bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turning behaviors of T cells climbing up ramp-like structures are regulated by myosin light chain kinase activity and lamellipodia formation
Authors: Song Kwang Hoon , Lee Jaehyun , Jung Hong-Ryul , Park HyoungJun , Doh Junsang 
Published: September 2017

AbstractT cells navigate diverse microenvironments to perform immune responses. Micro-scale topographical structures within the tissues, which may inherently exist in normal tissues or may be formed by inflammation or injury, can influence T cell migration, but how T cell migration is affected by such topographical structures have not been investigated. In this study, we fabricated ramp-like structures with a 5 μm height and various slopes, and observed T cells climbing up the ramp-like structures. T cells encountering the ramp-like structures exhibited MLC accumulation near head-tail junctions contacting the ramp-like structures, and made turns to the direction perpendicular to the ramp-like structures. Pharmacological study revealed that lamellipodia formation mediated by arp2/3 and contractility regulated by myosin light chain kinase (MLCK) were responsible for the intriguing turning behavior of T cells climbing the ramp-like structures. Arp2/3 or MLCK inhibition substantially reduced probability of T cells climbing sharp-edged ramp-like structures, indicating intriguing turning behavior of T cells mediated by lamellipodia formation and MLCK activity may be important for T cells to access inflamed or injured tissues with abrupt topographical changes.
Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis
Authors: Giardina Giorgio , Paiardini Alessandro , Montioli Riccardo , Cellini Barbara , Voltattorni Carla Borri , Cutruzzolà Francesca 
Published: September 2017

AbstractThe alanine:glyoxylate aminotransferase (AGT), a hepatocyte-specific pyridoxal-5′-phosphate (PLP) dependent enzyme, transaminates L-alanine and glyoxylate to glycine and pyruvate, thus detoxifying glyoxylate and preventing pathological oxalate precipitation in tissues. In the widely accepted catalytic mechanism of the aminotransferase family, the lysine binding to PLP acts as a catalyst in the stepwise 1,3-proton transfer, interconverting the external aldimine to ketimine. This step requires protonation by a conserved aspartate of the pyridine nitrogen of PLP to enhance its ability to stabilize the carbanionic intermediate. The aspartate residue is also responsible for a significant geometrical distortion of the internal aldimine, crucial for catalysis. We present the structure of human AGT in which complete X-ray photoreduction of the Schiff base has occurred. This result, together with two crystal structures of the conserved aspartate pathogenic variant (D183N) and the molecular modeling of the transaldimination step, led us to propose that an interplay of opposite forces, which we named spring mechanism, finely tunes PLP geometry during catalysis and is essential to move the external aldimine in the correct position in order for the 1,3-proton transfer to occur.
Hybrid Ag nanowire transparent conductive electrodes with randomly oriented and grid-patterned Ag nanowire networks
Authors: Ha Bonhee , Jo Sungjin 
Published: September 2017

AbstractTo improve the electrical properties of silver nanowire (Ag NW) transparent conductive electrodes (TCEs), the density of Ag NW networks should be increased, to increase the number of percolation paths. However, because of the inverse relationship between optical transmittance and electrical resistivity, the optical properties of Ag NW TCEs deteriorate with increasing density of the Ag NW network. In this study, a hybrid Ag NW electrode composed of randomly oriented and grid-patterned Ag NW networks is demonstrated. The hybrid Ag NW electrodes exhibit significantly improved sheet resistances and slightly decreased transmittances compared to randomly oriented Ag NW networks. Hybrid Ag NW TCEs show excellent mechanical flexibilities and durabilities in bending tests with a 5 mm radius of curvature. Moreover, flexible transparent film heaters (TFHs) based on the hybrid Ag NW electrodes show elevated maximum temperatures relative to TFHs based on randomly oriented Ag NW electrodes, when operated at the same input voltages.
Comparative analysis reveals regulatory motifs at the ainS/ainR pheromone-signaling locus of Vibrio fischeri
Authors: Kimbrough John H. , Stabb Eric V. 
Published: September 2017

AbstractVibrio fischeri uses the AinS/AinR pheromone-signaling system to control bioluminescence and other symbiotic colonization factors. The Ain system is thought to initiate cell-cell signaling at moderate cell densities and to prime the LuxI/LuxR signaling system. Here we compared and analyzed the ain locus from two V. fischeri strains and a Vibrio salmonicida strain to explore ain regulation. The ainS and ainR genes were predicted to constitute an operon, which we corroborated using RT-PCR. Comparisons between strains revealed a stark area of conservation across the ainS-ainR junction, including a large inverted repeat in ainR. We found that this inverted repeat in cis can affect accumulation of the AinS-generated pheromone N-octanoyl homoserine lactone, which may account for the previously unexplained low-signal phenotype of a ∆ainR mutant, although the mechanism behind this regulation remains elusive. We also extended the previous observation of a possible “lux box” LuxR binding site upstream of ainS by showing the conservation of this site as well as a second putative lux box. Using a plasmid-based reporter we found that LuxR can mediate repression of ainS, providing a negative feedback mechanism in the Ain/Lux signaling cascade. Our results provide new insights into the regulation, expression, and evolution of ainSR.
Meiotic arrest with roscovitine and follicular fluid improves cytoplasmic maturation of porcine oocytes by promoting chromatin de-condensation and gene transcription
Authors: Zhang Min , Zhang Chuan-Xin , Pan Liu-Zhu , Gong Shuai , Cui Wei , Yuan Hong-Jie , Zhang Wei-Ling , Tan Jing-He 
Published: September 2017

AbstractThe developmental capacity of in vitro matured oocytes is inferior to that of the in vivo matured ones due to insufficient cytoplasmic maturation. Although great efforts were made to accomplish better cytoplasmic maturation by meiotic arrest maintenance (MAM) before in vitro maturation (IVM), limited progress has been achieved in various species. This study showed that MAM of porcine oocytes was better achieved with roscovitine than with dibutyryl cyclic adenosine monophosphate (db-cAMP) or 3-isobutyl-1-methylxanthine. Oocyte developmental competence after IVM was significantly improved following MAM in 199 + FF medium (TCM-199 containing 10% porcine follicular fluid and 25 µM roscovitine) to a level even higher than that in control oocytes matured without pre-MAM. Observations on other markers further confirmed the positive effects of MAM in 199 + FF on oocyte cytoplasmic maturation. During MAM culture in 199 + FF, re-decondensation (RDC) of condensed chromatin occurred, and transcription of genes beneficial to cytoplasmic maturation was evident in some of the oocytes with surrounded nucleoli (SN). However, MAM with db-cAMP neither induced RDC nor improved oocyte developmental potential. Together, the results suggest that MAM in the presence of FF and roscovitine improved the developmental competence of porcine oocytes by promoting a pre-GVBD chromatin de-condensation and expression of beneficial genes.
The importance of simulated lung fluid (SLF) extractions for a more relevant evaluation of the oxidative potential of particulate matter
Authors: Calas Aude , Uzu Gaëlle , Martins Jean M. F. , Voisin Didier , Spadini Lorenzo , Lacroix Thomas , Jaffrezo Jean-Luc 
Published: September 2017

AbstractParticulate matter (PM) induces oxidative stress in vivo, leading to adverse health effects. Oxidative potential (OP) of PM is increasingly studied as a relevant metric for health impact (instead of PM mass concentration) as much of the ambient particle mass do not contribute to PM toxicity. Several assays have been developed to quantify PM oxidative potential and a widely used one is the acellular dithiothreitol (DTT) assay. However in such assays, particles are usually extracted with methanol or Milli-Q water which is unrepresentative of physiological conditions. For this purpose, OPDTT measurements after simulated lung fluids (SLF) extraction, in order to look at the impact of simulated lung fluid constituents, were compared to Milli-Q water extraction measurements. Our major finding is a significant decrease of the OPDTT when the artificial lysosomal fluid (ALF) solution was used. Indeed, ligand compounds are present in the SLF solutions and some induce a decrease of the OP when compared to water extraction. Our results suggest that the effect of ligands and complexation in lining fluids towards PM contaminants probably has been underestimated and should be investigated further.
Size-dependent electrical transport properties in Co nanocluster-assembled granular films
Authors: Zhang Q. F. , Wang X. Z. , Wang L. S. , Zheng H. F. , Lin L. , Xie J. , Liu X. , Qiu Y. L. , Chen Y. Z. , Peng D. L. 
Published: September 2017

AbstractA series of Co nanocluster-assembled films with cluster sizes ranging from 4.5 nm to 14.7 nm were prepared by the plasma-gas-condensation method. The size-dependent electrical transport properties were systematically investigated. Both of the longitudinal resistivity ($${\rho }_{xx}$$

ρ

x
x

) and saturated anomalous Hall resistivity ($${\rho }_{xy}^{A}$$

ρ

x
y

A

) continuously increased with the decrease of the cluster sizes (d). The $${\rho }_{xx}$$

ρ

x
x

firstly increased and then decreased with increasing the temperature for all samples, which could be well described by involving the thermally fluctuation-induced tunneling (FIT) process and scattering. The tunneling effect was verified to result in the invalidation of classical anomalous Hall effect (AHE) scaling relation. After deducting the contribution from tunneling effect to $${\rho }_{xx}$$

ρ

x
x

, the AHE scaling relation between $${\rho }_{xy}^{A}$$

ρ

x
y

A

and the scattering resistivity ($${\rho }_{S}$$

ρ

S

) by varying the temperature was reconstructed. The value of scaling exponent γ increased with increasing Co cluster sizes. The size dependence of γ might be qualitatively interpreted by the interface and surface-induced spin flip scattering. We also determined the scaling relation between $${\rho }_{xy}^{A}$$

ρ

x
y

A

and $${\rho }_{S}$$

ρ

S

at 5 K by changing the Co cluster sizes, and a large value of γ = 3.6 was obtained which might be ascribed to the surface and interfacial scattering.
Distributed Acoustic Sensing for Seismic Monitoring of The Near Surface: A Traffic-Noise Interferometry Case Study
Authors: Dou Shan , Lindsey Nate , Wagner Anna M. , Daley Thomas M. , Freifeld Barry , Robertson Michelle , Peterson John , Ulrich Craig , Martin Eileen R. , Ajo-Franklin Jonathan B. 
Published: September 2017

AbstractAmbient-noise-based seismic monitoring of the near surface often has limited spatiotemporal resolutions because dense seismic arrays are rarely sufficiently affordable for such applications. In recent years, however, distributed acoustic sensing (DAS) techniques have emerged to transform telecommunication fiber-optic cables into dense seismic arrays that are cost effective. With DAS enabling both high sensor counts (“large N”) and long-term operations (“large T”), time-lapse imaging of shear-wave velocity (V
S
) structures is now possible by combining ambient noise interferometry and multichannel analysis of surface waves (MASW). Here we report the first end-to-end study of time-lapse V
S
imaging that uses traffic noise continuously recorded on linear DAS arrays over a three-week period. Our results illustrate that for the top 20 meters the V
S
models that is well constrained by the data, we obtain time-lapse repeatability of about 2% in the model domain—a threshold that is low enough for observing subtle near-surface changes such as water content variations and permafrost alteration. This study demonstrates the efficacy of near-surface seismic monitoring using DAS-recorded ambient noise.
In Vitro and In Vivo Biocompatibility Evaluation of Polyallylamine and Macromolecular Heparin Conjugates Modified Alginate Microbeads
Authors: Vaithilingam Vijayaganapathy , Steinkjer Bjørg , Ryan Liv , Larsson Rolf , Tuch Bernard Edward , Oberholzer Jose , Rokstad Anne Mari 
Published: September 2017

AbstractHost reactivity to biocompatible immunoisolation devices is a major challenge for cellular therapies, and a human screening model would be of great value. We designed new types of surface modified barium alginate microspheres, and evaluated their inflammatory properties using human whole blood, and the intraperitoneal response after three weeks in Wistar rats. Microspheres were modified using proprietary polyallylamine (PAV) and coupled with macromolecular heparin conjugates (Corline Heparin Conjugate, CHC). The PAV-CHC strategy resulted in uniform and stable coatings with increased anti-clot activity and low cytotoxicity. In human whole blood, PAV coating at high dose (100 µg/ml) induced elevated complement, leukocyte CD11b and inflammatory mediators, and in Wistar rats increased fibrotic overgrowth. Coating of high dose PAV with CHC significantly reduced these responses. Low dose PAV (10 µg/ml) ± CHC and unmodified alginate microbeads showed low responses. That the human whole blood inflammatory reactions paralleled the host response shows a link between inflammatory potential and initial fibrotic response. CHC possessed anti-inflammatory activity, but failed to improve overall biocompatibility. We conclude that the human whole blood assay is an efficient first-phase screening model for inflammation, and a guiding tool in development of new generation microspheres for cell encapsulation therapy.
Stimulatory Secretions of Airway Epithelial Cells Accelerate Early Repair of Tracheal Epithelium
Authors: Kardia Egi , Mohamed Rafeezul , Yahaya Badrul Hisham 
Published: September 2017

AbstractAirway stem/progenitor epithelial cells (AECs) are notable for their differentiation capacities in response to lung injury. Our previous finding highlighted the regenerative capacity of AECs following transplantation in repairing tracheal injury and reducing the severity of alveolar damage associated acute lung injury in a rabbit model. The goal of this study is to further investigate the potential of AECs to re-populate the tracheal epithelium and to study their stimulatory effect on inhibiting pro-inflammatory cytokines, epithelial cell migration and proliferation, and epithelial-to-mesenchymal transition (EMT) process following tracheal injury. Two in vitro culture assays were applied in this study; the direct co-culture assay that involved a culture of decellularised tracheal epithelium explants and AECs in a rotating tube, and indirect co-culture assay that utilized microporous membrane-well chamber system to separate the partially decellularised tracheal epithelium explants and AEC culture. The co-culture assays provided evidence of the stimulatory behaviour of AECs to enhance tracheal epithelial cell proliferation and migration during early wound repair. Factors that were secreted by AECs also markedly suppressed the production of IL-1β and IL-6 and initiated the EMT process during tracheal remodelling.
Mapping the Atomistic Structure of Graded Core/Shell Colloidal Nanocrystals
Authors: Yarema Maksym , Xing Yunhua , Lechner Rainer T. , Ludescher Lukas , Dordevic Nikola , Lin Weyde M. M. , Yarema Olesya , Wood Vanessa 
Published: September 2017

AbstractEngineering the compositional gradient for core/shell semiconductor nanocrystals improves their optical properties. To date, however, the structure of graded core/shell nanocrystal emitters has only been qualitatively described. In this paper, we demonstrate an approach to quantify nanocrystal structure, selecting graded Ag-In-Se/ZnSe core/shell nanocrystals as a proof-of-concept material. A combination of multi-energy small-angle X-ray scattering and electron microscopy techniques enables us to establish the radial distribution of ZnSe with sub-nanometer resolution. Using ab initio shape-retrieval analysis of X-ray scattering spectra, we further determine the average shape of nanocrystals. These results allow us to generate three-dimensional, atomistic reconstructions of graded core/shell nanocrystals. We use these reconstructions to calculate solid-state Zn diffusion in the Ag-In-Se nanocrystals and the lattice mismatch between nanocrystal monolayers. Finally, we apply these findings to propose design rules for optimal shell structure and record-luminescent core/shell nanocrystals.
Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation
Authors: Chun Byung Hee , Kim Kyung Hyun , Jeon Hye Hee , Lee Se Hee , Jeon Che Ok 
Published: September 2017

AbstractThe genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu. mesenteroides harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The reconstruction of fermentative metabolic pathways for Leu. mesenteroides strains showed that Leu. mesenteroides produces various metabolites such as lactate, ethanol, acetate, CO2, mannitol, diacetyl, acetoin, and 2,3-butanediol through an obligate heterolactic fermentation from various carbohydrates. Fermentative metabolic features of Leu. mesenteroides during kimchi fermentation were investigated through transcriptional analyses for the KEGG pathways and reconstructed metabolic pathways of Leu. mesenteroides using kimchi metatranscriptomic data. This was the first study to investigate the genomic and metabolic features of Leu. mesenteroides through pan-genomic and metatranscriptomic analyses, and may provide insights into its genomic and metabolic features and a better understanding of kimchi fermentations by Leu. mesenteroides.
Three-dimensional combined biomarkers assay could improve diagnostic accuracy for gastric cancer
Authors: Sun Liping , Tu Huakang , Chen Tiejun , Yuan Quan , Liu Jingwei , Dong Nannan , Yuan Yuan 
Published: September 2017

AbstractSo far, stomach-specific biomarkers, gastric cancer(GC)-related environmental factors, and cancer-associated biomarkers are three major classes of serological biomarkers with GC warning potential, joint detection of which is expected to increase the diagnosis efficiency. We investigated whether the combination of serum pepsinogens(PGs), IgG anti-Helicobacter pylori (HpAb), and osteopontin (OPN) can be used as a panel for GC diagnose. Serum was collected from 365 GC patients and 729 healthy individuals,furtherly 332 cases and 332 age- and sex-matched controls were selected for the matched analysis. Serum levels were measured by ELISA. Logistic regression and receiver operator characteristic curve (ROC) were used to assess the associations of biomarkers with GC and the discriminative performance of biomarkers for GC. The area under ROC from three-dimensional combination of PGI/II-HpAb-OPN (0.826) was significantly higher than two-dimensional combination of PGI/II-HpAb (0.786, P < 0.001), PGI/II-OPN (0.787, P < 0.001), and OPN-HpAb (0.801, P = 0.006), as well as one-biomarker of PGI/II (0.735, P < 0.001), HpAb (0.737, P < 0.001) and OPN(0.713, P < 0.001), respectively. The combination of PGI/II-HpAb-OPN, yielded a sensitivity of 70.2% and specificity of 78.3% at the predicted probability of 0.493 as the optimal cutoff point. Three-dimensional combined biomarkers assay could improve diagnostic accuracy for gastric cancer.
Genetic variants in PPP2CA are associated with gastric cancer risk in a Chinese population
Authors: Huang Tongtong , He Kexin , Mao Yingying , Zhu Meng , Yan Caiwang , Yu Fei , Qi Qi , Wang Tianpei , Wang Yan , Du Jiangbo , Liu Li 
Published: September 2017

AbstractProtein phosphatase 2A (PP2A), a tumor suppressor protein, has been implicated in cell cycle and apoptosis. Additionally, studies have illustrated its crucial roles in transformation of normal human cells to tumorigenic status. PPP2CA, which encodes the alpha isoform of the catalytic subunit of PP2A, has been recently reported to be associated with several types of cancers. Therefore, we hypothesized that genetic variants in PPP2CA might influence susceptibility of gastric cancer. To test this hypothesis, three tagging single nucleotide polymorphisms (SNPs) in PPP2CA were genotyped in a case-control study including 1,113 cases and 1,848 controls in a Chinese population. Three tagging SNPs in PPP2CA were genotyped using Illumina Human Exome BeadChip. We observed that the A allele of rs13187105 was associated with an increased risk of gastric cancer (adjusted odds ratio (OR) = 1.14, 95% confidence interval (CI): 1.02–1.28, P = 0.017). Further analyses showed that rs13187105 [A] was associated with decreased expression of PPP2CA mRNA (P = 5.1 × 10−6), and PPP2CA mRNA was significantly lower in gastric tumor tissues when comparing that in their adjacent normal tissues (P = 0.037). These findings support our hypothesis that genetic variants in PPP2CA may be implicated in gastric cancer susceptibility in Chinese population.
Profiling of cocaine using ratios of GC-MS peaks
Authors: Villesen Palle , Stride Nielsen Louise 
Published: September 2017

AbstractIllicit cocaine seizures are often compared to each other by using gas chromatography-mass spectrometry (GC-MS) data from cocaine alkaloid compounds to determine whether two specimens originate from the same production batch or not. This can provide intelligence or investigative information at the early stages of an investigation or evidence in court. Traditional classification methods assume high stability of all alkaloids, use all of them to calculate the correlation between two profiles and use a threshold to classify samples. Unstable alkaloids will have a strong influence on the performance. We show that comparing each alkaloid target compound individually improves the classification. Unfortunately, it requires normalization and is also sensitive to the stability. Instead we suggest to use ratios of all possible pairwise combinations of the GC-MS peaks. These ratios are scale free and directly comparable between samples. The peaks can be given different weights in the comparison of profiles using appropriate classification methods and we show that randomForest classification using these ratios have a high and reproducible performance in comparison with other methods. The performance of this method is not affected by noise, transformation or normalization and should be considered for future comparison of chromatographic profiles in general.