bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrogen Sulphide Treatment Increases Insulin Sensitivity and Improves Oxidant Metabolism through the CaMKKbeta-AMPK Pathway in PA-Induced IR C2C12 Cells
Authors: Chen Xubo , Zhao Xueyan , Lan Fazhang , Zhou Tao , Cai Hua , Sun Haiying , Kong Weijia , Kong Wen 
Published: October 2017

AbstractStudies have reported attenuation of insulin resistance (IR) by improving phosphorylation of the insulin signalling pathway. However, the upstream molecular signalling pathway is still elusive. In this study, Western blot was used to evaluate the phosphorylation level of the insulin signalling pathway and the AMPK pathway. 2-NBDG was used to evaluate glucose uptake. Ca2+ imaging was used to assess change of intracellular Ca2+ concentration. We found that NaHS enhanced the intracellular Ca2+ concentration and glucose uptake and activated the insulin signalling cascade in a palmitic acid (PA)-induced IR model in C2C12 cells. Furthermore, activation of the IRS1/PI3K/AKT pathway and glucose uptake were decreased when AMPK or CaMKKβ was inhibited. Our study also showed that the mitochondrial electron transport chain, ATP production, and intramitochondrial cAMP declined in the IR model but that this effect was reversed by NaHS, an effect that may be mediated by the Ca2+/CaMKK2/AMPK and PI3K/AKT pathways. Our data indicate that H2S improves activation of the insulin signalling cascade and glucose uptake via activation of the Ca2+/CaMKK2/AMPK pathway and mitochondrial metabolism in C2C12 cells. Furthermore, NaHS protects mitochondrial function and maintains normal ATP production by activating the cAMP system and the Ca2+/CaMKK2/AMPK and PI3K/ATK pathways.
Controlling the Quantum State with a time varying potential
Authors: Carrasco Sebastián , Rogan José , Valdivia Juan Alejandro 
Published: October 2017

AbstractThe problem of controlling the quantum state of a system is investigated using a time varying potential. As a concrete example we study the problem of a particle in a box with a periodically oscillating infinite square-well potential, from which we obtain results that can be applied to systems with periodically oscillating boundary conditions. We derive an analytic expression for the frequencies of resonance between states, and against standard intuition, we show how to use this behavior to control the quantum state of the system at will. In particular, we offer as an example the transition from the ground state to the first excited state of the square well potential. At first sight, it may be counter intuitive that we can control the state of such a quantum Hamiltonian, as the Schrödinger equation conserves the norm of the wave function. In this manuscript, we show how that can be achieved.
Analysis of Nkx3.1:Cre-driven Erk5 deletion reveals a profound spinal deformity which is linked to increased osteoclast activity
Authors: Loveridge Carolyn J. , van ’t Hof Rob J. , Charlesworth Gemma , King Ayala , Tan Ee Hong , Rose Lorraine , Daroszewska Anna , Prior Amanda , Ahmad Imran , Welsh Michelle , Mui Ernest J. , Ford Catriona , Salji Mark , Sansom Owen , Blyth Karen , Leung Hing Y. 
Published: October 2017

AbstractExtracellular signal-regulated protein kinase 5 (ERK5) has been implicated during development and carcinogenesis. Nkx3.1-mediated Cre expression is a useful strategy to genetically manipulate the mouse prostate. While grossly normal at birth, we observed an unexpected phenotype of spinal protrusion in Nkx3.1:Cre;Erk5fl/fl (Erk5fl/fl) mice by ~6–8 weeks of age. X-ray, histological and micro CT (µCT) analyses showed that 100% of male and female Erk5fl/fl mice had a severely deformed curved thoracic spine, with an associated loss of trabecular bone volume. Although sex-specific differences were observed, histomorphometry measurements revealed that both bone resorption and bone formation parameters were increased in male Erk5fl/fl mice compared to wild type (WT) littermates. Osteopenia occurs where the rate of bone resorption exceeds that of bone formation, so we investigated the role of the osteoclast compartment. We found that treatment of RANKL-stimulated primary bone marrow-derived macrophage (BMDM) cultures with small molecule ERK5 pathway inhibitors increased osteoclast numbers. Furthermore, osteoclast numbers and expression of osteoclast marker genes were increased in parallel with reduced Erk5 expression in cultures generated from Erk5fl/fl mice compared to WT mice. Collectively, these results reveal a novel role for Erk5 during bone maturation and homeostasis in vivo.
Effects of charge-modifying mutations in histone H2A α3-domain on nucleosome stability assessed by single-pair FRET and MD simulations
Authors: Lehmann Kathrin , Zhang Ruihan , Schwarz Nathalie , Gansen Alexander , Mücke Norbert , Langowski Jörg , Toth Katalin 
Published: October 2017

AbstractNucleosomes are important for chromatin compaction and gene regulation; their integrity depends crucially on the structural properties of the histone tails. Recent all-atom molecular dynamics simulations revealed that removal of the N-terminal tails of histone H3, known to destabilize nucleosomes, causes a rearrangement of two arginines of histone H2A, namely R81 and R88 by altering the electrostatic environment of the H2A α3 domain. Whether this rearrangement is the cause or the effect of decreased stability, is unclear. Here, we emulate the altered electrostatic environment that was found after H3 tail clipping through charge-modifying mutations to decouple its impact on intranucleosomal interactions from that of the histone tails. Förster resonance energy transfer experiments on recombinant nucleosomes and all-atom molecular dynamics simulations reveal a compensatory role of those amino acids in nucleosome stability. The simulations indicate a weakened interface between H2A-H2B dimers and the (H3-H4)2 tetramer, as well as between dimers and DNA. These findings agree with the experimental observations of position and charge dependent decreased nucleosome stability induced by the introduced mutations. This work highlights the importance of the H2A α3 domain and suggests allosteric effects between this domain and the outer DNA gyre as well as the H3 N-terminal tail.
Anti-Infective Effect of Adhesive Probiotic Lactobacillus in Fish is Correlated With Their Spatial Distribution in the Intestinal Tissue
Authors: He Suxu , Ran Chao , Qin Chubin , Li Shuning , Zhang Hongling , de Vos Willem M. , Ringø Einar , Zhou Zhigang 
Published: October 2017

AbstracrIn this study, we tested the distribution of 49 Lactobacillus strains in the mucus and mucosa of the intestine tissue of zebrafish. We observed a progressive change in the spatial distribution of Lactobacillus strains, and suggested a division of the strains into three classes: mucus type (>70% in mucus), mucosa type (>70% in mucosa) and hybrid type (others). The hybrid type strains were more efficient in protection of zebrafish against Aeromonas hydrophila infection. Three strains representing different distribution types (JCM1149, CGMCC1.2028, and JCM 20300) were selected. The mucosa type strain JCM1149 induced higher intestinal expression of inflammatory cytokines and Hsp70 than the other strains. Furthermore, we used L. rhamnosus GG and its mutant (PB22) lacking SpaCBA pili to investigate the influence of pili on spatial distribution. LGG showed a mucosa type distribution, while PB22 revealed a hybrid distribution and the disease protection was accordingly improved. The different protection ability between LGG and PB22 did not involve the intestinal microbiota, however, LGG induced injury to the mucosa of zebrafish. Collectively, the disease protection activity of Lactobacillus in zebrafish is correlated with their spatial distribution in the intestinal tissue, with strains showing a balanced distribution (hybrid type) more efficient in protection.
Barocaloric effect on graphene
Authors: Ma Ning , Reis Mario S. 
Published: October 2017

AbstractWe describe how mechanical strain is able to control the flow of heat on a graphene sheet, since this material can either absorb or expel heat from/to a thermal reservoir, depending on the strain energy. In a similar fashion as the magneto- and electro-caloric effects, the present case considers the fact that a mechanical strain produces a pseudo-magnetic field that, on its turn, is responsible for the barocaloric effect. This result pushes graphene to the list of multicaloric materials.
Phylogenetic analysis of the metazoan carotenoid oxygenase superfamily: a new ancestral gene assemblage of BCO-like (BCOL) proteins
Authors: Poliakov Eugenia , Soucy Joseph , Gentleman Susan , Rogozin Igor B. , Redmond T. Michael 
Published: October 2017

AbstractHere we describe a new family of carotenoid cleavage oxygenases (CCOs) in metazoans, the BCO2-like (BCOL) clade, which contains lancelet, nematode, and molluscan carotenoid oxygenase sequences. Phylogenetic analysis of CCOs in all kingdoms of life confirmed that the BCOL enzymes are an independent clade of ancient origin. One of the predicted lancelet BCOL proteins, cloned and analyzed for carotenoid cleavage activity in a bacterial carotenoid expression system, had activity similar to lancelet BCO2 proteins, although with a preference forcis isomers. Our docking predictions correlated well with thecis-favored activity. The extensive expansions of the new animal BCOL family in some species (e.g., lancelet) suggests that the carotenoid cleavage oxygenase superfamily has evolved in the “extremely high turnover” fashion: numerous losses and duplications of this family are likely to reflect complex regulation processes during development, and interactions with the environment. These findings also serve to provide a rationale for the evolution of the BCO-related outlier RPE65 retinol isomerase, an enzyme that does not utilize carotenoids as substrate or perform double-bond cleavage.
The major outer sheath protein forms distinct conformers and multimeric complexes in the outer membrane and periplasm of Treponema denticola
Authors: Puthenveetil Robbins , Kumar Sanjiv , Caimano Melissa J. , Dey Abhishek , Anand Arvind , Vinogradova Olga , Radolf Justin D. 
Published: October 2017

AbstractThe major outer sheath protein (MOSP) is a prominent constituent of the cell envelope of Treponema denticola (TDE) and one of its principal virulence determinants. Bioinformatics predicts that MOSP consists of N- and C-terminal domains, MOSPN and MOSPC. Biophysical analysis of constructs refolded in vitro demonstrated that MOSPC, previously shown to possess porin activity, forms amphiphilic trimers, while MOSPN forms an extended hydrophilic monomer. In TDE and E. coli expressing MOSP with a PelB signal sequence (PelB-MOSP), MOSPC is OM-embedded and surface-exposed, while MOSPN resides in the periplasm. Immunofluorescence assay, surface proteolysis, and novel cell fractionation schemes revealed that MOSP in TDE exists as outer membrane (OM) and periplasmic trimeric conformers; PelB-MOSP, in contrast, formed only OM-MOSP trimers. Although both conformers form hetero-oligomeric complexes in TDE, only OM-MOSP associates with dentilisin. Mass spectrometry (MS) indicated that OM-MOSP interacts with proteins in addition to dentilisin, most notably, oligopeptide-binding proteins (OBPs) and the β-barrel of BamA. MS also identified candidate partners for periplasmic MOSP, including TDE1658, a spirochete-specific SurA/PrsA ortholog. Collectively, our data suggest that MOSP destined for the TDE OM follows the canonical BAM pathway, while formation of a stable periplasmic conformer involves an export-related, folding pathway not present in E. coli.
Human rickettsial pathogen modulates arthropod organic anion transporting polypeptide and tryptophan pathway for its survival in ticks
Authors: Taank Vikas , Dutta Shovan , Dasgupta Amrita , Steeves Tanner K. , Fish Durland , Anderson John F. , Sultana Hameeda , Neelakanta Girish 
Published: October 2017

AbstractThe black-legged tick Ixodes scapularis transmits the human anaplasmosis agent, Anaplasma phagocytophilum. In this study, we show that A. phagocytophilum specifically up-regulates I. scapularis organic anion transporting polypeptide, isoatp4056 and kynurenine amino transferase (kat), a gene involved in the production of tryptophan metabolite xanthurenic acid (XA), for its survival in ticks. RNAi analysis revealed that knockdown of isoatp4056 expression had no effect on A. phagocytophilum acquisition from the murine host but affected the bacterial survival in tick cells. Knockdown of the expression of kat mRNA alone or in combination with isoatp4056 mRNA significantly affected A. phagocytophilum survival and isoatp4056 expression in tick cells. Exogenous addition of XA induces isoatp4056 expression and A. phagocytophilum burden in both tick salivary glands and tick cells. Electrophoretic mobility shift assays provide further evidence that A. phagocytophilum and XA influences isoatp4056 expression. Collectively, this study provides important novel information in understanding the interplay between molecular pathways manipulated by a rickettsial pathogen to survive in its arthropod vector.
Simultaneous visualisation of calcified bone microstructure and intracortical vasculature using synchrotron X-ray phase contrast-enhanced tomography
Authors: Núñez Juan A. , Goring Alice , Hesse Eric , Thurner Philipp J. , Schneider Philipp , Clarkin Claire E. 
Published: October 2017

Abstract3D imaging of the bone vasculature is of key importance in the understanding of skeletal disease. As blood vessels in bone are deeply encased in the calcified matrix, imaging techniques that are applicable to soft tissues are generally difficult or impossible to apply to the skeleton. While canals in cortical bone can readily be identified and characterised in X-ray computed tomographic data in 3D, the soft tissue comprising blood vessels that are putatively contained within the canal structures does not provide sufficient image contrast necessary for image segmentation. Here, we report an approach that allows for rapid, simultaneous visualisation of calcified bone tissue and the vasculature within the calcified bone matrix. Using synchrotron X-ray phase contrast-enhanced tomography we show exemplar data with intracortical capillaries uncovered at sub-micrometre level without the need for any staining or contrast agent. Using the tibiofibular junction of 15 week-old C57BL/6 mice post mortem, we show the bone cortical porosity simultaneously along with the soft tissue comprising the vasculature. Validation with histology confirms that we can resolve individual capillaries. This imaging approach could be easily applied to other skeletal sites and transgenic models, and could improve our understanding of the role the vasculature plays in bone disease.
The Incipient Motion Features of Sediment from Yangtze Estuary: Annular Flume Experiments
Authors: Wei Huang , Ya-kun Liu , Hua-lin Wu , Yuan-yang Wan 
Published: October 2017

AbstractIn this study, annular flume experiments are carried out, using the sediment samples collected from Yangtze estuary. The incipient velocity and the incipient shear stress of three different groups of median grain size of sediment are given. The turbulent kinetic energy method (TKE) is used to determine the bed shear stress (τ), by evaluating variations in the suspended sediment concentration (SSC) within the water column. The suspended sediment concentration increases with the increase of the bed shear stress. When the sediment concentration reaches a certain concentration, the rate of change in τ obviously slows down. As the concentration increasing again, the bed shear stress grows rapidly with different growth rate attributed to different grain size. The results of the experiments indicate that SSC and grain size have strong influence on τ.
Invariant nature of substituted element in metal-hexacyanoferrate
Authors: Niwa Hideharu , Kobayashi Wataru , Shibata Takayuki , Nitani Hiroaki , Moritomo Yutaka 
Published: October 2017

AbstractThe chemical substitution of a transition metal (M) is an effective method to improve the functionality of materials. In order to design the highly functional materials, we first have to know the local structure and electronic state around the substituted element. Here, we systematically investigated the local structure and electronic state of the host (Mh) and guest (Mg) transition metals in metal-hexacyanoferrate (M-HCF), Na
x
(Mh, Mg)[Fe(CN)6]
y
(1.40 < x < 1.60 and 0.85 < y < 0.90), by means of extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) analyses. The EXAFS and XANES analyses revealed that the local structure and electronic state around Mg are essentially the same as those in the pure compound, i.e, Mg-HCF. Such an invariant nature of Mg in M-HCF is in sharp contrast with that in layered oxide, in which the Mg valence changes so that local Mg-O distance (d
M-Og) approaches the Mh-O distance (d
M-Oh).
Estimation of the age of human bloodstains under the simulated indoor and outdoor crime scene conditions by ATR-FTIR spectroscopy
Authors: Lin Hancheng , Zhang Yinming , Wang Qi , Li Bing , Huang Ping , Wang Zhenyuan 
Published: October 2017

AbstractEstimation of the age of human bloodstains is of great importance in forensic practices, but it is a challenging task because of the lack of a well-accepted, reliable, and established method. Here, the attenuated total reflection (ATR)-Fourier transform infrared (FTIR) technique combined with advanced chemometric methods was utilized to determine the age of indoor and outdoor bloodstains up to 107 days. The bloodstain storage conditions mimicked crime scene scenarios as closely as possible. Two partial least squares regression models—indoor and outdoor models with 7–85 days—exhibited good performance for external validation, with low values of predictive root mean squared error (5.83 and 4.77) and high R2 values (0.94 and 0.96) and residual predictive deviation (4.08 and 5.14), respectively. Two partial least squares–discriminant analysis classification models were built and demonstrated excellent distinction between fresh (age ≤1 d) and older (age >1 d) bloodstains, which is highly valuable for forensic investigations. These findings demonstrate that ATR-FTIR spectroscopy coupled with advanced chemometric methods can be employed as a rapid and non-destructive tool for age estimation of bloodstains in real-world forensic investigation.
Structural and Morphological Evolution for Water-resistant Organic Thermoelectrics
Authors: Oh Hyeon Jin , Jang Jae Gyu , Kim Jong-Gyu , Hong Jong-In , Kim Jaeyun , Kwak Jeonghun , Kim Sung Hyun , Shin Seunghan 
Published: October 2017

AbstractWe systematically investigated the effect of 2,5-bis(2-hydroxy-3-methacryloyloxypropoxy)-1,4:3,6-dianhydro-sorbitol (Iso-GMA) with different concentrations on the structural and morphological evolution of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) containing a fixed volume of dimethyl sulfoxide (DMSO) to realize water-resistant organic thermoelectric devices. As an additive, Iso-GMA is a hydrophilic and crosslinking agent that can interact with PEDOT and PSS chains by hydrogen bonding and/or dipole-dipole- or dipole-charge-interaction. The Seebeck coefficient and power factor in the film incorporating 3.0 vol% DMSO and 0.8 vol% Iso-GMA were respectively 1.82 × 102 and 1.53 × 105% higher than those of the pristine PEDOT:PSS film without additives (DMSO and Iso-GMA). These results can be attributed to the self-assembled and crosslinked fibril networks with optimized phase separation, where the film has densely-packed PEDOT and highly lamellar-stacked PSS. Also, the reduced charge carrier concentration from the structural characteristics originated in the higher thermoelectric properties. We introduced the schematic illustration to understand the chemical bonding among the components and the morphological evolution according to the Iso-GMA concentration. The increased mechanical strength by the interchain stacking degree of PEDOT and the crosslinking of Iso-GMA facilitate the film remained in a water bath for 0.5 h without physical degradation, and sustain the thermoelectric properties during 12 h in humid conditons.
Interplay between the gold nanoparticle sub-cellular localization, size, and the photon energy for radiosensitization
Authors: Lechtman Eli , Pignol Jean-Philippe 
Published: October 2017

AbstractThere are large variations in the reported efficiency of gold nanoparticle (GNP) radiosensitization. We have previously reported on a predictive model, which accounts for the detailed Auger and photoelectron tracks to calculate the cell survival probability. After validating our model using PC-3 cells incubated with 2 mg/ml of 30 nm GNPs and irradiated with 100 kVp or 300 kVp beams, we evaluated the interplay between photon energy, GNP size (1.9 and 100 nm) and sub-cellular localization. Experiments were in excellent agreement with the model. In predictive modeling, using a 100 kVp source and 1.9 nm nanoparticles, GNP localization had a significant impact on cell survival. A sensitizer enhancement ratio of 1.34 was achieved when GNPs were localized outside the cells, increasing to 2.56 when GNPs were also distributed in the cytoplasm and nucleus. Using a 300 kVp source, which emits photons mainly above the gold K-edge, the dependence on GNP localization and size was barely detectable, since long ranged electrons dominate the energy deposition. In summary, achieving intracellular uptake with targeted-GNPs can significantly enhance radiosensitization for photon energies below the gold K-edge, where Auger electrons contribute significantly to the local energy deposition. For higher energies, this is much less important.
Graphene-based nanolaminates as ultra-high permeation barriers
Authors: Sagade Abhay A. , Aria Adrianus I. , Edge Steven , Melgari Paolo , Gieseking Bjoern , Bayer Bernhard C. , Meyer Jannik C. , Bird David , Brewer Paul , Hofmann Stephan 
Published: October 2017

AbstractPermeation barrier films are critical to a wide range of applications. In particular, for organic electronics and photovoltaics not only ultra-low permeation values are required but also optical transparency. A laminate structure thereby allows synergistic effects between different materials. Here, we report on a combination of chemical vapor deposition (CVD) and atomic layer deposition (ALD) to create in scalable fashion few-layer graphene/aluminium oxide-based nanolaminates. The resulting ~10 nm contiguous, flexible graphene-based films are >90% optically transparent and show water vapor transmission rates below 7 × 10−3 g/m2/day measured over areas of 5 × 5 cm2. We deploy these films to provide effective encapsulation for organic light-emitting diodes (OLEDs) with measured half-life times of 880 h in ambient.
Whole genome DNA methylation sequencing of the chicken retina, cornea and brain
Authors: Lee Isac , Rasoul Bejan A. , Holub Ashton S. , Lejeune Alannah , Enke Raymond A. , Timp Winston 
Published: October 2017

AbstractWhole genome bisulfite sequencing (WGBS) analysis of DNA methylation uses massively parallel next generation sequencing technology to characterize global epigenetic patterns and fluctuations throughout a range of tissue samples. Development of the vertebrate retina is thought to involve extensive epigenetic reprogramming during embryogenesis. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal methylome. Here we used Illumina WGBS analysis to characterize genome-wide patterns of DNA methylation in the developing chicken retina as well as cornea and brain in an effort to further our understanding of retina-specific epigenetic regulation. These data will be valuable to the vision research community for correlating global changes in DNA methylation to differential gene expression between ocular and neural tissues during critical developmental time points of retinogenesis in the chicken retina.