bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph distance for complex networks
Authors: Shimada Yutaka , Hirata Yoshito , Ikeguchi Tohru , Aihara Kazuyuki 
Published: October 2016

AbstractNetworks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions.
Highly stable, extremely high-temperature, nonvolatile memory based on resistance switching in polycrystalline Pt nanogaps
Authors: Suga Hiroshi , Suzuki Hiroya , Shinomura Yuma , Kashiwabara Shota , Tsukagoshi Kazuhito , Shimizu Tetsuo , Naitoh Yasuhisa 
Published: October 2016

AbstractHighly stable, nonvolatile, high-temperature memory based on resistance switching was realized using a polycrystalline platinum (Pt) nanogap. The operating temperature of the memory can be drastically increased by the presence of a sharp-edged Pt crystal facet in the nanogap. A short distance between the facet edges maintains the nanogap shape at high temperature, and the sharp shape of the nanogap densifies the electric field to maintain a stable current flow due to field migration. Even at 873 K, which is a significantly higher temperature than feasible for conventional semiconductor memory, the nonvolatility of the proposed memory allows stable ON and OFF currents, with fluctuations of less than or equal to 10%, to be maintained for longer than eight hours. An advantage of this nanogap scheme for high-temperature memory is its secure operation achieved through the assembly and disassembly of a Pt needle in a high electric field.
Swiss identity smells like chocolate: Social identity shapes olfactory judgments
Authors: Coppin Géraldine , Pool Eva , Delplanque Sylvain , Oud Bastiaan , Margot Christian , Sander David , Van Bavel Jay J. 
Published: October 2016

AbstractThere is extensive evidence that social identities can shape people’s attitudes and behavior, but what about sensory judgments? We examined the possibility that social identity concerns may also shape the judgment of non-social properties—namely, olfactory judgment. In two experiments, we presented Swiss and non-Swiss participants with the odor of chocolate, for which Switzerland is world-famous, and a control odor (popcorn). Swiss participants primed with Swiss identity reported the odor of chocolate (but not popcorn) as more intense than non-Swiss participants (Experiments 1 and 2) and than Swiss participants primed with individual identity or not primed (Experiment 2). The self-reported intensity of chocolate smell tended to increase as identity accessibility increased—but only among Swiss participants (Experiment 1). These results suggest that identity priming can counter-act classic sensory habituation effects, allowing identity-relevant smells to maintain their intensity after repeated presentations. This suggests that social identity dynamically influences sensory judgment. We discuss the potential implications for models of social identity and chemosensory perception.
Quantitative analysis of hydrogen sites and occupancy in deep mantle hydrous wadsleyite using single crystal neutron diffraction
Authors: Purevjav Narangoo , Okuchi Takuo , Tomioka Naotaka , Wang Xiaoping , Hoffmann Christina 
Published: October 2016

AbstractEvidence from seismological and mineralogical studies increasingly indicates that water from the oceans has been transported to the deep earth to form water-bearing dense mantle minerals. Wadsleyite [(Mg, Fe2+)2SiO4] has been identified as one of the most important host minerals incorporating this type of water, which is capable of storing the entire mass of the oceans as a hidden reservoir. To understand the effects of such water on the physical properties and chemical evolution of Earth’s interior, it is essential to determine where in the crystal structure the hydration occurs and which chemical bonds are altered and weakened after hydration. Here, we conduct a neutron time-of-flight single-crystal Laue diffraction study on hydrous wadsleyite. Single crystals were grown under pressure to a size suitable for the experiment and with physical qualities representative of wet, deep mantle conditions. The results of this neutron single crystal diffraction study unambiguously demonstrate the method of hydrogen incorporation into the wadsleyite, which is qualitatively different from that of its denser polymorph, ringwoodite, in the wet mantle. The difference is a vital clue towards understanding why these dense mantle minerals show distinctly different softening behaviours after hydration.
The unravelling of the complex pattern of tyrosinase inhibition
Authors: Deri Batel , Kanteev Margarita , Goldfeder Mor , Lecina Daniel , Guallar Victor , Adir Noam , Fishman Ayelet 
Published: October 2016

AbstractTyrosinases are responsible for melanin formation in all life domains. Tyrosinase inhibitors are used for the prevention of severe skin diseases, in skin-whitening creams and to avoid fruit browning, however continued use of many such inhibitors is considered unsafe. In this study we provide conclusive evidence of the inhibition mechanism of two well studied tyrosinase inhibitors, KA (kojic acid) and HQ (hydroquinone), which are extensively used in hyperpigmentation treatment. KA is reported in the literature with contradicting inhibition mechanisms, while HQ is described as both a tyrosinase inhibitor and a substrate. By visualization of KA and HQ in the active site of TyrBm crystals, together with molecular modeling, binding constant analysis and kinetic experiments, we have elucidated their mechanisms of inhibition, which was ambiguous for both inhibitors. We confirm that while KA acts as a mixed inhibitor, HQ can act both as a TyrBm substrate and as an inhibitor.
Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition
Authors: Choi Sung-Jin , Ban Changill 
Published: October 2016

AbstractStructural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base–phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.
Cleaning patch-clamp pipettes for immediate reuse
Authors: Kolb I. , Stoy W. A. , Rousseau E. B. , Moody O. A. , Jenkins A. , Forest C. R. 
Published: October 2016

AbstractPatch-clamp recording has enabled single-cell electrical, morphological and genetic studies at unparalleled resolution. Yet it remains a laborious and low-throughput technique, making it largely impractical for large-scale measurements such as cell type and connectivity characterization of neurons in the brain. Specifically, the technique is critically limited by the ubiquitous practice of manually replacing patch-clamp pipettes after each recording. To circumvent this limitation, we developed a simple, fast, and automated method for cleaning glass pipette electrodes that enables their reuse within one minute. By immersing pipette tips into Alconox, a commercially-available detergent, followed by rinsing, we were able to reuse pipettes 10 times with no degradation in signal fidelity, in experimental preparations ranging from human embryonic kidney cells to neurons in culture, slices, and in vivo. Undetectable trace amounts of Alconox remaining in the pipette after cleaning did not affect ion channel pharmacology. We demonstrate the utility of pipette cleaning by developing the first robot to perform sequential patch-clamp recordings in cell culture and in vivo without a human operator.
Global metabolomics reveals potential urinary biomarkers of esophageal squamous cell carcinoma for diagnosis and staging
Authors: Xu Jing , Chen Yanhua , Zhang Ruiping , He Jiuming , Song Yongmei , Wang Jingbo , Wang Huiqing , Wang Luhua , Zhan Qimin , Abliz Zeper 
Published: October 2016

AbstractWe performed a metabolomics study using liquid chromatography-mass spectrometry (LC-MS) combined with multivariate data analysis (MVDA) to discriminate global urine profiles in urine samples from esophageal squamous cell carcinoma (ESCC) patients and healthy controls (NC). Our work evaluated the feasibility of employing urine metabolomics for the diagnosis and staging of ESCC. The satisfactory classification between the healthy controls and ESCC patients was obtained using the MVDA model, and obvious classification of early-stage and advanced-stage patients was also observed. The results suggest that the combination of LC-MS analysis and MVDA may have potential applications for ESCC diagnosis and staging. We then conducted LC-MS/MS experiments to identify the potential biomarkers with large contributions to the discrimination. A total of 83 potential diagnostic biomarkers for ESCC were screened out, and 19 potential biomarkers were identified; the variations between the differences in staging using these potential biomarkers were further analyzed. These biomarkers may not be unique to ESCCs, but instead result from any malignant disease. To further elucidate the pathophysiology of ESCC, we studied related metabolic pathways and found that ESCC is associated with perturbations of fatty acid β-oxidation and the metabolism of amino acids, purines, and pyrimidines.
Good Biocompatibility and Sintering Properties of Zirconia Nanoparticles Synthesized via Vapor-phase Hydrolysis
Authors: Wang Jigang , Yin Wenyan , He Xiao , Wang Qiang , Guo Ming , Chen Shaowei 
Published: October 2016

AbstractZrO2 nanoparticles were synthesized by a vapor-phase hydrolysis process, and characterized in terms of crystalline structures, hardness and microstructures by X-ray diffraction, Vickers hardness test method, and atomic force microscopy (AFM) measurements. Moreover, in vitro cytotoxicity evaluation and hemolysis assay showed that the nanoparticles possessed good biocompatibility. Hardness investigations and AFM measurements indicated that both the sintering temperature and compression force played an important role in determining the physical behaviors (hardness, roughness and density) of flakes of the ZrO2 nanoparticles. When ZrO2 nanoparticles synthesized at 500 °C were pressed into flakes under 6 MPa and sintered at 1400 °C, the resulting flakes exhibited an optimal combination of hardness (534.58 gf·mm−2), roughness (0.07 μm) and density (4.41 g·cm−3). As the Vickers hardness value of human bones is of 315~535 gf·mm−2 and the density of adult femuris about 1.3~1.7 g·cm−3, the experimental results showed that the ZrO2 flakes were comparable to human bones with a higher density. As a result, the synthesized ZrO2 NPs may be useful for biomedical applications, especially for bone repair and replacement in future.
Microstructural characterization of random packings of cubic particles
Authors: Malmir Hessam , Sahimi Muhammad , Tabar M. Reza Rahimi 
Published: October 2016

AbstractUnderstanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders. In addition, packing of cubic salt crystals arise in various problems involving preservation of pavements, paintings, and historical monuments, mineral-fluid interactions, CO2 sequestration in rock, and intrusion of groundwater aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We have developed a version of the random sequential addition algorithm to generate such packings, and have computed a variety of microstructural descriptors, including the radial distribution function, two-point probability function, orientational correlation function, specific surface, and mean chord length, and have studied the effect of finite system size and porosity on such characteristics. The results indicate the existence of both spatial and orientational long-range order in the packing, which is more distinctive for higher packing densities. The maximum packing fraction is about 0.57.
Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River
Authors: Wang Wenhui , Wang Hui , Feng Youzhi , Wang Lei , Xiao Xingji , Xi Yunguan , Luo Xue , Sun Ruibo , Ye Xianfeng , Huang Yan , Zhang Zhengguang , Cui Zhongli 
Published: October 2016

AbstractSoil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compared with conventional farming, organic farming significantly increased soil nutrients, soil enzyme activities, and bacterial richness and diversity. A Venn diagram and principal component analysis revealed that the soils with 3 different crops under organic farming have more number and percent of shared OTUs (operational taxonomic units), and shared a highly similar microbial community structure. Under organic farming, several predominant guilds and major bacterial lineages (Rhizobiales, Thiotrichaceae, Micromonosporaceae, Desulfurellaceae and Myxococcales) contributing to nutrient (C, N, S and P) cycling were enriched, whereas the relative abundances of acid and alkali resistant microorganisms (Acidobacteriaceae and Sporolactobacillaceae) were increased under conventional farming practices. Our results indicated that, for all three crops, organic farming have a more stable microflora and the uniformity of the bacterial community structure. Organic agriculture significantly increased the abundance of some nutrition-related bacteria, while reducing some of the abundance of acid and alkali resistant bacteria.
Safety Evaluation and Imaging Properties of Gadolinium-Based Nanoparticles in nonhuman primates
Authors: Kotb Shady , Piraquive Joao , Lamberton Franck , Lux François , Verset Michael , Di Cataldo Vanessa , Contamin Hugues , Tillement Olivier , Canet-Soulas Emmanuelle , Sancey Lucie 
Published: October 2016

AbstractIn this article, we report the safety evaluation of gadolinium-based nanoparticles in nonhuman primates (NHP) in the context of magnetic resonance imaging (MRI) studies in atherosclerosis bearing animals and healthy controls. In healthy NHP, the pharmacokinetics and toxicity profiles demonstrated the absence of dose, time, and sex-effects, as well as a suitable tolerance of intravenous administration of the nanoparticles. We investigated their imaging properties for arterial plaque imaging in a standard diet or a high cholesterol diet NHP, and compared their characteristics with clinically applied Gd-chelate. This preliminary investigation reports the efficient and safe imaging of atherosclerotic plaques.
Three-dimensional X-ray visualization of axonal tracts in mouse brain hemisphere
Authors: Mizutani Ryuta , Saiga Rino , Ohtsuka Masato , Miura Hiromi , Hoshino Masato , Takeuchi Akihisa , Uesugi Kentaro 
Published: October 2016

AbstractNeurons transmit active potentials through axons, which are essential for the brain to function. In this study, the axonal networks of the murine brain were visualized with X-ray tomographic microscopy, also known as X-ray microtomography or micro-CT. Murine brain samples were freeze-dried to reconstitute the intrinsic contrast of tissue constituents and subjected to X-ray visualization. A whole brain hemisphere visualized by absorption contrast illustrated three-dimensional structures including those of the striatum, corpus callosum, and anterior commissure. Axonal tracts observed in the striatum start from the basal surface of the cerebral cortex and end at various positions in the basal ganglia. The distribution of X-ray attenuation coefficients indicated that differences in water and phospholipid content between the myelin sheath and surrounding tissue constituents account for the observed contrast. A rod-shaped cutout of brain tissue was also analyzed with a phase retrieval method, wherein tissue microstructures could be resolved with up to 2.7 μm resolution. Structures of axonal networks of the striatum were reconstructed by tracing axonal tracts. Such an analysis should be able to delineate the functional relationships of the brain regions involved in the observed network.
Three-dimensional electron microscopy reveals the evolution of glomerular barrier injury
Authors: Randles Michael J. , Collinson Sophie , Starborg Tobias , Mironov Aleksandr , Krendel Mira , Königshausen Eva , Sellin Lorenz , Roberts Ian S. D. , Kadler Karl E. , Miner Jeffrey H. , Lennon Rachel 
Published: October 2016

AbstractGlomeruli are highly sophisticated filters and glomerular disease is the leading cause of kidney failure. Morphological change in glomerular podocytes and the underlying basement membrane are frequently observed in disease, irrespective of the underlying molecular etiology. Standard electron microscopy techniques have enabled the identification and classification of glomerular diseases based on two-dimensional information, however complex three-dimensional ultrastructural relationships between cells and their extracellular matrix cannot be easily resolved with this approach. We employed serial block face-scanning electron microscopy to investigate Alport syndrome, the commonest monogenic glomerular disease, and compared findings to other genetic mouse models of glomerular disease (Myo1e−/−, Ptpro−/−). These analyses revealed the evolution of basement membrane and cellular defects through the progression of glomerular injury. Specifically we identified sub-podocyte expansions of the basement membrane with both cellular and matrix gene defects and found a corresponding reduction in podocyte foot process number. Furthermore, we discovered novel podocyte protrusions invading into the glomerular basement membrane in disease and these occurred frequently in expanded regions of basement membrane. These findings provide new insights into mechanisms of glomerular barrier dysfunction and suggest that common cell-matrix-adhesion pathways are involved in the progression of disease regardless of the primary insult.
Microfluidics-based point-of-care test for serodiagnosis of Lyme Disease
Authors: Nayak Samiksha , Sridhara Archana , Melo Rita , Richer Luciana , Chee Natalie H. , Kim Jiyoon , Linder Vincent , Steinmiller David , Sia Samuel K. , Gomes-Solecki Maria 
Published: October 2016

AbstractCurrently, diagnostic testing for Lyme disease is done by determination of the serologic responses to Borrelia burgdorferi antigens, with the exception of the early localized phase of disease where diagnosis must be done clinically. Here, we describe the use of microfluidics technology to develop a multiplexed rapid lab-on-a-chip point of care (POC) assay for the serologic diagnosis of human Lyme disease. Following ELISA screening of 12 candidate antigens, we tested 8 on a microfluidic diagnostic system, called mChip-Ld, using a set of 60 serological samples. The mChip-Ld test, which can be performed in 15 minutes at the point of care, showed promising performance for detection of antibodies to B. burgdorferi using the PPO triplex test (rP100 + PepVF + rOspC-K, AUC of 0.844) compared to a gold-standard reference of culture confirmed clinical samples. The performance is comparable to the commonly used C6 peptide by lab-based ELISA. In addition, the mChip-Ld test showed promising performance for early-stage diagnosis of the disease using the antigen OspC-K (sensitivity and specificity of 84% and 92%, respectively; AUC of 0.877). Overall, this study underscores the potential of using microfluidics to aid the diagnosis of Lyme disease at the point of care.
RAMAN spectroscopy imaging improves the diagnosis of papillary thyroid carcinoma
Authors: Rau Julietta V. , Graziani Valerio , Fosca Marco , Taffon Chiara , Rocchia Massimiliano , Crucitti Pierfilippo , Pozzilli Paolo , Onetti Muda Andrea , Caricato Marco , Crescenzi Anna 
Published: October 2016

AbstractRecent investigations strongly suggest that Raman spectroscopy (RS) can be used as a clinical tool in cancer diagnosis to improve diagnostic accuracy. In this study, we evaluated the efficiency of Raman imaging microscopy to discriminate between healthy and neoplastic thyroid tissue, by analyzing main variants of Papillary Thyroid Carcinoma (PTC), the most common type of thyroid cancer. We performed Raman imaging of large tissue areas (from 100 × 100 μm2 up to 1 × 1 mm2), collecting 38 maps containing about 9000 Raman spectra. Multivariate statistical methods, including Linear Discriminant Analysis (LDA), were applied to translate Raman spectra differences between healthy and PTC tissues into diagnostically useful information for a reliable tissue classification. Our study is the first demonstration of specific biochemical features of the PTC profile, characterized by significant presence of carotenoids with respect to the healthy tissue. Moreover, this is the first evidence of Raman spectra differentiation between classical and follicular variant of PTC, discriminated by LDA with high efficiency. The combined histological and Raman microscopy analyses allow clear-cut integration of morphological and biochemical observations, with dramatic improvement of efficiency and reliability in the differential diagnosis of neoplastic thyroid nodules, paving the way to integrative findings for tumorigenesis and novel therapeutic strategies.