bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Discrete Element Methods to Approximate Sea Ice Dynamics
Authors: Damsgaard A. , Adcroft A. , Sergienko O. 
Published: August 2018

AbstractLagrangian models of sea ice dynamics have several advantages over Eulerian continuum models. Spatial discretization on the ice floe scale is natural for Lagrangian models and offers exact solutions for mechanical nonlinearities with arbitrary sea ice concentrations. This allows for improved model performance in ice‐marginal zones, where sea ice is fragmented. Furthermore, Lagrangian models can explicitly simulate jamming processes that occur when sea ice moves through narrow confinements. While difficult to parameterize in continuum formulations, jamming emerges spontaneously in dense granular systems simulated in a Lagrangian framework. Here we present a flexible discrete element framework for approximating Lagrangian sea ice mechanics at the ice floe scale, forced by ocean and atmosphere velocity fields. Our goal is to evaluate the potential of models simpler than the traditional discrete element methods for granular dynamics. We demonstrate that frictionless contact models based on compressive stiffness alone are unlikely to produce jamming and describe two different approaches based on Coulomb friction and cohesion which both result in increased bulk shear strength of the granular assemblage. The frictionless but cohesive contact model displays jamming behavior which is similar to the more complex model with Coulomb friction and ice floe rotation at larger scales and has significantly lower computational cost.
“To Be, or Not to Be, That Is the Question”—The Cretan Extensional Detachment, Greece
Authors: Ring Uwe , Yngwe Frej 
Published: August 2018

AbstractWe present new structural data from the contact zone between the high‐pressure Phyllite‐Quartzite unit (PQ) and the overlying non‐high‐pressure Tripolitza unit in east‐central Crete for testing propositions that this contact represents the top‐to‐the‐north Cretan extensional detachment. Detailed mapping in the Neapoli valley shows that the PQ/Tripolitza contact is associated with a shallowly dipping penetrative foliation and associated south‐southwest (SSW)‐trending stretching lineation in the PQ. Kinematic indicators yielded a consistent top‐to‐the‐SSW sense of shear. The Tripolitza unit above was brittlely deformed, and top‐to‐the‐SSW thrust faults sole out in the contact zone. Undoing the effects of subsequent large‐wavelength, low‐amplitude folding about west‐northwest‐trending axes of the contact indicates that the top‐to‐the‐SSW kinematics resulted from crustal shortening. Therefore, the PQ/Tripolitza contact in the Neapoli valley is an out‐of‐sequence thrust, the Tripolitza thrust. We discuss a tectonic model in which the high‐pressure PQ was first exhumed in a shortening‐related extrusion wedge between about 22 and 17 Ma. The top of the exhuming extrusion wedge was then cut off by out‐of‐sequence thrusts in the upper crust at ≥17–11 Ma during sustained N‐S shortening. Subsequently, extensional graben in Crete formed after 11 Ma.
Modeling of Interactions Between Floating Particles and Emergent Stems in Slow Open Channel Flow
Authors: Liu Xiaoguang , Zeng Yuhong , Huai Wenxin 
Published: August 2018

AbstractIn slow open channel flow that features emergent vegetation, the dispersal of floating particles is affected by hydrodynamic characteristics at the free surface (e.g., surface tension), fluid drag, and inertial impaction. We investigated the interaction mechanism between floating particles and emergent stems. A mechanical model that considers the combined effect of fluid drag and inertial impaction has been presented to predict the probability that a particle collides with emergent stems. This model correctly captures the expected positive correlation between collision probability and vegetation density for dense emergent canopies. Furthermore, a new definition of the probability that a floating particle interacts with a stem is proposed. A statistical model to predict the probability that particles are permanently captured by stems is also proposed where the physical characteristics of particles (such as density and shape) are explicitly treated. Flume experiments have been conducted to explore the simultaneous effects of stem density and flow velocity on the approach and retention of slow‐moving inertial particles. These experiments are used to evaluate the scaling assumptions and the proposed model performance.
Water Repellency Decreases Vapor Sorption of Clay Minerals
Authors: Chen Jingjing , Shang Chao , Eick Matthew J. , Stewart Ryan D. 
Published: August 2018

AbstractAs soils become dry, water primarily exists as vapor that adsorbs to and desorbs from particle surfaces. The drying process also often enhances soil water repellency, yet the effects of repellency on soil water vapor sorption and exchange are not well understood. The objective of this study was to quantify the water vapor sorption dynamics of two minerals (Ca2+ saturated kaolinite and montmorillonite), in which water repellency was induced using two organic agents: cetyl trimethylammonium bromide (~4% by mass) and stearic acid (0.5%, 5%, 10%, 20%, and 35% by mass). Samples were then analyzed for water vapor sorption isotherms, solid‐water contact angles, organic carbon content, mineral surface morphology, hydrophobic functional groups (using Fourier transform infrared spectroscopy), zeta potential, and particle size distributions. The results showed that the water repellent treatments altered particle surface potentials and decreased surface areas relative to the controls. As a result, those samples adsorbed significantly less water and had less hysteresis between adsorption and desorption isotherms than the nontreated controls (p < 0.05). Differences in water adsorption were most pronounced for water activities >0.6, where hydrophobic compounds may have inhibited water vapor condensation, even at low concentrations. In contrast, solid‐water contact angles were small in montmorillonite treatments with <10% stearic acid, suggesting that low levels of hydrophobic compounds may have greater effect on vapor sorption compared to liquid water imbibition. Altogether, these results imply that repellency may reduce water retention in dry soils and enhance water vapor losses.
Effectiveness of EGFR/HER2-targeted drugs is influenced by the downstream interaction shifts of PTPIP51 in HER2-amplified breast cancer cells
Authors: Dietel Eric , Brobeil Alexander , Tag Claudia , Gattenloehner Stefan , Wimmer Monika 
Published: August 2018

AbstractBreast cancer is the most common female cancerous disease and the second most cause of cancer death in women. About 20–30% of these tumors exhibit an amplification of the HER2/ErbB2 receptor, which is coupled to a more aggressive and invasive growth of the cancer cells. Recently developed tyrosine kinase inhibitors and therapeutic antibodies targeting the HER2 receptor improved the overall survival time compared with sole radio- and chemotherapy. Upcoming resistances against the HER2-targeted therapy make a better understanding of the receptor associated downstream pathways an absolute need. In earlier studies, we showed the involvement of Protein Tyrosine Phosphatase Interacting Protein 51 (PTPIP51) in the mitogen-activated protein kinase (MAPK) pathway. The MAPK pathway is one of the most frequently overactivated pathways in HER2-amplified breast cancer cells. This study is aimed to elucidate the effects of four different TKIs on the interactome of PTPIP51, namely with the receptors EGFR and HER2, 14-3-3/Raf1 (MAPK pathway), its regulating enzymes, and the mitochondria-associated interaction partners in HER2 breast cancer cell lines (SK-BR3 and BT474) by using the Duolink proximity ligation assay, immunoblotting and knockdown of PTPIP51. Inhibition of both EGFR and HER2/ErbB2R shifted PTPIP51 into the MAPK pathway, but left the mitochondria-associated interactome of PTPIP51 unattended. Exclusively inhibiting HER2/ErbB2 by Mubritinib did not affect the interaction of PTPIP51 with the MAPK signaling. Selective inhibition of HER2 induced great alterations of mitochondria-associated interactions of PTPIP51, which ultimately led to the most-effective reduction of cell viability of SK-BR3 cells of all tested TKIs. The results clearly reveal the importance of knowing the exact mechanisms of the inhibitors affecting receptor tyrosine kinases in order to develop more efficient anti-HER2-targeted therapies.
Divergent accumulation of microbial necromass and plant lignin components in grassland soils
Authors: Ma Tian , Zhu Shanshan , Wang Zhiheng , Chen Dima , Dai Guohua , Feng Bowei , Su Xiangyan , Hu Huifeng , Li Kaihui , Han Wenxuan , Liang Chao , Bai Yongfei , Feng Xiaojuan 
Published: August 2018

AbstractThe means through which microbes and plants contribute to soil organic carbon (SOC) accumulation remain elusive due to challenges in disentangling the complex components of SOC. Here we use amino sugars and lignin phenols as tracers for microbial necromass and plant lignin components, respectively, and investigate their distribution in the surface soils across Mongolian grasslands in comparison with published data for other grassland soils of the world. While lignin phenols decrease, amino sugars increase with SOC contents in all examined grassland soils, providing continental-scale evidence for the key role of microbial necromass in SOC accumulation. Moreover, in contrast to clay’s control on amino sugar accumulation in fine-textured soils, aridity plays a central role in amino sugar accrual and lignin decomposition in the coarse-textured Mongolian soils. Hence, aridity shifts may have differential impacts on microbial-mediated SOC accumulation in grassland soils of varied textures.
Intermolecular selective carboacylation of alkenes via nickel-catalyzed reductive radical relay
Authors: Zhao Xian , Tu Hai-Yong , Guo Lei , Zhu Shengqing , Qing Feng-Ling , Chu Lingling 
Published: August 2018

AbstractThe development of catalytic carboacylation of simple olefins, which would enable the rapid construction of ketones with high levels of complexity and diversity, is very challenging. To date, the vast majority of alkene carboacylation reactions are typically restricted to single- and two-component methodologies. Here we describe a three-component carboacylation of alkenes via the merger of radical chemistry with nickel catalysis. This reaction manifold utilizes a radical relay strategy involving radical addition to an alkene followed by alkyl radical capture by an acyl-nickel complex to forge two vicinal C−C bonds under mild conditions. Excellent chemoselectivity and regioselectivity have been achieved by utilizing a pendant weakly chelating group. This versatile protocol allows for facile access to a wide range of important β-fluoroalkyl ketones from simple starting materials.
Megahertz data collection from protein microcrystals at an X-ray free-electron laser
Authors: Grünbein Marie Luise , Bielecki Johan , Gorel Alexander , Stricker Miriam , Bean Richard , Cammarata Marco , Dörner Katerina , Fröhlich Lars , Hartmann Elisabeth , Hauf Steffen , Hilpert Mario , Kim Yoonhee , Kloos Marco , Letrun Romain , Messerschmidt Marc , Mills Grant , Nass Kovacs Gabriela , Ramilli Marco , Roome Christopher M. , Sato Tokushi , Scholz Matthias , Sliwa Michel , Sztuk-Dambietz Jolanta , Weik Martin , Weinhausen Britta , Al-Qudami Nasser , Boukhelef Djelloul , Brockhauser Sandor , Ehsan Wajid , Emons Moritz , Esenov Sergey , Fangohr Hans , Kaukher Alexander , Kluyver Thomas , Lederer Max , Maia Luis , Manetti Maurizio , Michelat Thomas , Münnich Astrid , Pallas Florent , Palmer Guido , Previtali Gianpietro , Raab Natascha , Silenzi Alessandro , Szuba Janusz , Venkatesan Sandhya , Wrona Krzysztof , Zhu Jun , Doak R. Bruce , Shoeman Robert L. , Foucar Lutz , Colletier Jacques-Philippe , Mancuso Adrian P. , Barends Thomas R. M. , Stan Claudiu A. , Schlichting Ilme 
Published: August 2018

AbstractX-ray free-electron lasers (XFELs) enable novel experiments because of their high peak brilliance and femtosecond pulse duration. However, non-superconducting XFELs offer repetition rates of only 10–120 Hz, placing significant demands on beam time and sample consumption. We describe serial femtosecond crystallography experiments performed at the European XFEL, the first MHz repetition rate XFEL, delivering 1.128 MHz X-ray pulse trains at 10 Hz. Given the short spacing between pulses, damage caused by shock waves launched by one XFEL pulse on sample probed by subsequent pulses is a concern. To investigate this issue, we collected data from lysozyme microcrystals, exposed to a ~15 μm XFEL beam. Under these conditions, data quality is independent of whether the first or subsequent pulses of the train were used for data collection. We also analyzed a mixture of microcrystals of jack bean proteins, from which the structure of native, magnesium-containing concanavalin A was determined.
Redox-responsive self-assembly PEG nanoparticle enhanced triptolide for efficient antitumor treatment
Authors: Wang Yanchun , Liu Xuewei , Wang Xuemei , Zheng Wei , Zhang Junping , Shi Feng , Liu Junbao 
Published: August 2018

AbstractChemotherapy induces tumor cell death by directly damaging DNA or hindering cell mitosis. Some of the drawbacks of most chemotherapy are lack of target selectivity to tumor cells, and adverse drug reaction, which limit the treatment intensity and frequency. Herein, we synthesized the prodrug of triptolide (TP) coupled to vitamin E (VE) using dithiodiglycolic acid and co-dissolved with PEG2000- linoleic acid (MPEG200-LD) in ethanol. The PEGylated TP prodrug self-assembly nanoparticles (PTPPSN) were prepared via nanoprecipitation method. Besides, characterization, stability and in vitro release of the PEGylated nanometer prodrug were investigated. Furthermore, in vitro and in vivo antitumor efficacy of PTPPSN explored showed that the cytotoxicity of triptolide was significantly reduced in vitro preparation. However, in vitro and in vivo antitumor effect of PTPPSN was significantly improved compared to the original triptolide. In summary, the PEGylated nanoparticle successfully encapsulated triptolide yielded suitable cell microenvironment, and nanotechnology-related achievements. This study, therefore, provides a new method for antitumor research as well as an innovative technology for clinical treatment of malignant tumor.
Human Plasma Metabolomics Implicates Modified 9-cis-Retinoic Acid in the Phenotype of Left Main Artery Lesions in Acute ST-Segment Elevated Myocardial Infarction
Authors: Huang Lei , Zhang Lei , Li Tong , Liu Ying-wu , Wang Yu , Liu Bo-jiang 
Published: August 2018

AbstractThe detection of left main coronary artery disease (LMCAD) is crucial before ST-segment elevated myocardial infarction (STEMI) or sudden cardiac death. The aim of this study was to identify characteristic metabolite modifications in the LMCAD phenotype, using the metabolomics technique. Metabolic profiles were generated based on ultra-performance liquid chromatography and mass spectrometry, combined with multivariate statistical analysis. Plasma samples were collected prospectively from a propensity-score matched cohort including 44 STEMI patients (22 consecutive LMCAD and 22 non-LMCAD), and 22 healthy controls. A comprehensive metabolomics data analysis was performed with Metaboanalyst 3.0 version. The retinol metabolism pathway was shown to have the strongest discriminative power for the LMCAD phenotype. According to biomarker analysis through receiver-operating characteristic curves, 9-cis-retinoic acid (9cRA) dominated the first page of biomarkers, with area under the curve (AUC) value 0.888. Next highest were a biomarker panel consisting of 9cRA, dehydrophytosphingosine, 1H-Indole-3-carboxaldehyde, and another seven variants of lysophosphatidylcholines, exhibiting the highest AUC (0.933). These novel data propose that the retinol metabolism pathway was the strongest differential pathway for the LMCAD phenotype. 9cRA was the most critical biomarker of LMCAD, and a ten-metabolite plasma biomarker panel, in which 9cRA remained the weightiest, may help develop a potent predictive model for LMCAD in clinic.
Energy metabolism in the intestinal crypt epithelial cells of piglets during the suckling period
Authors: Wang Qiye , Xiong Xia , Li Jianzhong , Tu Qiang , Yang Huansheng , Yin Yulong 
Published: August 2018

AbstractWe tested the hypothesis that energy metabolism in the intestinal crypt epithelial cells of piglets changes during the suckling period. The experiment began with 24 piglets from 8 litters (3 piglets per litter). One piglet from each litter was randomly selected and euthanized at 7, 14, or 21 d of age, respectively. Crypt cells were isolated from the mid-jejunum and protein synthesis was analyzed using isobaric tags for relative and absolute quantification. The production of proteins related to glycolysis was mainly decreased from Days 7 to 14 before increasing up to Day 21. Synthesis of proteins involved in fatty acids, amino acids (glutamate and glutamine), and citrate cycle metabolism was generally down-regulated for samples collected on Days 14 and 21 when compared with levels on Day 7. These results indicate that energy metabolism in the intestinal crypt epithelial cells changes during the suckling period. Furthermore, this pattern of metabolism varies among glucose, fatty acids, and amino acids. Therefore, these findings may be useful in efforts to regulate the intestinal development of piglets.
Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus
Authors: Nöldeke Erik R. , Muckenfuss Lena M. , Niemann Volker , Müller Anna , Störk Elena , Zocher Georg , Schneider Tanja , Stehle Thilo 
Published: August 2018

AbstractThe peptidoglycan of Staphylococcus aureus is highly amidated. Amidation of α-D-isoglutamic acid in position 2 of the stem peptide plays a decisive role in the polymerization of cell wall building blocks. S. aureus mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin, indicating that targeting the amidation reaction could be a useful strategy to combat this pathogen. The enzyme complex that catalyzes the formation of α-D-isoglutamine in the Lipid II stem peptide was identified recently and shown to consist of two subunits, the glutamine amidotransferase-like protein GatD and the Mur ligase homolog MurT. We have solved the crystal structure of the GatD/MurT complex at high resolution, revealing an open, boomerang-shaped conformation in which GatD is docked onto one end of MurT. Putative active site residues cluster at the interface between GatD and MurT and are contributed by both proteins, thus explaining the requirement for the assembled complex to carry out the reaction. Site-directed mutagenesis experiments confirm the validity of the observed interactions. Small-angle X-ray scattering data show that the complex has a similar conformation in solution, although some movement at domain interfaces can occur, allowing the two proteins to approach each other during catalysis. Several other Gram-positive pathogens, including Streptococcus pneumoniae, Clostridium perfringens and Mycobacterium tuberculosis have homologous enzyme complexes. Combined with established biochemical assays, the structure of the GatD/MurT complex provides a solid basis for inhibitor screening in S. aureus and other pathogens.
Association of plasma microRNA expression with age, genetic background and functional traits in dairy cattle
Authors: Ioannidis Jason , Sánchez-Molano Enrique , Psifidi Androniki , Donadeu F. Xavier , Banos Georgios 
Published: August 2018

AbstractA number of blood circulating microRNAs (miRNAs) are proven disease biomarkers and have been associated with ageing and longevity in multiple species. However, the role of circulating miRNAs in livestock species has not been fully studied. We hypothesise that plasma miRNA expression profiles are affected by age and genetic background, and associated with health and production traits in dairy cattle. Using PCR arrays, we assessed 306 plasma miRNAs for effects of age (calves vs mature cows) and genetic background (control vs select lines) in 18 animals. We identified miRNAs which were significantly affected by age (26 miRNAs) and genetic line (5 miRNAs). Using RT-qPCR in a larger cow population (n = 73) we successfully validated array data for 12 age-related miRNAs, one genetic line-related miRNA, and utilised expression data to associate their levels in circulation with functional traits in these animals. Plasma miRNA levels were associated with telomere length (ageing/longevity indicator), milk production and composition, milk somatic cell count (mastitis indicator), fertility, lameness, and blood metabolites linked with body energy balance and metabolic stress. In conclusion, circulating miRNAs could provide useful selection markers for dairy cows to help improve health, welfare and production performance.
Correlation of Color Fundus Photograph Grading with Risks of Early Age-related Macular Degeneration by using Automated OCT-derived Drusen Measurements
Authors: Cheung Chui Ming Gemmy , Shi Yuan , Tham Yih Chung , Sabanayagam Charumathi , Neelam Kumari , Wang Jie Jin , Mitchell Paul , Cheng Ching-Yu , Wong Tien Yin , Cheung Carol Yim Lui 
Published: August 2018

AbstractWe evaluated automated OCT-derived drusen volume measures in a population-based study (n = 4,512) aged ≥40 years, and its correlation with conventional color fundus photographs (CFP)-derived early AMD features. Participants had protocol-based assessment to capture medical and ocular history, genotyping for SNPs in CFH, ARMS2, and CETP, CFP-based AMD grading and automated drusen volume based on SD-OCT using built-in software (Cirrus OCT advanced RPE analysis software). Significantly fewer eyes with early AMD features (drusen, hyperpigmentation, soft or reticular drusen) had drusen volume = 0 mm3 (p < 0.001). In eyes with drusen volume > 0 mm3, increasing AMD severity was associated with increase in drusen volume (correlation coefficient 0.17, p < 0.001). However 220 (59.14%) of 372 participants with AMD based on CFP grading had drusen volume = 0 mm3. Factors associated with drusen volume included age (OR 1.42 per 5 years, 95% confidence interval [CI] 2.76, 4.48), systolic blood pressure (OR1.00, 95% CI 1.00, 1.01), ethnic Malay (OR 1.54, 95% CI 1.29, 1.83) and Chinese (OR 1.66, 95% CI 1.37, 2.01) compared to Indian. The ARMS2 rs10490924 T allele was associated with increased drusen volume in subjects with AMD (multivariable adjusted OR1.54, 95% CI 1.08, 2.19). Automated OCT-derived drusen volume is correlated with CFP-based AMD grading in many, but not all subjects. However the agreement is not good. These two modalities provide complementary information and should be incorporated into future studies.