bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single Cell Transfection through Precise Microinjection with Quantitatively Controlled Injection Volumes
Authors: Chow Yu Ting , Chen Shuxun , Wang Ran , Liu Chichi , Kong Chi-wing , Li Ronald A. , Cheng Shuk Han , Sun Dong 
Published: April 2016

AbstractCell transfection is a technique wherein foreign genetic molecules are delivered into cells. To elucidate distinct responses during cell genetic modification, methods to achieve transfection at the single-cell level are of great value. Herein, we developed an automated micropipette-based quantitative microinjection technology that can deliver precise amounts of materials into cells. The developed microinjection system achieved precise single-cell microinjection by pre-patterning cells in an array and controlling the amount of substance delivered based on injection pressure and time. The precision of the proposed injection technique was examined by comparing the fluorescence intensities of fluorescent dye droplets with a standard concentration and water droplets with a known injection amount of the dye in oil. Injection of synthetic modified mRNA (modRNA) encoding green fluorescence proteins or a cocktail of plasmids encoding green and red fluorescence proteins into human foreskin fibroblast cells demonstrated that the resulting green fluorescence intensity or green/red fluorescence intensity ratio were well correlated with the amount of genetic material injected into the cells. Single-cell transfection via the developed microinjection technique will be of particular use in cases where cell transfection is challenging and genetically modified of selected cells are desired.
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
Authors: Lin Hsin-Hung , Liao Yu-Chieh 
Published: April 2016

AbstractMetagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or ‘bin’ sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/.
Universal quantum gates for photon-atom hybrid systems assisted by bad cavities
Authors: Wang Guan-Yu , Liu Qian , Wei Hai-Rui , Li Tao , Ai Qing , Deng Fu-Guo 
Published: April 2016

AbstractWe present two deterministic schemes for constructing a CNOT gate and a Toffoli gate on photon-atom and photon-atom-atom hybrid quantum systems assisted by bad cavities, respectively. They are achieved by cavity-assisted photon scattering and work in the intermediate coupling region with bad cavities, which relaxes the difficulty of their implementation in experiment. Also, bad cavities are feasible for fast quantum operations and reading out information. Compared with previous works, our schemes do not need any auxiliary qubits and measurements. Moreover, the schematic setups for these gates are simple, especially that for our Toffoli gate as only a quarter wave packet is used to interact the photon with each of the atoms every time. These atom-cavity systems can be used as the quantum nodes in long-distance quantum communication as their relatively long coherence time is suitable for multi-time operations between the photon and the system. Our calculations show that the average fidelities and efficiencies of our two universal hybrid quantum gates are high with current experimental technology.
Adsorbing/dissolving Lyoprotectant Matrix Technology for Non-cryogenic Storage of Archival Human Sera
Authors: Solivio Morwena J. , Less Rebekah , Rynes Mathew L. , Kramer Marcus , Aksan Alptekin 
Published: April 2016

AbstractDespite abundant research conducted on cancer biomarker discovery and validation, to date, less than two-dozen biomarkers have been approved by the FDA for clinical use. One main reason is attributed to inadvertent use of low quality biospecimens in biomarker research. Most proteinaceous biomarkers are extremely susceptible to pre-analytical factors such as collection, processing and storage. For example, cryogenic storage imposes very harsh chemical, physical and mechanical stresses on biospecimens, significantly compromising sample quality. In this communication, we report the development of an electrospun lyoprotectant matrix and isothermal vitrification methodology for non-cryogenic stabilization and storage of liquid biospecimens. The lyoprotectant matrix was mainly composed of trehalose and dextran (and various low concentration excipients targeting different mechanisms of damage) and it was engineered to minimize heterogeneity during vitrification. The technology was validated using five biomarkers; LDH, CRP, PSA, MMP-7 and C3a. Complete recovery of LDH, CRP and PSA levels was achieved post-rehydration while more than 90% recovery was accomplished for MMP-7 and C3a, showing promise for isothermal vitrification as a safe, efficient and low-cost alternative to cryogenic storage.
An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes
Authors: Guldner Ian H. , Yang Lin , Cowdrick Kyle R. , Wang Qingfei , Alvarez Barrios Wendy V. , Zellmer Victoria R. , Zhang Yizhe , Host Misha , Liu Fang , Chen Danny Z. , Zhang Siyuan 
Published: April 2016

AbstractMetastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.
Systematic characterization of seminal plasma piRNAs as molecular biomarkers for male infertility
Authors: Hong Yeting , Wang Cheng , Fu Zheng , Liang Hongwei , Zhang Suyang , Lu Meiling , Sun Wu , Ye Chao , Zhang Chen-Yu , Zen Ke , Shi Liang , Zhang Chunni , Chen Xi 
Published: April 2016

AbstractAlthough piwi-interacting RNAs (piRNAs) play pivotal roles in spermatogenesis, little is known about piRNAs in the seminal plasma of infertile males. In this study, we systematically investigated the profiles of seminal plasma piRNAs in infertile males to identify piRNAs that are altered during infertility and evaluate their diagnostic value. Seminal plasma samples were obtained from 211 infertile patients (asthenozoospermia and azoospermia) and 91 fertile controls. High-throughput sequencing technology was employed to screen piRNA profiles in seminal plasma samples pooled from healthy controls and infertile patients. The results identified 61 markedly altered piRNAs in infertile patient groups compared with control group. Next, a quantitative RT-PCR assay was conducted in the training and validation sets to measure and confirm the concentrations of altered piRNAs. The results identified a panel of 5 piRNAs that were significantly decreased in seminal plasma of infertile patients compared with healthy controls. ROC curve analysis and risk score analysis revealed that the diagnostic potential of these 5 piRNAs to distinguish asthenozoospermic and azoospermic individuals from healthy controls was high. In summary, this study identifies a panel of piRNAs that can accurately distinguish fertile from infertile males. This finding may provide pathophysiological clues about the development of infertility.
C/EBPβ-Thr217 Phosphorylation Stimulates Macrophage Inflammasome Activation and Liver Injury
Authors: Buck Martina , Solis-Herruzo Jose , Chojkier Mario 
Published: April 2016

AbstractAmplification of liver injury is mediated by macrophages but the signaling by which the macrophage inflammasome enhances liver injury is not completely understood. The CCAAT/Enhancer Binding Protein-β (C/EBPβ) is a critical signaling molecule for macrophages because expression of a dominant inhibitor of C/EBPβ DNA-binding sites or a targeted deletion of C/EBPβ results in impaired macrophage differentiation. We reported that expression of the phosphorylation-mutant C/EBPβ-Glu217, which mimics phosphorylated C/EBPβ-Thr217, was sufficient to confer macrophage survival to Anthrax lethal toxin. Here, using primary hepatocytes, primary liver macrophages, dominant positive and negative transgenic mice of the C/EBPβ-Thr217 phosphoacceptor, macrophage ablation and an inhibitory peptide of C/EBPβ-Thr217 phosphorylation, we determined that this phosphorylation is essential for the activation of the inflammasome in liver macrophages and for the hepatocyte apoptosis induced by hepatotoxins that results in liver injury. Similar findings were observed in the livers of patients with acute injury induced by Toxic Oil Syndrome.
Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells
Authors: Jones M. W. M. , Elgass K. D. , Junker M. D. , de Jonge M. D. , van Riessen G. A. 
Published: April 2016

AbstractRecent developments in biological X-ray microscopy have allowed structural information and elemental distribution to be simultaneously obtained by combining X-ray ptychography and X-ray fluorescence microscopy. Experimentally, these methods can be performed simultaneously; however, the optimal conditions for each measurement may not be compatible. Here, we combine two distinct measurements of ultrastructure and elemental distribution, with each measurement performed under optimised conditions. By combining optimised ptychography and fluorescence information we are able to determine molar concentrations from two-dimensional images, allowing an investigation into the interactions between the environment sensing filopodia in fibroblasts and extracellular calcium. Furthermore, the biological ptychography results we present illustrate a point of maturity where the technique can be applied to solve significant problems in structural biology.
Theory of Thomson scattering in inhomogeneous media
Authors: Kozlowski P. M. , Crowley B. J. B. , Gericke D. O. , Regan S. P. , Gregori G. 
Published: April 2016

AbstractThomson scattering of laser light is one of the most fundamental diagnostics of plasma density, temperature and magnetic fields. It relies on the assumption that the properties in the probed volume are homogeneous and constant during the probing time. On the other hand, laboratory plasmas are seldom uniform and homogeneous on the temporal and spatial dimensions over which data is collected. This is particularly true for laser-produced high-energy-density matter, which often exhibits steep gradients in temperature, density and pressure, on a scale determined by the laser focus. Here, we discuss the modification of the cross section for Thomson scattering in fully-ionized media exhibiting steep spatial inhomogeneities and/or fast temporal fluctuations. We show that the predicted Thomson scattering spectra are greatly altered compared to the uniform case, and may lead to violations of detailed balance. Therefore, careful interpretation of the spectra is necessary for spatially or temporally inhomogeneous systems.
Nox Complex signal and MAPK cascade pathway are cross-linked and essential for pathogenicity and conidiation of mycoparasite Coniothyrium minitans
Authors: Wei Wei , Zhu Wenjun , Cheng Jiasen , Xie Jiatao , Jiang Daohong , Li Guoqing , Chen Weidong , Fu Yanping 
Published: April 2016

AbstractThe NADPH oxidase complex of a sclerotial mycoparasite Coniothyrium minitans, an important biocontrol agent against crop diseases caused by Sclerotinia sclerotiorum, was identified and its functions involved in conidiation and mycoparasitism were studied. Gene knock-out and complementary experiments indicated that CmNox1, but not CmNox2, is necessary for conidiation and parasitism, and its expression could be significantly induced by its host fungus. CmNox1 is regulated by CmRac1-CmNoxR and interacts with CmSlt2, a homolog of Saccharomyces cerevisiae Slt2 encoding cell wall integrity-related MAP kinase. In ΔCmNox1, CmSlt2-GFP fusion protein lost the ability to localize to the cell nucleus accurately. The defect of conidiation in ΔCmRac1 could be partially restored by over-expressing CmSlt2, indicating that CmSlt2 was a downstream regulatory factor of CmNox1 and was involved in conidiation and parasitism. The expressions of mycoparasitism-related genes CmPks1, Cmg1 and CH1 were suppressed in the knock-out mutants of the genes in CmNox1-CmSlt2 signal pathway when cultivated either on PDA. Therefore, our study infers that CmRac1-CmNoxR regulates CmNox1-CmSlt2 pathway in regulating conidiation and pathogenicity of C. minitans.
Matrine displayed antiviral activity in porcine alveolar macrophages co-infected by porcine reproductive and respiratory syndrome virus and porcine circovirus type 2
Authors: Sun Na , Sun Panpan , Lv Haipeng , Sun Yaogui , Guo Jianhua , Wang Zhirui , Luo Tiantian , Wang Shaoyu , Li Hongquan 
Published: April 2016

AbstractThe co-infection of porcine reproductive respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) is quite common in clinical settings and no effective treatment to the co-infection is available. In this study, we established the porcine alveolar macrophages (PAM) cells model co-infected with PRRSV/PCV2 with modification in vitro, and investigated the antiviral activity of Matrine on this cell model and further evaluated the effect of Matrine on virus-induced TLR3,4/NF-κB/TNF-α pathway. The results demonstrated PAM cells inoculated with PRRSV followed by PCV2 2 h later enhanced PRRSV and PCV2 replications. Matrine treatment suppressed both PRRSV and PCV2 infection at 12 h post infection. Furthermore, PRRSV/PCV2 co- infection induced IκBα degradation and phosphorylation as well as the translocation of NF-κB from the cytoplasm to the nucleus indicating that PRRSV/PCV2 co-infection induced NF-κB activation. Matrine treatment significantly down-regulated the expression of TLR3, TLR4 and TNF-α although it, to some extent, suppressed p-IκBα expression, suggesting that TLR3,4/NF-κB/TNF-α pathway play an important role of Matrine in combating PRRSV/PCV2 co-infection. It is concluded that Matrine possesses activity against PRRSV/PCV2 co-infection in vitro and suppression of the TLR3,4/NF-κB/TNF-α pathway as an important underlying molecular mechanism. These findings warrant Matrine to be further explored for its antiviral activity in clinical settings.
Genipin cross-linked decellularized tracheal tubular matrix for tracheal tissue engineering applications
Authors: Sun Fei , Jiang Yuan , Xu Yanfei , Shi Hongcan , Zhang Siquan , Liu Xingchen , Pan Shu , Ye Gang , Zhang Weidong , Zhang Fangbiao , Zhong Chonghao 
Published: April 2016

AbstractDecellularization techniques have been widely used as an alternative strategy for organ reconstruction. This study investigated the mechanical, pro-angiogenic and in vivo biocompatibility properties of decellularized airway matrices cross-linked with genipin. New Zealand rabbit tracheae were decellularized and cross-linked with genipin, a naturally derived agent. The results demonstrated that, a significant (p < 0.05) increase in the secant modulus was computed for the cross-linked tracheae, compared to the decellularized samples. Angiogenic assays demonstrated that decellularized tracheal scaffolds and cross-linked tracheae treated with 1% genipin induce strong in vivo angiogenic responses (CAM analysis). Seven, 15 and 30 days after implantation, decreased (p < 0.01) inflammatory reactions were observed in the xenograft models for the genipin cross-linked tracheae matrices compared with control tracheae and no increase in the IgM or IgG content was observed in rats. In conclusion, treatment with genipin improves the mechanical properties of decellularized airway matrices without altering the pro-angiogenic properties or eliciting an in vivo inflammatory response.
Functional traits help to explain half-century long shifts in pollinator distributions
Authors: Aguirre-Gutiérrez Jesús , Kissling W. Daniel , Carvalheiro Luísa G. , WallisDeVries Michiel F. , Franzén Markus , Biesmeijer Jacobus C. 
Published: April 2016

AbstractChanges in climate and land use can have important impacts on biodiversity. Species respond to such environmental modifications by adapting to new conditions or by shifting their geographic distributions towards more suitable areas. The latter might be constrained by species’ functional traits that influence their ability to move, reproduce or establish. Here, we show that functional traits related to dispersal, reproduction, habitat use and diet have influenced how three pollinator groups (bees, butterflies and hoverflies) responded to changes in climate and land-use in the Netherlands since 1950. Across the three pollinator groups, we found pronounced areal range expansions (>53%) and modelled range shifts towards the north (all taxa: 17–22 km), west (bees: 14 km) and east (butterflies: 11 km). The importance of specific functional traits for explaining distributional changes varied among pollinator groups. Larval diet preferences (i.e. carnivorous vs. herbivorous/detritivorous and nitrogen values of host plants, respectively) were important for hoverflies and butterflies, adult body size for hoverflies and flight period length for all groups. Moreover, interactions among multiple traits were important to explain species’ geographic range shifts, suggesting that taxon-specific multi-trait analyses are needed to predict how global change will affect biodiversity and ecosystem services.
Facile fabrication of properties-controllable graphene sheet
Authors: Choi Jin Sik , Choi Hongkyw , Kim Ki-Chul , Jeong Hu Young , Yu Young-Jun , Kim Jin Tae , Kim Jin-Soo , Shin Jin-Wook , Cho Hyunsu , Choi Choon-Gi 
Published: April 2016

AbstractGraphene has been received a considerable amount of attention as a transparent conducting electrode (TCE) which may be able to replace indium tin oxide (ITO) to overcome the significant weakness of the poor flexibility of ITO. Given that graphene is the thinnest 2-dimensional (2D) material known, it shows extremely high flexibility, and its lateral periodic honeycomb structure of sp2-bonded carbon atoms enables ~2.3% of incident light absorption per layer. However, there is a trade-off between the electrical resistance and the optical transmittance, and the fixed absorption rate in graphene limits is use when fabricating devices. Therefore, a more efficient method which continuously controls the optical and electrical properties of graphene is needed. Here, we introduce a method which controls the optical transmittance and the electrical resistance of graphene through various thicknesses of the top Cu layers with a Cu/Ni metal catalyst structure used to fabricate a planar mesh pattern of single and multi-layer graphene. We exhibit a continuous transmittance change from 85% (MLG) to 97.6% (SLG) at an incident light wavelength of 550 nm on graphene samples simultaneously grown in a CVD quartz tube. We also investigate the relationships between the sheet resistances.
Simultaneous Determination of Size and Quantification of Gold Nanoparticles by Direct Coupling Thin layer Chromatography with Catalyzed Luminol Chemiluminescence
Authors: Yan Neng , Zhu Zhenli , He Dong , Jin Lanlan , Zheng Hongtao , Hu Shenghong 
Published: April 2016

AbstractThe increasing use of metal-based nanoparticle products has raised concerns in particular for the aquatic environment and thus the quantification of such nanomaterials released from products should be determined to assess their environmental risks. In this study, a simple, rapid and sensitive method for the determination of size and mass concentration of gold nanoparticles (AuNPs) in aqueous suspension was established by direct coupling of thin layer chromatography (TLC) with catalyzed luminol-H2O2 chemiluminescence (CL) detection. For this purpose, a moving stage was constructed to scan the chemiluminescence signal from TLC separated AuNPs. The proposed TLC-CL method allows the quantification of differently sized AuNPs (13 nm, 41 nm and 100 nm) contained in a mixture. Various experimental parameters affecting the characterization of AuNPs, such as the concentration of H2O2, the concentration and pH of the luminol solution, and the size of the spectrometer aperture were investigated. Under optimal conditions, the detection limits for AuNP size fractions of 13 nm, 41 nm and 100 nm were 38.4 μg L−1, 35.9 μg L−1 and 39.6 μg L−1, with repeatabilities (RSD, n = 7) of 7.3%, 6.9% and 8.1% respectively for 10 mg L−1 samples. The proposed method was successfully applied to the characterization of AuNP size and concentration in aqueous test samples.