Functional and Structural Segregation of Overlapping Helices in HIV-1

Overlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1.

Angle Effect on Typical Optical Remote Sensing Indices in Vegetation Monitoring

Optical remote sensing indices play an important role in vegetation information extraction and have been widely serving ecology, agriculture and forestry, urban monitoring, and other communities. Remote sensing indices are constructed from individual bands depending on special characteristics to enhance the typical spectral features for the identification or distinction of surface land covers. With the development of quantitative remote sensing, there is a rapidly increasing requirement for accurate data processing and modeling. It is well known that the geometry-induced variation observed on surface reflectance is not ignorable, but the situation of uncertainty thereby introduced into these indices still needs further detailed understanding. We adopted the ground multi-angle hyperspectrum, spectral response function (SRF) of Thematic Mapper (TM), Enhanced Thematic Mapper (ETM+), Operational Land Imager (OLI), Moderate-Resolution Imaging Spectroradiometer (MODIS), and Multi-Spectral Instrument (MSI) optical sensors and simulated their sensor-like spectral reflectance; then, we investigated the potential angle effect uncertainty on optical indices that have been frequently involved in vegetation monitoring and examined the forward/backward effect over both the ground-based level and the actual Landsat TM/ETM+ overlapped region. Our results on the discussed indices and sensors show the following: (1) Identifiable angle effects exist with a more elevated influence than that introduced by band difference among sensors; (2) The absolute difference of forward and backward direction can reach up to −0.03 to 0.1 within bands of the TM/ETM+ overlapped region; (3) The investigation at ground level indicates that there are different variations of angle effect transmitted to each remote sensing index. Regarding cases of crop canopy at various growth phases, most of the discussed indices have more than a 20% relative difference in nadir value except Normalized Difference Vegetation Index (NDVI) and Normalized Difference Water Index (NDWI), at less than 10%, and Normalized Burn Ratio (NBR) at less than 16%. For the case of wax maturity stage, the relative difference in nadir value of Enhanced Vegetation Index (EVI), Soil-Adjusted Vegetation Index (SAVI), Ratio Vegetation Index (RVI), Char Soil Index (CSI), NBR, Normalized Difference Moisture Index (NDMI), and SWIR2/NIR exceeded 50%, among which the values for NBR and NDMI reached up to 115.8% and 206.7%, respectively; (4) Various schemes of index construction imply different developments of angle effect uncertainty. The “difference” indices can partially suppress the directional influence, while the “ratio” indices show high potential to amplify the angle effect. This study reveals that the angle-induced uncertainty of these indices is greater than that induced by the spectrum mismatch among sensors, especially under the senescence period. In addition, based on this work, indices with a suppressed potential of angle effect are recommended for vegetation monitoring or information retrieval to avoid unexpected effects.

Image Stitching Based on Nonrigid Warping for Urban Scene

Image stitching based on a global alignment model is widely used in computer vision. However, the resulting stitched image may look blurry or ghosted due to parallax. To solve this problem, we propose a parallax-tolerant image stitching method based on nonrigid warping in this paper. Given a group of putative feature correspondences between overlapping images, we first use a semiparametric function fitting, which introduces a motion coherence constraint to remove outliers. Then, the input images are warped according to a nonrigid warp model based on Gaussian radial basis functions. The nonrigid warping is a kind of elastic deformation that is flexible and smooth enough to eliminate moderate parallax errors. This leads to high-precision alignment in the overlapped region. For the nonoverlapping region, we use a rigid similarity model to reduce distortion. Through effective transition, the nonrigid warping of the overlapped region and the rigid warping of the nonoverlapping region can be used jointly. Our method can obtain more accurate local alignment while maintaining the overall shape of the image. Experimental results on several challenging data sets for urban scene show that the proposed approach is better than state-of-the-art approaches in both qualitative and quantitative indicators.

Effects of nozzle hole configuration of a multi-hole type gasoline direct injector on spray development under flash boiling conditions

The flash boiling phenomenon is critically affected by not only injection conditions such as fuel temperature, ambient pressure and physical properties of fuel but also the nozzle hole configurations of the injector. In this research, two kinds of injectors, having different nozzle hole configurations (a closed type and a opened type) were used to analyze the influence of flash boiling. Near-field and far-field spray visualization was performed using a high-speed camera based on the Mie-scattering imaging technique. Test parameters were injection pressure, ambient pressure, and fuel temperature. The spray length, spray width, length-to-width ratio, and axial velocity of spray development depending on time were measured using the MATLAB program for quantitative and objective analysis. Finally, the prediction equation for the spray length was derived using the least-squares method based on the experimental results. In the case of the closed type injector, the spray center contained a wide overlapped region because of the strong links between plumes. On the other hand, with the opened type injector, there was a relatively narrow overlapped region between plumes due to weak interaction between plumes. As a result, the closed type injector had a narrow and long spray structure and the opened type injector had a partially long and wide spray structure. According to the prediction equation, the spray develops depending on time more linearly under flash boiling conditions than under non-flash boiling conditions. The influence of flash boiling was smaller in the closed type injector because the closed type injector has less variation of the spray structure with varying injection conditions, ranging from non-flash boiling conditions to non-flash boiling conditions.

Optimising Prediction in Overlapping and Non-Overlapping Regions

Researchers working on real world classification data have identified that a combination of class overlap with class imbalance and high dimensional data is a crucial problem and are important factors for degrading performance of the classifier. Hence, it has received significant attention in recent years. Misclassification often occurs in the overlapped region as there is no clear distinction between the class boundaries and the presence of high dimensional data with an imbalanced proportion poses an additional challenge. Only a few studies have ever been attempted to address all these issues simultaneously; therefore; a model is proposed which initially divides the data space into overlapped and non-overlapped regions using a K-means algorithm, then the classifier is allowed to learn from two data space regions separately and finally, the results are combined. The experiment is conducted using the Heart dataset selected from the Keel repository and results prove that the proposed model improves the efficiency of the classifier based on accuracy, kappa, precision, recall, f-measure, FNR, FPR, and time.

Transfer Tiling of Nanostructures for Large-Area Fabrication

The fabrication of nanoscale patterns over a large area has been considered important but difficult, because there are few ways to satisfy both conditions. Previously, visually tolerable tiling (VTT) for fabricating nanopatterns for optical applications has been reported as a candidate for large area fabrication. The essence of VTT is the inevitable stitching of the nanoscale optical component, which is not seen by the naked eye if the boundary is very narrow while the tiles are overlapped. However, it had been difficult to control the shape of the spread of liquid prepolymers in the previous work, and there was room for the development of tiling. Here, we propose a method for transferring various shapes of tiles, which can be defined with a shadow mask. The method of using a transparent shadow mask can provide a wide process window, because it allows the spreading of a liquid prepolymer to be more easily controlled. We optimize the coating condition of a liquid prepolymer and the ultraviolet (UV) exposure time. Using this method, we can attach tiles of various shapes without a significant visible trace in the overlapped region.

Measurement of High Numerical Aperture Cylindrical Surface with Iterative Stitching Algorithm

There are some limitations in null test measurements in stitching interferometry. In order to meet the null test conditions, the moving distance between the sub-apertures often deviates from the theoretical preset distance, which leads to a position deviation of sub-apertures when measured. To overcome this problem, an algorithm for data processing is proposed in this paper. An optimal estimation of the deviation between sub-apertures is used to update their positions, and then a new overlapped region is obtained and again optimized. This process is repeated until the algorithm converges to an acceptable tolerance, and finally exact stitching is realized. A cylindrical lens was taken as an object for experimental examination of the proposed method. The obtained results demonstrate the validity, reliability, and feasibility of our iterative stitching algorithm.

A Novel Seam Finding Method Using Downscaling and Cost for Image Stitching

Seaming finding is an important step for creating panorama images because it smoothes away differences observed at boundaries between stitched images. We propose an improved seam finding method in which we define a cost function to measure the discrepancies that boundary pixels cause. We are also able to improve computing complexity by avoiding finding a seam over the whole area of overlapped region. Instead, we use a downscaled version of overlapped area to approximate a seam and then interpolate the seam to the original region. From experiments to generate panorama images, we compare our method with three other existing seam finding algorithms and observe that our method is able to produce better quality panorama image than the existing methods, while the processing time is comparable to those of the others.

Total Body Irradiation with Step Translation and Dynamic Field Matching

The purpose of this study is to develop a total body irradiation technique that does not require additional devices or sophisticated processes to overcome the space limitation of a small treatment room. The technique aims to deliver a uniform dose to the entire body while keeping the lung dose within the tolerance level. The technique treats the patient lying on the floor anteriorly and posteriorly. For each AP/PA treatment, two complementary fields with dynamic field edges are matched over an overlapped region defined by the marks on the body surface. A compensator, a spoiler, and lung shielding blocks were used during the treatment. Moreover, electron beams were used to further boost the chest wall around the lungs. The technique was validated in a RANDO phantom using GAFCHROMIC films. Dose ratios at different body sites along the midline ranged from 0.945 to 1.076. The dose variation in the AP direction ranged from 96.0% to 104.6%. The dose distribution in the overlapped region ranged from 98.5% to 102.8%. Lateral dose profiles at abdomen and head revealed 109.8% and 111.7% high doses, respectively, at the body edges. The results confirmed that the technique is capable of delivering a uniform dose distribution to the midline of the body in a small treatment room while keeping the lung dose within the tolerance level.