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Background Xinjiang is one of the regions with a high incidence of cervical cancer, and the genetic variation of human papillomavirus may increase its ability to infect the human body and enhance virus-mediated immune escape ability. Methods Sanger sequencing of the HPV16 genome from 165 samples positive for HPV16 infection and phylogenetic analysis of the E1 and E2 genes revealed the gene polymorphism of HPV16 in Xinjiang. Results The results showed that there were 109 samples with variations in HPV16 E1, 48 sites with nucleotide variations (19 missense variations and 29 synonymous variations), and 91 samples with variations in HPV16 E2, 25 sites with nucleotide variations (20 missense variations and five synonymous variations). Conclusions From the phylogenetic tree results, 149 samples were of the European variant and 16 samples were of the Asian variant. No African or North American/Asian variant types were found.

Molecular dynamics (MD) simulations that rely on force field methods has been widely used to explore the structure and function of RNAs. However, the current commonly used force fields are limited by the electrostatic description offered by atomic charge, dipole and at most quadrupole moments, failing to capture the anisotropic picture of electronic features. Actually, the distribution of electrons around atomic nuclei is not spherically symmetric but is geometry dependent. A multipolar electrostatic model based on high rank multipole moments is described in this work, which allows us to combine polarizability and anisotropy of electron density. RNA secondary structure was taken as a research system, and its substructures including stem, loops (hairpin loop, bulge loop, internal loop, and multi-branch loop), and pseudoknots (H-type and K-type) were investigated, respectively, as well as the hairpin. First, the atom-atom electrostatic properties derived from one chain of a duplex RNA 2MVY in our previous work (Ref. 58) were measured by the pilot RNA systems of hairpin, hairpin loop, stem, and H-type pseudoknot, respectively. The prediction results were not satisfactory. Consequently, to obtain a general set of electrostatic parameters for RNA force fields, the convergence behavior of the atom-atom electrostatic interactions in the pilot RNA systems was explored using high rank atomic multipole moments. The pilot RNA systems were cut into four types of different-sized molecular fragments, and the single nucleotide fragment and nucleotide-paired fragment proved to be the most reasonable systems for base-unpairing regions and base-pairing regions to investigate the convergence behavior of all types of atom-atom electrostatic interactions, respectively. Transferability of the electrostatic properties drawn from the pilot RNA systems to the corresponding test systems was also investigated. Furthermore, the convergence behavior of atomic electrostatic interactions in other substructures including bulge loop, internal loop, multi-branch loop, and K-type pseudoknot was expected to be modeled via the hairpin.

In this paper, a surface measurement method based on dual-scan positioning strategy is presented to address the challenges of irregular surface patterns and complex geometries. A confocal sensor with an internal scanning mechanism was used in this study. By synchronizing the local scan, enabled by the internal actuator in the confocal sensor, and the global scans, enabled by external positioners, the developed system was able to perform noncontact line scan and area scan. Thus, this system was able to measure both surface roughness and surface uniformity. Unlike laboratory surface measurement equipment, the proposed system is reconfigurable for in situ measurement and able to scan free-form surfaces with a proper stand-off distance and approaching angle. For long-travel line scan, which is needed for rough surfaces, a surface form tracing algorithm was developed to ensure that the data were always captured within the sensing range of the confocal sensor. It was experimentally verified that in a scanning length of 100 mm, where the surface fluctuation in vertical direction is around 10 mm, the system was able to perform accurate surface measurement. For area scan, XY coordinates provided by the lateral positioning system and the Z coordinate captured by the confocal sensor were plotted into one coordinate system for 3D reconstruction. A coherence scanning interferometer and a confocal microscope were employed as the reference measurement systems to verify the performance of the proposed system in a scanning area of 1 mm by 1 mm. Experimental data showed that the proposed system was able to achieve comparable accuracy with laboratory systems. The measurement deviation was within 0.1 &micro, m. Because line scan mechanisms are widely used in sensor design, the presented work can be generalized to expand the applications of line scan sensors.

Chunhe Zhang,1,* Shaowei Fu,1,* Luyue Wang,1,* Fang Wang,1 Dan Wu,1 Xiangyi Zhe,1 Huizhen Xin,1 Hongtao Li,1 Dongmei Li,1 Fuyuan Jin,1 Renfu Shao,2 Zemin Pan1 1Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang 832002, People’s Republic of China; 2School of Science, Technology and Engineering, Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia*These authors contributed equally to this workCorrespondence: Zemin Pan; Xiangyi ZheDepartment of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, People’s Republic of ChinaEmail panteacher89@sina.com; 342480821@qq.comIntroduction: The aim of this study was to determine whether ZNF582 gene methylation and tissue protein expression can be used as a tool with high sensitivity and specificity for cervical cancer screening. We analyzed the correlation between promoter methylation of ZNF582 gene and cervical cancer and high risk HPV16/18 infection.Methods: Tissue samples of normal cervical or chronic cervicitis (n=51), CIN (cervical intraepithelial neoplasia) (n=35), and cervical carcinoma (n=68) were tested for HPV16/18 infection by polymerase chain reaction (PCR). We also detected the methylation status of the ZNF582 gene promoter in the same tissues by methylation-specific PCR (MSP), then analyzed the correlation between ZNF582 promoter methylation and HPV16/18 infection. Immunohistochemistry was used to analyze ZNF582 gene expression in 152 cervical tissues. We detected ZNF582 mRNA expression in cervical tissues (including cancer and non-cancer) by real-time fluorescence quantitative PCR (qPCR).Results: Among 93 high-grade cervical lesions (CINII and above) and cervical cancer samples, 57 cases were positive for HPV16/18 infection and 36 cases were negative. ZNF582 gene methylation occurred in 9 out of 51 cases in normal cervical tissues (17.6%), 16 of 35 cases in CIN tissues (45.7%), and 50 of 68 cases in cervical cancer (73.5%). The differences in methylation rate of the three groups were statistically significant (P< 0.05). The ZNF582 methylation rate in the positive HPV16/18 infection group was 73.7%, while the negative group was 63.9%. Compared with normal tissues, ZNF582 protein was highly expressed in cervical cancer tissues, but mRNA expression was low.Conclusion: While ZNF582 protein is highly expressed in cervical cancer tissues, it was not sufficient for use as a standard for cervical cancer staging. On the other hand, ZNF582 promoter methylation had high specificity and sensitivity in detecting CINII and highly diseased cervical lesions and could be used as a diagnostic marker for cervical cancer of women.Keywords: cervical cancer, ZNF582 gene, promoter methylation, HPV16/18, gene expression

A novel position measurement system, the so-called image grating system, is presented in this research paper. It features an adjustable measurement range, flexible standoff distance and in-line measurement capabilities. The developed position measurement system includes an image grating attached to the moving stage as the target feature and a line scan camera as the stationary displacement reader. By observing the position of the target feature in the image and applying subpixel image registration, the position of the moving stage can be determined. In order to improve the measurement efficiency, the computations for pattern correlation and subpixel registration are performed in the frequency domain. Calibration and error correction methods are also developed to compensate for the measurement error caused by optical distortion. Experimental data confirms the capability of the image grating technology of ±0.2 μm measurement accuracy within 25 mm measurement range. By applying different optics, the standoff distance and the measurement range can be customized for different precision measurement applications.

Mirror finish surface products are widely used in many industries such as aerospace, optics, semiconductor and biomedical device manufacturing. The surface texture of mirror finish products is usually measured by off-line instruments such as coherence scanning or phase shifting interferometers. However, most commercial interferometers are expensive and must be operated in a clean and vibration-free laboratory environment. In order to achieve both in-situ surface quality control and automated tool changing for the polishing process, fast and non-contact surface texture measurement are required. To address these in-situ measurement challenges, a surface texture measuring system based on fringe pattern illumination method is proposed in this paper. By analyzing the luminance contrast ratio of the fringe pattern reflection image and comparing to the measurement results from the referenced coherence scanning interferometer, the experimental results showed that the proposed system was able to measure different mirror finish surfaces with Sa and Sq values in the range of 15 nm to 120 nm and 30 nm to 160 nm respectively. In addition, the luminance contrast ratio was also correlated with directions of the machining marks and the projected fringes at different measurement angles. The surface texture aspect ratio parameter Str which provides information about the strength of the machining marks was experimentally evaluated and compared with luminance contrast change. In conclusion, the proposed measuring system was able to measure surface texture with a relative error less than 10% at measurement angle between 20° to 160°, and indicate machining pattern effects on the mirror finish surface.

Background Primary familial brain calcification (PFBC) is a rare calcifying disorder of the brain with extensive clinical and genetic heterogeneity. Its prevalence is underestimated due to clinical selection bias (compared with symptomatic PFBC patients, asymptomatic ones are less likely to undergo genetic testing). Methods A total of 273 PFBC probands were enrolled in a multicenter retrospective cohort study by two different approaches. In Group I (nonsystematic approach), 37 probands diagnosed at our clinic were enrolled. In Group II (systematic approach), 236 probands were enrolled by searching the medical imaging databases of 50 other hospitals using specific keywords. Genetic testing of four genes known to be causative of autosomal dominant PFBC was performed in all probands using cDNA. All identified variants were further confirmed using genomic DNA and classified according to ACMG-AMP recommendations. Results Thirty-two variants including 22 novel variants were detected in 37 probands. Among these probands, 83.8% (31/37) were asymptomatic. Two probands with homozygous pathogenic SLC20A2 variants presented more severe brain calcification and symptoms. Based on the variant detection rate of probands in Group II, we extrapolated an overall minimal prevalence of PFBC of 6.6 per 1,000, much higher than previously reported (2.1 per 1000). Conclusions We identified a higher proportion of genetically confirmed PFBC probands who were asymptomatic. These patients would be overlooked due to clinical selection bias, leading to underestimation of the disease prevalence. Considering that PFBC patients with biallelic variants had more severe phenotypes, this specific condition should be focused on in genetic counseling.

Mirror-finished surface products have a wide range of applications in different engineering industries, such as power generation, aerospace, semiconductors and optics. The surface topography of mirror-finished products is typically measured in a metrology laboratory, which is typically time consuming and cannot be integrated into the manufacturing process. To allow for in-situ product quality assurance and automatic tool change for manufacturing processes, a more accurate and responsive surface-measurement method is needed. For highly polished surfaces, a sub-micron surface fluctuation makes it possible to use light-scattering effects and image processing for surface texture analysis. A non-contact surface inspection system using a fringe-patterned illumination method is proposed in this paper. A predesigned pattern was projected onto the target surface, and its reflected image was captured by a camera. It was found that the surface parameters Sa and Sq, which are widely used to evaluate surface quality, are significantly correlated with luminous-intensity distribution. Another parameter, Str, which quantifies the uniformity of surface-texture directions due to polishing or grinding marks, was traditionally quantified after a complete-surface topographic measurement. In this research, a new approach is proposed to determine surface isotropy through a luminance-intensity distribution analysis. By rotating the test coupon, the variation of specular reflection showed correlation with the significance of surface-texture direction. The experimental results demonstrate that mirror-finished surfaces with a large deviation in luminance intensity across the pattern possess low Str values, which indicates low uniformity in surface texture.

Background Xinjiang is one of the areas with the highest incidence of cervical cancer in China. Genetic variation in Human papillomavirus type 16 (HPV16) may increase the ability of the virus to mediate carcinogenesis and immune escape, which are risk factors for the progression of cervical cancer. We investigated polymorphism in HPV16 and the distribution of its sub-lineages in the region by analyzing the E6, E7 and long control region (LCR) gene sequences from women with HPV16-positive cervical samples in Xinjiang. Methods A total of 138 cases of cervical lesions and squamous cell carcinoma with infection of HPV16 virus were collected. The E6 and E7 genes and LCR of HPV16 virus were sequenced and compared with the HPV16 European prototype reference and other HPV16 mutants for single nucleotide polymorphisms. Neighbor-joining phylogenetic trees were constructed using E6, E7 and LCR sequences. Results Fourteen missense mutations were found in the E6 gene; the loci with the highest mutation frequency were T350G (36/75, 48%) and T178G (19/75, 25.3%). In the E7 gene, the locus with the highest mutation frequency was A647G (18/75, 24%). A total of 33 polymorphic sites were found in the LCR, of which T7447C (39/95, 40.1%) was the most frequent. Conclusion HPV16 in Xinjiang is mainly of the European variant, followed by the Asian variant type; no Africa 1, 2 or Asia–America variant types were found.

The characterization of surface topographic features on a component is typically quantified using two-dimensional roughness descriptors which are captured by off-line desktop instruments. Ideally any measurement system should be integrated into the manufacturing process to provide in-situ measurement and real-time feedback. A non-contact in-situ surface topography measuring system is proposed in this paper. The proposed system utilizes a laser confocal sensor in both lateral and vertical scanning modes to measure the height of the target features. The roughness parameters are calculated in the developed data processing software according to ISO 4287. To reduce the inherent disadvantage of confocal microscopy, e.g., scattering noise at steep angles and background noise from specular reflection from the optical elements, the developed system has been calibrated and a linear correction factor has been applied in this study. A particular challenge identified for this work is the in-situ measurement of features generated by a robotized surface finishing system. The proposed system was integrated onto a robotic arm with the measuring distance and angle adjusted during measurement based on a CAD model of the component in question. Experimental data confirms the capability of this system to measure the surface roughness within the Ra range of 0.2&ndash, 7 &mu, m (bandwidth &lambda, c/&lambda, s of 300), with a relative accuracy of 5%.

Surfaces made by Additive Manufacturing (AM) processes normally show higher roughness and more complicated microstructures than conventional machined surfaces. In this study, AM surface roughness measurements using both tactile and optical techniques are analyzed, theoretically and experimentally. Analytical results showed both techniques have comparable performance when measuring AM samples with good surface integrity. For surfaces with steep features, coherence scanning interferometry showed more reliable performance especially when peak-to-valley value was required. In addition of the benchmarking study, development of a low-cost measurement system, using laser confocal technology, is also presented in this paper. By comparing the measurement results with those from a coherent scanning interferometer, accuracy levels of the proposed system can be evaluated. It was concluded that with comparable accuracy, the proposed low-cost optical system was able to achieve much faster measurements, which would make it possible for in-situ surface quality checking. Published version

In this research paper, a precision position-measurement system based on the image grating technique is presented. The system offers a better robustness and flexibility for 1D position measurement compared to a conventional optical encoder. It is equipped with an image grating attached to a linear stage as the target feature and a line scan camera as the stationary displacement reader. By measuring the position of the specific feature in the image and applying a subpixel image registration method, the position of the linear stage can be obtained. In order to improve the computational efficiency, the calculations for pattern correlation and subpixel registration are performed in the frequency domain. An error compensation method based on a lens distortion model is investigated and implemented to improve the measurement accuracy of the proposed system. Experimental data confirms the capability of the developed image grating system as &plusmn, 0.3&nbsp, &micro, m measurement accuracy within a 50 mm range and &plusmn, 0.2 &micro, m measurement accuracy within a 25 mm range. By applying different optics, the standoff distance, measurement range, and resolution can be customized to conform to different precision measurement applications.

Adjusting components of the display system to reproduce colors observed in the original scene is difficult and expensive. We know that a color can be matched in hue (H), luminance (L), and saturation (S) by a mixture of three primary colors, red (R), green (G), and blue (B). The color senses to the mixture are various for different observations as the senses are psychophysical characters. In this paper we describe a psychophysical method of transforming the ideal primary colors X, Y, and Z making up the colors in the original scene into the colors R, G and B of the display system. The R, G, and B value corresponding to the X, Y, and Z values come from statistical data of standard observations. By means of a polynomial regression analysis, the transform relating the X, Y, and Z to the R, G, and B can be reached on those standard observations. Sufficient observation data and effective color samples are essential to find the psychophysical relation between the two sets of colors. Adaptation of a color lookup table to enhance the fidelity of color reproduction with the method is easier and more straightforward. This method can avoid the obstacles which occur in hardware methods of color reproduction.© (1992) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.