bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progranulin inhibits expression and release of chemokines CXCL9 and CXCL10 in a TNFR1 dependent manner
Authors: Mundra Jyoti Joshi , Jian Jinlong , Bhagat Priyal , Liu Chuan-ju 
Published: February 2016

AbstractProgranulin (PGRN), a pleiotrophic growth factor, is known to play an important role in the maintenance and regulation of the homeostatic dynamics of normal tissue development, proliferation, regeneration and host-defense. PGRN also has potent anti-inflammatory functionality and deregulated PGRN is associated with rheumatoid arthritis and inflammatory bowel disease. We have previously reported that PGRN directly binds to TNFR and significantly enhances Treg population and stimulatesIL-10 production. To further investigate PGRN’s function in the immune system we performed a gene array analysis on CD4+ T cells from wild type B6 mice and PGRN −/− mice. We identified many chemokines and their receptors, among which CXCL9 and CXCL10 were most prominent, that were significantly induced in PGRN null mice. Administration of recombinant PGRN protein strongly inhibited TNF and IFN-γ-induced CXCL9 and CXCL10 expression. In addition, CXCL9 expression is strongly upregulated in PGRN KO mice and its level is correlated with severity of inflammation in a dermatitis model. Further, we have demonstrated that PGRN-mediated inhibition of chemokine expression largely depends on TNFR1. Taken together, this study provides new insights into the mechanisms underlying PGRN mediated regulation of various inflammatory and autoimmune diseases.
Risk Prediction Modeling of Sequencing Data Using a Forward Random Field Method
Authors: Wen Yalu , He Zihuai , Li Ming , Lu Qing 
Published: February 2016

AbstractWith the advance in high-throughput sequencing technology, it is feasible to investigate the role of common and rare variants in disease risk prediction. While the new technology holds great promise to improve disease prediction, the massive amount of data and low frequency of rare variants pose great analytical challenges on risk prediction modeling. In this paper, we develop a forward random field method (FRF) for risk prediction modeling using sequencing data. In FRF, subjects’ phenotypes are treated as stochastic realizations of a random field on a genetic space formed by subjects’ genotypes, and an individual’s phenotype can be predicted by adjacent subjects with similar genotypes. The FRF method allows for multiple similarity measures and candidate genes in the model, and adaptively chooses the optimal similarity measure and disease-associated genes to reflect the underlying disease model. It also avoids the specification of the threshold of rare variants and allows for different directions and magnitudes of genetic effects. Through simulations, we demonstrate the FRF method attains higher or comparable accuracy over commonly used support vector machine based methods under various disease models. We further illustrate the FRF method with an application to the sequencing data obtained from the Dallas Heart Study.
Tuning Liposome Membrane Permeability by Competitive Peptide Dimerization and Partitioning-Folding Interactions Regulated by Proteolytic Activity
Authors: Lim Seng Koon , Sandén Camilla , Selegård Robert , Liedberg Bo , Aili Daniel 
Published: February 2016

AbstractMembrane active peptides are of large interest for development of drug delivery vehicles and therapeutics for treatment of multiple drug resistant infections. Lack of specificity can be detrimental and finding routes to tune specificity and activity of membrane active peptides is vital for improving their therapeutic efficacy and minimize harmful side effects. We describe a de novo designed membrane active peptide that partition into lipid membranes only when specifically and covalently anchored to the membrane, resulting in pore-formation. Dimerization with a complementary peptide efficiently inhibits formation of pores. The effect can be regulated by proteolytic digestion of the inhibitory peptide by the matrix metalloproteinase MMP-7, an enzyme upregulated in many malignant tumors. This system thus provides a precise and specific route for tuning the permeability of lipid membranes and a novel strategy for development of recognition based membrane active peptides and indirect enzymatically controlled release of liposomal cargo.
High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus
Authors: Wang Ruanlin , Xiong Jie , Wang Wei , Miao Wei , Liang Aihua 
Published: February 2016

AbstractProgrammed −1 ribosomal frameshifting (−1 PRF) has been identified as a mechanism to regulate the expression of many viral genes and some cellular genes. The slippery site of −1 PRF has been well characterized, whereas the +1 PRF signal and the mechanism involved in +1 PRF remain poorly understood. Previous study confirmed that +1 PRF is required for the synthesis of protein products in several genes of ciliates from the genus Euplotes. To accurately assess the frequency of genes requiring frameshift in Euplotes, the macronuclear genome and transcriptome of Euplotes octocarinatus were analyzed in this study. A total of 3,700 +1 PRF candidate genes were identified from 32,353 transcripts and the gene products of these putative +1 PRFs were mainly identified as protein kinases. Furthermore, we reported a putative suppressor tRNA of UAA which may provide new insights into the mechanism of +1 PRF in euplotids. For the first time, our transcriptome-wide survey of +1 PRF in E. octocarinatus provided a dataset which serves as a valuable resource for the future understanding of the mechanism underlying +1 PRF.
Suicide Gene-Engineered Stromal Cells Reveal a Dynamic Regulation of Cancer Metastasis
Authors: Shen Keyue , Luk Samantha , Elman Jessica , Murray Ryan , Mukundan Shilpaa , Parekkadan Biju 
Published: February 2016

AbstractCancer-associated fibroblasts (CAFs) are a major cancer-promoting component in the tumor microenvironment (TME). The dynamic role of human CAFs in cancer progression has been ill-defined because human CAFs lack a unique marker needed for a cell-specific, promoter-driven knockout model. Here, we developed an engineered human CAF cell line with an inducible suicide gene to enable selective in vivo elimination of human CAFs at different stages of xenograft tumor development, effectively circumventing the challenge of targeting a cell-specific marker. Suicide-engineered CAFs were highly sensitive to apoptosis induction in vitro and in vivo by the addition of a simple small molecule inducer. Selection of timepoints for targeted CAF apoptosis in vivo during the progression of a human breast cancer xenograft model was guided by a bi-phasic host cytokine response that peaked at early timepoints after tumor implantation. Remarkably, we observed that the selective apoptosis of CAFs at these early timepoints did not affect primary tumor growth, but instead increased the presence of tumor-associated macrophages and the metastatic spread of breast cancer cells to the lung and bone. The study revealed a dynamic relationship between CAFs and cancer metastasis that has counter-intuitive ramifications for CAF-targeted therapy.
Combined strategies for optimal detection of the contact point in AFM force-indentation curves obtained on thin samples and adherent cells
Authors: Gavara Núria 
Published: February 2016

AbstractAtomic Force Microscopy (AFM) is a widely used tool to study cell mechanics. Current AFM setups perform high-throughput probing of living cells, generating large amounts of force-indentations curves that are subsequently analysed using a contact-mechanics model. Here we present several algorithms to detect the contact point in force-indentation curves, a crucial step to achieve fully-automated analysis of AFM-generated data. We quantify and rank the performance of our algorithms by analysing a thousand force-indentation curves obtained on thin soft homogeneous hydrogels, which mimic the stiffness and topographical profile of adherent cells. We take advantage of the fact that all the proposed algorithms are based on sequential search strategies and show that a combination of them yields the most accurate and unbiased results. Finally, we also observe improved performance when force-indentation curves obtained on adherent cells are analysed using our combined strategy, as compared to the classical algorithm used in the majority of previous cell mechanics studies.
A Microstructured Fiber with Defined Borosilicate Regions to Produce a Radial Micronozzle Array for Nanoelectrospray Ionization
Authors: Fu Y. , Morency S. , Bachus K. , Simon D. , Hutama T. , Gibson G. T. T. , Messaddeq Y. , Oleschuk R. D. 
Published: February 2016

AbstractThis work highlights the possibility of using microstructured fibres with predefined doped regions to produce functional microstructures at a fibre facet with differential chemical etching. A specially designed silica microstructured fibre (MSF) that possesses specific boron-doped silica regions was fabricated for the purpose of generating a radial micronozzle array. The MSF was drawn from a preform comprising pure silica capillaries surrounded by boron-doped silica rods. Different etching rates of the boron-doped and silica regions at the fiber facet produces raised nozzles where the silica capillaries were placed. Fabrication parameters were explored in relation to the fidelity and protrusion length of the nozzle. Using etching alone, the nozzle protrusion length was limited and the inner diameter of the channels in the array is expanded. However with the addition of a protective water counter flow, nozzle protrusion is increased to 60 μm with a limited increase in hole diameter. The radial micronozzle array generated nine individual electrosprays which were characterized using spray current measurements and related to theoretical prediction. Signal enhancement for the higher charge state ions for two peptides showed a substantial signal enhancement compared to conventional emitter technology.
Early detection of germinated wheat grains using terahertz image and chemometrics
Authors: Jiang Yuying , Ge Hongyi , Lian Feiyu , Zhang Yuan , Xia Shanhong 
Published: February 2016

AbstractIn this paper, we propose a feasible tool that uses a terahertz (THz) imaging system for identifying wheat grains at different stages of germination. The THz spectra of the main changed components of wheat grains, maltose and starch, which were obtained by THz time spectroscopy, were distinctly different. Used for original data compression and feature extraction, principal component analysis (PCA) revealed the changes that occurred in the inner chemical structure during germination. Two thresholds, one indicating the start of the release of α-amylase and the second when it reaches the steady state, were obtained through the first five score images. Thus, the first five PCs were input for the partial least-squares regression (PLSR), least-squares support vector machine (LS-SVM) and back-propagation neural network (BPNN) models, which were used to classify seven different germination times between 0 and 48 h, with a prediction accuracy of 92.85%, 93.57% and 90.71%, respectively. The experimental results indicated that the combination of THz imaging technology and chemometrics could be a new effective way to discriminate wheat grains at the early germination stage of approximately 6 h.
Increased risk of hepatic complications in kidney transplantation with chronic virus hepatitis infection: A nationwide population-based cohort study
Authors: Yu Tung-Min , Lin Che-Chen , Shu Kuo-Hsiung , Chuang Ya-Wen , Huang Shih-Ting , Chen Cheng-Hsu , Wu Ming-Ju , Chung Mu-Chi , Chang Chao-Hsiang , Li Chi-Yuan , Chung Chi-Jung 
Published: February 2016

AbstractData regarding the risk of various liver diseases among different hepatitis viruses in kidney transplantation have not yet been identified.We selected individuals with kidney transplantation (ICD-9-CM V420 or 996.81) from 2000–2009 from the catastrophic illness registry of National Health Insurance Research Database (NHIRD)as the study cohort. The two end-points in the study included overall death and post-transplant occurrence of hepatic disease. After adjustment for other risk factors, the risk of mortality was increased in patients with HBV infection (N = 352) and with HCV infection (N = 275) compared to those with neither HBV nor HCV infection (N = 3485). In addition,renal transplant recipients with HBV alone,HCV alone and both with HBV and HCVinfectionrespectively had an approximately 10-fold hazard ratio (HR) = 9.84, 95% confidence interval (CI): 4.61–21.0, 4-fold increased risk (HR = 4.40, 95% CI: 1.85–10.5)and 5-fold increased risk (HR = 4.63, 95% CI: 1.06–20.2)of hepatocellular carcinoma (HCC)compared to those with neither HBV nor HCV infection. Our findings showed a significant risk of de novo liver disease in recipients with hepatitis virus infection. Based on our findings, we reinforce the importance and impact of hepatitis virus in renal transplantation.
An embryonic atrazine exposure results in reproductive dysfunction in adult zebrafish and morphological alterations in their offspring
Authors: Wirbisky Sara E. , Weber Gregory J. , Sepúlveda Maria S. , Lin Tsang-Long , Jannasch Amber S. , Freeman Jennifer L. 
Published: February 2016

AbstractThe herbicide atrazine, a suspected endocrine disrupting chemical (EDC), frequently contaminates potable water supplies. Studies suggest alterations in the neuroendocrine system along the hypothalamus-pituitary-gonadal axis; however, most studies address either developmental, pubertal, or adulthood exposures, with few investigations regarding a developmental origins hypothesis. In this study, zebrafish were exposed to 0, 0.3, 3, or 30 parts per billion (ppb) atrazine through embryogenesis and then allowed to mature with no additional chemical exposure. Reproductive function, histopathology, hormone levels, offspring morphology, and the ovarian transcriptome were assessed. Embryonic atrazine exposure resulted in a significant increase in progesterone levels in the 3 and 30 ppb groups. A significant decrease in spawning and a significant increase in follicular atresia in the 30 ppb group were observed. In offspring, a decrease in the head length to body ratio in the 30 ppb group, along with a significant increase in head width to body ratio in the 0.3 and 3 ppb groups occurred. Transcriptomic alterations involved genes associated with endocrine system development and function, tissue development, and behavior. This study provides evidence to support atrazine as an EDC causing reproductive dysfunction and molecular alterations in adults exposed only during embryogenesis and morphological alterations in their offspring.
The Critical Criterion on Runaway Shear Banding in Metallic Glasses
Authors: Sun B. A. , Yang Y. , Wang W. H. , Liu C. T. 
Published: February 2016

AbstractThe plastic flow of metallic glasses (MGs) in bulk is mediated by nanoscale shear bands, which is known to proceed in a stick-slip manner until reaching a transition state causing catastrophic failures. Such a slip-to-failure transition controls the plasticity of MGs and resembles many important phenomena in natural science and engineering, such as friction, lubrication and earthquake, therefore has attracted tremendous research interest over past decades. However, despite the fundamental and practical importance, the physical origin of this slip-to-failure transition is still poorly understood. By tracking the behavior of a single shear band, here we discover that the final fracture of various MGs during compression is triggered as the velocity of the dominant shear band rises to a critical value, the magnitude of which is independent of alloy composition, sample size, strain rate and testing frame stiffness. The critical shear band velocity is rationalized with the continuum theory of liquid instability, physically originating from a shear-induced cavitation process inside the shear band. Our current finding sheds a quantitative insight into deformation and fracture in disordered solids and, more importantly, is useful to the design of plastic/tough MG-based materials and structures.
Synthesis of Highly Crystalline Multilayered Boron Niride Microflakes
Authors: Ahmad Pervaiz , Khandaker Mayeen Uddin , Amin Yusoff Mohd , Muhammad Nawshad 
Published: February 2016

AbstractBoron niride microflakes of 2–5 μm in diameter and greater than 40 μm in length with multilayer structure and highly crystalline nature are synthesized in two states of catalysts and dual role of nitrogen at 1100 °C. Most of the microflakes are flat, smooth and vertically aligned with a wall-like view from the top. Transmission electron microscopy shows overlapped layers of microflakes with an interlayer spacing of 0.34 nm. The h-BN components of the synthesized microflakes are verified from B 1s and N1 s peaks at 190. 7 and 397.9 eV. Raman shift at 1370 (cm−1) and sharp peaks in the XRD pattern further confirm the h-BN phase and crystalline nature of the synthesized microflakes. Microflakes of h-BN with the above characteristics are highly desirable for the development of a solid state neutron detector with higher detection efficiency.
Surface Molecularly Imprinted Polymer of Chitosan Grafted Poly(methyl methacrylate) for 5-Fluorouracil and Controlled Release
Authors: Zheng Xue-Fang , Lian Qi , Yang Hua , Wang Xiuping 
Published: February 2016

AbstractThe molecular surface imprinted graft copolymer of chitosan with methyl methacrylate (MIP-CS-g-PMMA) were prepared by free radical polymerization with 5-fluorouracil (5-FU) as the template molecule using initiator of ammonium persulfate as adsorption system. MIPs were characterized by FTIR, X-ray diffraction, thermo-gravimetric analysis, 1H NMR and SEM. The mechanism of graft copolymerization and factors affected graft reaction were studied in details and the optimum reaction conditions (to the highest %G and %E as the standard) were obtained at [MMA] 1.2 mol/L, [Chitosan] 16.67 mol/L, [initiator] 0.0062 mol/L, temperature 60 °C and reaction time 7 h. MIPs exhibited high recognition selectivity and excellent combining affinity to template molecular. The in vitro release of the 5-FU was highly pH-dependent and time delayed. The release behavior showed that the drugs did not release in simulated gastric fluid (pH = 1.0) and the drug release was small in the simulated small intestinal fluid (pH = 6.8) and drug abrupt release will be produced in the simulated colon fluid (pH = 7.4), indicating excellent colon-specific drug delivery behavior.
Combining the absorptive and radiative loss in metasurfaces for multi-spectral shaping of the electromagnetic scattering
Authors: Pan Wenbo , Huang Cheng , Pu Mingbo , Ma Xiaoliang , Cui Jianhua , Zhao Bo , Luo Xiangang 
Published: February 2016

AbstractThe absorptive and radiative losses are two fundamental aspects of the electromagnetic responses, which are widely occurring in many different systems such as waveguides, solar cells and antennas. Here we proposed a metasurface to realize the control of the absorptive and radiative loss and to reduce the radar cross section (RCS) in multi-frequency bands. The anti-phase gradient and absorptive metasurfaces were designed that consists of metallic square patch and square loop structure inserted with resistors, acting as an phase gradient material in the X and Ku band, while behaving as an absorber in the S band. The simulation and experiment results verified the double-band, wideband and polarization-independent RCS reduction by the absorptive and anti-phase gradient metasurfaces.
DDX3 promotes tumor invasion in colorectal cancer via the CK1ε/Dvl2 axis
Authors: He Tsung-Ying , Wu De-Wei , Lin Po-Lin , Wang Lee , Huang Chi-Chou , Chou Ming-Chih , Lee Huei 
Published: February 2016

AbstractDDX3, a subunit of CK1ε, phosphorylates Dvl2 to promote β-catenin activation. Overexpression of the Dvl2 protein results in potent activation of β-catenin/TCF signaling in colorectal cancer. Therefore, we hypothesized that DDX3 might promote tumor invasion via the CK1ε/Dvl2 axis due to β-catenin/TCF activation. Western blotting showed that β-catenin expression was decreased by DDX3 knockdown and increased by DDX3 overexpression in colorectal cancer cells. The TCF promoter activity and invasion capability were concomitantly increased and decreased by DDX3 manipulation in these cells. The invasion capability in colon cancer cells and xenograft lung tumor nodules induced by a DDX3-overexpressing T84 stable clone in tail-vein injection model were nearly suppressed by inhibitors of CK1ε (PF4800567) and β-catenin/TCF signaling (XAV939). Among colorectal cancer patients, DDX3 expression was positively correlated with the expression of pDvl2 and nuclear β-catenin in tumor tissues. The expression of pDvl2 occurred more frequently in high-nuclear than in low-nuclear β-catenin tumors. A prognostic significance of DDX3, pDvl2 and nuclear β-catenin on overall survival and relapse free survival was observed in this study population. We therefore suggest CK1ε or β-catenin/TCF signaling as potential targets for improving tumor regression and outcomes in colorectal cancer, particularly tumors with high-DDX3/high-nuclear β-catenin or high-DDX3/high-pDvl2/high-nuclear β-catenin expression.
Self-arrangement of nanoparticles toward crystalline metal oxides with high surface areas and tunable 3D mesopores
Authors: Lee Hyung Ik , Lee Yoon Yun , Kang Dong-Uk , Lee Kirim , Kwon Young-Uk , Kim Ji Man 
Published: February 2016

AbstractWe demonstrate a new design concept where the interaction between silica nanoparticles (about 1.5 nm in diameter) with titania nanoparticles (anatase, about 4 nm or 6 nm in diameter) guides a successful formation of mesoporous titania with crystalline walls and controllable porosity. At an appropriate solution pH (~1.5, depending on the deprotonation tendencies of two types of nanoparticles), the smaller silica nanoparticles, which attach to the surface of the larger titania nanoparticles and provide a portion of inactive surface and reactive surface of titania nanoparticles, dictate the direction and the degree of condensation of the titania nanoparticles, resulting in a porous 3D framework. Further crystallization by a hydrothermal treatment and subsequent removal of silica nanoparticles result in a mesoporous titania with highly crystalline walls and tunable mesopore sizes. A simple control of the Si/Ti ratio verified the versatility of the present method through the successful control of mean pore diameter in the range of 2–35 nm and specific surface area in the ranges of 180–250 m2 g−1. The present synthesis method is successfully extended to other metal oxides, their mixed oxides and analogues with different particle sizes, regarding as a general method for mesoporous metal (or mixed metal) oxides.