Brain atlas fusion from high-thickness diagnostic magnetic resonance images by learning-based super-resolution

Zhang, Jinpeng,Zhang, Lichi,Xiang, Lei,Shao, Yeqin,Wu, Guorong,Zhou, Xiaodong,Shen, Dinggang,Wang, Qian Elsevier 2017 Pattern recognition Vol.63 No.-

<P><B>Abstract</B></P> <P>It is fundamentally important to fuse the brain atlas from magnetic resonance (MR) images for many imaging-based studies. Most existing works focus on fusing the atlases from high-quality MR images. However, for low-quality diagnostic images (i.e., with high inter-slice thickness), the problem of atlas fusion has not been addressed yet. In this paper, we intend to fuse the brain atlas from the high-thickness diagnostic MR images that are prevalent for clinical routines. The main idea of our works is to extend the conventional groupwise registration by incorporating a novel super-resolution strategy. The contribution of the proposed super-resolution framework is two-fold. First, each high-thickness subject image is reconstructed to be isotropic by the patch-based sparsity learning. Then, the reconstructed isotropic image is enhanced for better quality through the random-forest-based regression model. In this way, the images obtained by the super-resolution strategy can be fused together by applying the groupwise registration method to construct the required atlas. Our experiments have shown that the proposed framework can effectively solve the problem of atlas fusion from the low-quality brain MR images.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We fuse the brain atlas from real diagnostic MR images with high inter-slice thickness. </LI> <LI> All images are processed through the two-stage learning-based super-resolution. </LI> <LI> Groupwise registration is applied for unbiased atlas fusion. </LI> </UL> </P>

Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota

Zhang Dao-Feng,Yao Yu-Fang,Xue Hua-Peng,Fu Zi-Yue,Zhang Xiao-Mei,Shao Zongze 한국미생물학회 2022 The journal of microbiology Vol.60 No.9

A novel bacterium, designated YYF0007T, was isolated from an agar-degrading co-culture. The strain was found harboring four CRISPR-Cas systems of two classes in the chromosome and subsequently subjected to a study on polyphasic taxonomy. Pairwise analyses of the 16S rRNA gene sequences indicated that strain YYF0007T had highest 16S rRNA gene sequence similarity (92.2%) to Jiulongibacter sediminis JN- 14-9T. The phylogenomic trees based on the 16S rRNA gene and 269 single-copy orthologous gene clusters (OCs) indicated that strain YYF0007T should be recognized as a novel genus of the family Spirosomaceae. The cells were Gramstain- negative, nonmotile, strictly aerobic, and straight long rods with no flagellum. Optimum growth occurred at 28°C and pH 7.0 with the presence of NaCl concentration 1.0–3.0% (w/v). The strain showed oxidase and catalase activities. The major fatty acids were C16:1ω5c, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant isoprenoid quinone was MK-7. The complete genome size was 4.64 Mb with a DNA G + C content of 44.4%. Further typing of CRISPR-Cas systems in the family Spirosomaceae and the phylum Bacteroidota indicated that it was remarkable for strain YYF0007T featured by such a set of CRISPR-Cas systems. This trait highlights the applications of strain YYF- 0007T in studies on the evolutionary dynamics and bacterial autoimmunity of CRISPR-Cas system as a potential model. The name Marinilongibacter aquaticus gen. nov., sp. nov. is proposed, and the type strain is YYF0007T (= MCCC 1K06017T = GDMCC 1.2428T = JCM 34683T).

Clinical Significance of SH2B1 Adaptor Protein Expression in Non-small Cell Lung Cancer

Zhang, Hang,Duan, Chao-Jun,Chen, Wei,Wang, Shao-Qiang,Zhang, Sheng-Kang,Dong, Shuo,Cheng, Yuan-Da,Zhang, Chun-Fang Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.5

The SH2B1 adaptor protein is recruited to multiple ligand-activated receptor tyrosine kinases that play important role in the physiologic and pathologic features of many cancers. The purpose of this study was to assess SH2B1 expression and to explore its contribution to the non-small cell lung cancer (NSCLC). Methods: SH2B1 expression in 114 primary NSCLC tissue specimens was analyzed by immunohistochemistry and correlated with clinicopathological parameters and patients' outcome. Additionally, 15 paired NSCLC background tissues, 5 NSCLC cell lines and a normal HBE cell line were evaluated for SH2B1 expression by RT-PCR and immunoblotting, immunofluorescence being applied for the cell lines. Results: SH2B1 was found to be overexpressed in NSCLC tissues and NSCLC cell lines. More importantly, high SH2B1 expression was significantly associated with tumor grade, tumor size, clinical stage, lymph node metastasis, and recurrence respectively. Survival analysis demonstrated that patients with high SH2B1 expression had both poorer disease-free survival and overall survival than other patients. Multivariate Cox regression analysis revealed that SH2B1 overexpression was an independent prognostic factor for patients with NSCLC. Conclusions: Our findings suggest that the SH2B1 protein may contribute to the malignant progression of NSCLC and could offer a novel prognostic indicator for patients with NSCLC.

VUV spectroscopic properties of rare-earth (RE³⁺ = Sm³⁺, Eu³⁺, Tb³⁺, Dy³⁺) -activated layered borate Ba₆Gd₉B₇₉O₁₃₈

Zhang, Zhi-Jun,Zhang, Shao-Lin,Zhang, Wei-Bin,Yang, Woochul Elsevier 2017 SOLID STATE SCIENCES Vol.64 No.-

<P><B>Abstract</B></P> <P>Vacuum ultraviolet (VUV) spectroscopic properties of rare-earth RE<SUP>3+</SUP>- activated (RE<SUP>3+</SUP> = Sm<SUP>3+</SUP>, Eu<SUP>3+</SUP>, Tb<SUP>3+</SUP> and Dy<SUP>3+</SUP>) Ba<SUB>6</SUB>Gd<SUB>9</SUB>B<SUB>79</SUB>O<SUB>138</SUB> borates (BGBO) are investigated. The strong absorption bands in the VUV range of un-doped and RE<SUP>3+</SUP>-activated BGBO were observed. The band range from 140 to 200 nm with a peak at about 173 nm results from the host lattice absorption. For Sm<SUP>3+</SUP>-activated BGBO, the charge transfer transition from O<SUP>2-</SUP> to Sm<SUP>3+</SUP> was observed at 202 nm. In addition, it exhibits bright red emission originating from the Sm<SUP>3+</SUP> <I>f</I>-<I>f</I> transitions of <SUP>4</SUP>G<SUB>5/2</SUB> → <SUP>6</SUP>H<SUB> <I>J</I> </SUB> (<I>J</I> = 5/2, 7/2 and 9/2). The O<SUP>2-</SUP>-Eu<SUP>3+</SUP> charge transfer (CT) at 249 nm is observed in the excitation spectrum for Eu<SUP>3+</SUP>-doped BGBO. For Tb<SUP>3+</SUP>-activated BGBO, the broad bands around 208 and 230 nm are due to the spin-allowed and spin-forbidden <I>f</I>-<I>d</I> transitions of Tb<SUP>3+</SUP>, respectively. In addition, the absence of the <I>f</I>-<I>d</I> transitions of Sm<SUP>3+</SUP> and Dy<SUP>3+</SUP> in the excitation spectra probably due to the photo-ionization effect. It is demonstrated that there are energy transfers from the BGBO host lattice to the luminescent activators depending on the activators.</P> <P><B>High lights</B></P> <P> <UL> <LI> VUV spectroscopic properties of rare-earth ions in Ba<SUB>6</SUB>Gd<SUB>9</SUB>B<SUB>79</SUB>O<SUB>138</SUB> have been investigated. </LI> <LI> The CT bands of O<SUP>2-</SUP>-Sm<SUP>3+</SUP> and O<SUP>2-</SUP>-Eu<SUP>3+</SUP> charge transfer bands were observed at 202 and 249 nm, respectively. </LI> <LI> The <I>f</I>-<I>d</I> spin-allowed (208 nm) and spin-forbidden (230 nm) transitions of Tb<SUP>3+</SUP> were observed. </LI> <LI> Energy transfer from the host to rare-earth activators has been demonstrated. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Surface polished of bulk methylammonium lead tribromide single crystal

Zhang Hang,Zhang Bohao,Wang Xiang,Shao Wenyi,Nie Jing,Liu Jun,Ouyang Xiaoping,Xu Qiang 한국물리학회 2020 Current Applied Physics Vol.20 No.10

Organic-inorganic halide perovskite materials have been demonstrated with wide applications in optoelectronics and ionization radiation detection. For bulk as-grown crystals, the existence of surface cracks and defects can significantly increase charges recombination and reduce the performance of the device. Herein, we polished the crystal surfaces with both mechanical and chemical mechanical methods at room temperature. After been chemical-mechanical polished, the crystal surface with root mean square roughness about 0.5 nm was obtained. Optical transmission and photoluminescence spectra indicate that chemical mechanical polishing technology can effectively reduce the density of crystal surface defects. The achieved low leakage current density on the surface and bulk crystal is 0.05 nA mm 2 and 0.07 nA mm 2, respectively. Furthermore, the current-voltage curve under visible photons and X-ray photons reveals that surface polishing treatment can suppress the charges recombination and increase the charges transportation.

Time-related Mapping of Quantitative Trait Loci Controlling Dry Matter Accumulation and Partitioning in Rice

Shao Bo Li,Zhi Hong Zhang,Shao Qing Li,Yang Sheng Li,You Lin Zhu,Ying Guo Zhu 한국유전학회 2008 Genes & Genomics Vol.30 No.4

Grain yield is a result of dry matter accumulation and partitioning in rice (Oryza sativa L.). To characterize the genetic basis of dynamics of traits representing dry matter accumulation and partitioning as well as their relationships with each other, composite interval mapping of quantitative trait loci (QTL) was conducted based on time-related phenotypic data obtained from a population of 258 recombinant inbred lines (F12), which was derived from a cross between Lemont (japonica var.) and Teqing (indica var.). A total of twenty-three QTL were identified for leaf weight, stem weight and panicle weight at four measuring stages after heading. However, these three dynamic traits were observed to be controlled by different QTL (genes) at different growth stages. An extreme example was that at least three types of QTL (genes) might be involved in the development of panicle weight. Growth duration, which is closely related to dry matter accumulation and partitioning, was also identified to be significantly affected by four QTL. The close correlations among the studied four traits were explained to some extent by six co-located QTL. Nevertheless, it would be of great importance to distinguish the pleiotropic or linked effects of the co-located QTL. In addition, the chromosome regions or QTL identified in this study were compared with those previously reported for the same or related traits with the same RIL population.

Selective Growth of ZnO Nanorods and Its Gas Sensor Application

Shao-Lin Zhang,Jeong-Ok Lim,Jeung-Soo Huh,Wooyoung Lee IEEE 2012 IEEE Sensors Journal Vol.12 No.11

<P>The facile sonochemical method has been used to selectively grow a ZnO nanorods sensing layer directly on an alumina substrate. The growth region of the ZnO nanorods array is precisely controlled by a pre-coated Pt/Zn seed layer on alumina substrate. No growth of ZnO nanostructure is found on the substrate without seed layer. The grown ZnO nanorods are well aligned and densely packed, with wurtzite crystal structure and flat hexagonal tip. The sensing properties of the obtained ZnO nanorods sensing layer to three kinds of toxic gases ( NH<SUB>3</SUB>, CO, and CH<SUB>4</SUB>) have been investigated. The sensing observation revealed that the selectively grown ZnO nanorods demonstrated good response, repeatability, and excellent linearity toward toxic gases. This result indicates that selective growth of ZnO nanorods directly on sensor substrate is an accessible and advantageous method for sensor fabrication.</P>

Analysis on Modeling and Motion Simulation Based on Manipulator End Executor of Small Satellite during the Grasping Process

Zhang Yuan,Shao Junpeng,Zhang Liyuan,Dai Ye,Lai Yinan 보안공학연구지원센터 2015 International Journal of Smart Home Vol.9 No.10

This paper introduces the components and functions of institution aiming at docking capture link of the small satellite manipulator end executor. Putting forward to Euler method and quaternion as the theoretical basis, kinetics of grasping institution the relative position and attitude are modeling and analyzed. The axial tilt grab conditions of the simulation analysis are finished by the ADAMS software. The results of the simulation analysis for the relative position and velocity and the hand-grasp collision force are concluded.

Controlled Synthesis of ZnO Nanostructures for Sub-ppm-Level VOC Detection

Shao-Lin Zhang,Hyung-Gi Byun,Jeong-Ok Lim,Jeung-Soo Huh,Wooyoung Lee IEEE 2012 IEEE Sensors Journal Vol.12 No.11

<P>Various ZnO nanostructures, including nanoparticles, nanorods, nanotubes, and nanorings, were synthesized via a controlled synthesis by a facile sonochemical method combined with a chemical etching process. The morphology and structure of the fabricated nanomaterials were characterized by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The sensing properties of different ZnO nanostructures toward volatile organic compounds gases at sub-ppm levels were investigated. The differences in the sensing responses of various nanostructures were compared, and reasonable mechanisms are proposed here.</P>

Novel Auto-regressive Measurement of Diamond Tool Wear in Ultra-precision Raster Milling

Shao-Jian Zhang,Suet To,Chi-Fai Cheung,Jian-Jun Du 한국정밀공학회 2012 International Journal of Precision Engineering and Vol. No.

In this paper, a new auto-regressive algorithm is proposed to reconstruct 3D topographic surface for diamond tool wear, using its in-process image. First, based on digital image processing technique, tool wear lands are separated from a tool wear image captured by a CCD camera under a 100X optical system; Second, a traverse search method of arc translation is put forward to eliminate feigned wear lands, and a least square polynomial method is adopted to fit inner- and outer-contours of the wear lands, self-adaptively filtering noises and connecting the discontinuous wear lands; Finally, the auto-regressive calibration method is developed to reconstruct its 3D topographic surface. The wear land is extracted self-adaptively, and the wear area, maximal wear width, average wear width and worn volume can be determined automatically by the algorithm. The reconstructed 3D topography of the tool wear land can be identified, based on the tool wear image captured by SEM. The result indicates that the method is capable of reconstructing 3D topography of the tool wear land and provides a possibility for in-process 3D-wear measurement in ultra-precision raster milling (UPRM) and the algorithm reliability is validated finally. And the influence of tool wear on surface roughness is discussed.