration into the magnetosphere. The general correspondence between the characteristics of the wave trains observed in the foreshock region and at two widely separated ground stations (namely, at low latitudes in the Northern Hemisphere and in Antarctica) confirms that the ground activity is ubiquitously determined and controlled by the upstream activity. At low latitudes, the direct propagation of the external waves through the subsolar point is sharply confined to the dayside hemisphere. In Antarctica, the wave activity is detected even on field lines stretched into the tail; here the polarization pattern suggests a significant contribution of sunward propagating waves in the postmidnight hours, consistent with a wave penetration through the magnetotail lobes. At both stations the wave energy is typically ≈5–10% of the external energy; in addition, in Antarctica the contribution of the cusp turbulence largely overcomes that one related to the penetration of the upstream waves.