bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonenzymatic Conversion of ADP-Ribosylated Arginines to Ornithine Alters the Biological Activities of Human Neutrophil Peptide-1
Authors: Stevens Linda A. , Barbieri Joseph T. , Piszczek Grzegorz , Otuonye Amy N. , Levine Rodney L. , Zheng Gang , Moss Joel 
Published: November 2014

Abstract
Activated neutrophils, recruited to the airway of diseased lung, release human neutrophil peptides (HNP1–4) that are cytotoxic to airway cells as well as microbes. Airway epithelial cells express arginine-specific ADP ribosyltransferase (ART)-1, a GPI-anchored ART that transfers ADP-ribose from NAD to arginines 14 and 24 of HNP-1. We previously reported that ADP-ribosyl-arginine is converted nonenzymatically to ornithine and that ADP-ribosylated HNP-1 and ADP-ribosyl-HNP-(ornithine) were isolated from bronchoalveolar lavage fluid of a patient with idiopathic pulmonary fibrosis, indicating that these reactions occur in vivo. To determine effects of HNP-ornithine on the airway, three analogs of HNP-1, HNP-(R14orn), HNP-(R24orn), and HNP-(R14,24orn), were tested for their activity against Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus; their cytotoxic effects on A549, NCI-H441, small airway epithelial-like cells, and normal human lung fibroblasts; and their ability to stimulate IL-8 and TGF-β1 release from A549 cells, and to serve as ART1 substrates. HNP and the three analogs had similar effects on IL-8 and TGF-β1 release from A549 cells and were all cytotoxic for small airway epithelial cells, NCI-H441, and normal human lung fibroblasts. HNP-(R14,24orn), when compared with HNP-1 and HNP-1 with a single ornithine substitution for arginine 14 or 24, exhibited reduced cytotoxicity, but it enhanced proliferation of A549 cells and had antibacterial activity. Thus, arginines 14 and 24, which can be ADP ribosylated by ART1, are critical to the regulation of the cytotoxic and antibacterial effects of HNP-1. The HNP analog, HNP-(R14,24orn), lacks the epithelial cell cytotoxicity of HNP-1, but partially retains its antibacterial activity and thus may have clinical applications in airway disease.
PARP-1 Mediates LPS-Induced HMGB1 Release by Macrophages through Regulation of HMGB1 Acetylation
Authors: Yang Zhiyong , Li Li , Chen Lijuan , Yuan Weiwei , Dong Liming , Zhang Yushun , Wu Heshui , Wang Chunyou 
Published: November 2014

Abstract
The high-mobility group box protein 1 (HMGB1) is increasingly recognized as an important inflammatory mediator. In some cases, the release of HMGB1 is regulated by poly(ADP-ribose) polymerase-1 (PARP-1), but the mechanism is still unclear. In this study, we report that PARP-1 activation contributes to LPS-induced PARylation of HMGB1, but the PARylation of HMGB1 is insufficient to direct its migration from the nucleus to the cytoplasm; PARP-1 regulates the translocation of HMGB1 to the cytoplasm through upregulating the acetylation of HMGB1. In mouse bone marrow–derived macrophages, genetic and pharmacological inhibition of PARP-1 suppressed LPS-induced translocation and release of HMGB1. Increased PARylation was accompanied with the nucleus-to-cytoplasm translocation and release of HMGB1 upon LPS exposure, but PARylated HMGB1 was located at the nucleus, unlike acetylated HMGB1 localized at the cytoplasm in an import assay. PARP inhibitor and PARP-1 depletion decreased the activity ratio of histone acetyltransferases to histone deacetylases that elevated after LPS stimulation and impaired LPS-induced acetylation of HMGB1. In addition, PARylation of HMGB1 facilitates its acetylation in an in vitro enzymatic reaction. Furthermore, reactive oxygen species scavenger (N-acetyl-l-cysteine) and the ERK inhibitor (FR180204) impaired LPS-induced PARP activation and HMGB1 release. Our findings suggest that PARP-1 regulates LPS-induced acetylation of HMGB1 in two ways: PARylating HMGB1 to facilitate the latter acetylation and increasing the activity ratio of histone acetyltransferases to histone deacetylases. These studies revealed a new mechanism of PARP-1 in regulating the inflammatory response to endotoxin.
Integration of altimetric lake levels and GRACE gravimetry over Africa: Inferences for terrestrial water storage change 2003–2011
Authors: Moore P. , Williams S. D. P. 
Published: November 2014

AbstractTerrestrial water storage (TWS) change for 2003–2011 is estimated over Africa from GRACE gravimetric data. The signatures from change in water of the major lakes are removed by utilizing kernel functions with lake heights recovered from retracked ENVISAT satellite altimetry. In addition, the contribution of gravimetric change due to soil moisture and biomass is removed from the total GRACE signal by utilizing the GLDAS land surface model. The residual TWS time series, namely groundwater and the surface waters in rivers, wetlands, and small lakes, are investigated for trends and the seasonal cycle using linear regression. Typically, such analyses assume that the data are temporally uncorrelated but this has been shown to lead to erroneous inferences in related studies concerning the linear rate and acceleration. In this study, we utilize autocorrelation and investigate the appropriate stochastic model. The results show the proper distribution of TWS change and identify the spatial distribution of significant rates and accelerations. The effect of surface water in the major lakes is shown to contribute significantly to the trend and seasonal variation in TWS in the lake basin. Lake Volta, a managed reservoir in Ghana, is seen to have a contribution to the linear trend that is a factor of three greater than that of Lake Victoria despite having a surface area one‐eighth of that of Lake Victoria. Analysis also shows the confidence levels of the deterministic trend and acceleration identifying areas where the signatures are most likely due to a physical deterministic cause and not simply stochastic variations.
Inverse modeling of geochemical and mechanical compaction in sedimentary basins through Polynomial Chaos Expansion
Authors: Porta G. , Tamellini L. , Lever V. , Riva M. 
Published: November 2014

AbstractWe present an inverse modeling procedure for the estimation of model parameters of sedimentary basins subject to compaction driven by mechanical and geochemical processes. We consider a sandstone basin whose dynamics are governed by a set of unknown key quantities. These include geophysical and geochemical system attributes as well as pressure and temperature boundary conditions. We derive a reduced (or surrogate) model of the system behavior based on generalized Polynomial Chaos Expansion (gPCE) approximations, which are directly linked to the variance‐based Sobol indices associated with the selected uncertain model parameters. Parameter estimation is then performed within a Maximum Likelihood (ML) framework. We then study the way the ML inversion procedure can benefit from the adoption of anisotropic polynomial approximations (a‐gPCE) in which the surrogate model is refined only with respect to selected parameters according to an analysis of the nonlinearity of the input‐output mapping, as quantified through the Sobol sensitivity indices. Results are illustrated for a one‐dimensional setting involving quartz cementation and mechanical compaction in sandstones. The reliability of gPCE and a‐gPCE approximations in the context of the inverse modeling framework is assessed. The effects of (a) the strategy employed to build the surrogate model, leading either to a gPCE or a‐gPCE representation, and (b) the type and quality of calibration data on the goodness of the parameter estimates is then explored.
Construction of Matryoshka‐Type Structures from Supercharged Protein Nanocages
Authors: Beck Tobias , Tetter Stephan , Künzle Matthias , Hilvert Donald 
Published: November 2014

AbstractDesigning nanoscaled hierarchical structures with increasing levels of complexity is challenging. Here we show that electrostatic interactions between two complementarily supercharged protein nanocages can be effectively utilized to create nested Matryoshka‐type structures. Cage‐within‐cage complexes containing spatially ordered iron oxide nanoparticles spontaneously self‐assemble upon mixing positively supercharged ferritin compartments with AaLS‐13, a larger shell‐forming protein with a negatively supercharged lumen. Exploiting engineered Coulombic interactions and protein dynamics in this way opens up new avenues for creating hierarchically organized supramolecular assemblies for application as delivery vehicles, reaction chambers, and artificial organelles.
Three‐Dimensional Mid‐Infrared Tomographic Imaging of Endogenous and Exogenous Molecules in a Single Intact Cell with Subcellular Resolution
Authors: Quaroni Luca , Obst Martin , Nowak Marcus , Zobi Fabio 
Published: November 2014

AbstractMicroscopy in the mid‐infrared spectral range provides detailed chemical information on a sample at moderate spatial resolution and is being used increasingly in the characterization of biological entities as challenging as single cells. However, a conventional cellular 2D imaging measurement is limited in its ability to associate specific compositional information to subcellular structures because of the interference from the complex topography of the sample. Herein we provide a method and protocols that overcome this challenge in which tilt‐series infrared tomography is used with a standard benchtop infrared microscope. This approach gives access to the quantitative 3D distribution of molecular components based on the intrinsic contrast provided by the sample. We demonstrate the method by quantifying the distribution of an exogenous metal carbonyl complex throughout the cell and by reporting changes in its coordination sphere in different locations in the cell.
Stepwise Halide‐Triggered Double and Triple Catenation of Self‐Assembled Coordination Cages
Authors: Zhu Rongmei , Lübben Jens , Dittrich Birger , Clever Guido H. 
Published: November 2014

AbstractA simple self‐assembled [Pd2L4] coordination cage consisting of four carbazole‐based ligands was found to dimerize into the interpenetrated double cage [3 X@Pd4L8] upon the addition of 1.5 equivalents of halide anions (X=Cl−, Br−). The halide anions serve as templates, as they are sandwiched by four PdII cations and occupy the three pockets of the entangled cage structure. The subsequent addition of larger amounts of the same halide triggers another structural conversion, now yielding a triply catenated link structure in which each PdII node is trans‐coordinated by two pyridine donors and two halide ligands. This simple system demonstrates how molecular complexity can increase upon a gradual change of the relative concentrations of reaction partners that are able to serve different structural roles.
Lime mud CaCO3 for use as a filler material in papermaking: Impact of its preflocculation with cationic polyacrylamide
Authors: Peng Yuan , He Beihai , Zhao Lihong 
Published: November 2014

ABSTRACTCationic polyacrylamide with different molecular weights were used to preflocculate the lime mud (LM) before it was added to the paper stock for handsheet preparation. The particle sizes, ζ potential, and morphology of the unpreflocculated and resulting preflocculated LM were studied. We found that high‐molecular‐weight cationic polyacrylamide (H‐CPAM) led to larger LM flocs with a more positive ζ potential. The scanning electron microscopy images indicated that the morphological structure of the filler hardly changed during the preflocculation process. The effects of the preflocculation on the filler retention and paper properties were also investigated. The results show that the handsheets filled with preflocculated LM had better hydrophobicity and strength properties compared to handsheets filled with unpreflocculated LM, especially for H‐CPAM‐preflocculated LM. The paper formation was also improved, and the optical properties nearly remained the same. In addition, the LM preflocculated with H‐CPAM had the highest filler retention. At a filler loading of 30%, the filler retention of the H‐CPAM‐preflocculated LM was higher than 86; it was less than 82.5% in other cases. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41640.
Connecting MPAs – eight challenges for science and management
Authors: Lagabrielle Erwann , Crochelet Estelle , Andrello Marco , Schill Steven R. , Arnaud‐Haond Sophie , Alloncle Neil , Ponge Benjamin 
Published: November 2014

ABSTRACTConnectivity is a crucial process underpinning the persistence, recovery, and productivity of marine ecosystems. The Convention on Biological Diversity, through the Aichi Target 11, has set the ambitious objective of implementing a ‘well connected system of protected areas’ by 2020.This paper identifies eight challenges toward the integration of connectivity into MPA network management and planning. A summary table lists the main recommendations in terms of method, tool, advice, or action to address each of these challenges. Authors belong to a science–management continuum including researchers, international NGO officers, and national MPA agency members.Three knowledge challenges are addressed: selecting and integrating connectivity measurement metrics; assessing the accuracy and uncertainty of connectivity measurements; and communicating and visualizing connectivity measurements.Three management challenges are described: integrating connectivity into the planning and management of MPA networks; setting quantitative connectivity targets; and implementing connectivity‐based management across scales and marine jurisdictions.Finally, two paths toward a better integration of connectivity science with MPA management are proposed: setting management‐driven priorities for connectivity research, bridging connectivity science, and MPA network management.There is no single method to integrate connectivity into marine spatial planning. Rather, an array of methods can be assembled according to the MPA network objectives, budget, available skills, data, and timeframe.Overall, setting up ‘boundary organizations’ should be promoted to organize complex cross‐disciplinary, cross‐sectoral and cross‐jurisdiction interactions that are needed between scientists, managers, stakeholders and decision‐makers to make informed decision regarding connectivity‐based MPA planning and management.Copyright © 2014 John Wiley & Sons, Ltd.
The Catlin Seaview Survey – kilometre‐scale seascape assessment, and monitoring of coral reef ecosystems
Authors: González‐Rivero Manuel , Bongaerts Pim , Beijbom Oscar , Pizarro Oscar , Friedman Ariell , Rodriguez‐Ramirez Alberto , Upcroft Ben , Laffoley Dan , Kline David , Bailhache Christophe , Vevers Richard , Hoegh‐Guldberg Ove 
Published: November 2014

ABSTRACTMarine ecosystems provide critically important goods and services to society, and hence their accelerated degradation underpins an urgent need to take rapid, ambitious and informed decisions regarding their conservation and management.The capacity, however, to generate the detailed field data required to inform conservation planning at appropriate scales is limited by time and resource consuming methods for collecting and analysing field data at the large scales required.The ‘Catlin Seaview Survey’, described here, introduces a novel framework for large‐scale monitoring of coral reefs using high‐definition underwater imagery collected using customized underwater vehicles in combination with computer vision and machine learning. This enables quantitative and geo‐referenced outputs of coral reef features such as habitat types, benthic composition, and structural complexity (rugosity) to be generated across multiple kilometre‐scale transects with a spatial resolution ranging from 2 to 6 m2.The novel application of technology described here has enormous potential to contribute to our understanding of coral reefs and associated impacts by underpinning management decisions with kilometre‐scale measurements of reef health.Imagery datasets from an initial survey of 500 km of seascape are freely available through an online tool called the Catlin Global Reef Record. Outputs from the image analysis using the technologies described here will be updated on the online repository as work progresses on each dataset.Case studies illustrate the utility of outputs as well as their potential to link to information from remote sensing. The potential implications of the innovative technologies on marine resource management and conservation are also discussed, along with the accuracy and efficiency of the methodologies deployed. Copyright © 2014 John Wiley & Sons, Ltd.
Evaluating official marine protected area coverage for Aichi Target 11: appraising the data and methods that define our progress
Authors: Thomas Hannah L , Macsharry Brian , Morgan Lance , Kingston Naomi , Moffitt Russell , Stanwell‐Smith Damon , Wood Louisa 
Published: November 2014

ABSTRACTThe adoption of the Convention on Biological Diversity (CBD) Strategic Plan for Biodiversity, along with the 20 Aichi Targets, is a strong political endorsement for integrating biodiversity strategy across the entire United Nations system. Aichi Targets represent specific, time‐bound drivers for governments to safeguard both marine and terrestrial biodiversity.For the marine environment, Aichi Target 11 represents a call to effectively conserve at least 10% of coastal and marine areas by 2020. The core indicator to measure Aichi Target 11 is the extent of protected area coverage, and therefore it is essential that MPA data used to calculate this metric are robust.The World Database on Protected Areas (WDPA) is the authoritative source of data for measuring Aichi Target coverage progress. The WDPA assimilates global protected areas data as officially reported by the UN Member States themselves.Analysis of the WDPA (August 2014) calculated that MPAs now cover approximately 12,300,000 km2 or 3.41% of the world's ocean. Only 0.59% of the global ocean area (2 163 661 km2 within 1124 areas) is protected in no‐take areas.Only gathering and using State-sanctioned information may affect the accuracy of the WDPA MPA data. However, it is essential to first and foremost recognize national sovereignty and the rights of the Member State data providers in order to maintain a comprehensive approach to data gathering while ensuring international support for the resulting coverage figures that are used to measure global environmental targets.Further improvements could be made to the MPA data, for example by refining current MPA attributes and working with Member States and conventions to reduce or remove point data in the system. Moreover, broadening the scope of the WDPA to allow the inclusion of clearly marked non‐State‐sanctioned sites would complement existing official data and facilitate dialogue between Member States and other data providers towards MPA data improvement. Copyright © 2014 John Wiley & Sons, Ltd.
Inhibitors of Polyhydroxyalkanoate (PHA) Synthases: Synthesis, Molecular Docking, and Implications
Authors: Zhang Wei , Chen Chao , Cao Ruikai , Maurmann Leila , Li Ping 
Published: November 2014

AbstractPolyhydroxyalkanoate (PHA) synthases (PhaCs) catalyze the formation of biodegradable PHAs that are considered to be ideal alternatives to non‐biodegradable synthetic plastics. However, study of PhaCs has been challenging because the rate of PHA chain elongation is much faster than that of initiation. This difficulty, along with lack of a crystal structure, has become the main hurdle to understanding and engineering PhaCs for economical PHA production. Here we report the synthesis of two carbadethia CoA analogues—sT‐CH2‐CoA (26 a) and sTet‐CH2‐CoA (26 b)—as well as sT‐aldehyde (saturated trimer aldehyde, 29), as new PhaC inhibitors. Study of these analogues with PhaECAv revealed that 26 a/b and 29 are competitive and mixed inhibitors, respectively. Both the CoA moiety and extension of PHA chain will increase binding affinity; this is consistent with our docking study. Estimation of the Kic values of 26 a and 26 b predicts that a CoA analogue incorporating an octameric hydroxybutanoate (HB) chain might facilitate the formation of a kinetically well‐behaved synthase.
A Regioselective Synthesis of Benzopinacolones through Aerobic Dehydrogenative α‐Arylation of the Tertiary sp3 CH Bond of 1,1‐Diphenylketones with Aromatic and Heteroaromatic Compounds
Authors: More Nagnath Yadav , Jeganmohan Masilamani 
Published: November 2014

AbstractA regioselective synthesis of symmetrical and unsymmetrical benzopinacolones through aerobic dehydrogenative α‐arylation at the tertiary sp3 CH bond of substituted 1,1‐diphenylketones with aromatic and heteroaromatic compounds, in the presence of K2S2O8 in CF3COOH at room temperature, is described. The reaction is proposed to go via a carbocation intermediate, which could be generated directly from cleavage of the sp3 CH bond of 1,1‐diphenylketone. Subsequent α‐arylation was achieved at the methene sp3 carbon atom of the substituted ketone. A variety of substituted aromatic and heteroaromatic compounds were compatible with this reaction. In addition, benzopinacolones were converted into sterically hindered, tetrasubstituted alkenes and polycyclic aromatic compounds.
A Heteroleptic Push–Pull Substituted Iron(II) Bis(tridentate) Complex with Low‐Energy Charge‐Transfer States
Authors: Mengel Andreas K. C. , Förster Christoph , Breivogel Aaron , Mack Katharina , Ochsmann Julian R. , Laquai Frédéric , Ksenofontov Vadim , Heinze Katja 
Published: November 2014

AbstractA heteroleptic iron(II) complex [Fe(dcpp)(ddpd)]2+ with a strongly electron‐withdrawing ligand (dcpp, 2,6‐bis(2‐carboxypyridyl)pyridine) and a strongly electron‐donating tridentate tripyridine ligand (ddpd, N,N′‐dimethyl‐N,N′‐dipyridine‐2‐yl‐pyridine‐2,6‐diamine) is reported. Both ligands form six‐membered chelate rings with the iron center, inducing a strong ligand field. This results in a high‐energy, high‐spin state (5T2, (t2g)4(eg*)2) and a low‐spin ground state (1A1, (t2g)6(eg*)0). The intermediate triplet spin state (3T1, (t2g)5(eg*)1) is suggested to be between these states on the basis of the rapid dynamics after photoexcitation. The low‐energy π* orbitals of dcpp allow low‐energy MLCT absorption plus additional low‐energy LL′CT absorptions from ddpd to dcpp. The directional charge‐transfer character is probed by electrochemical and optical analyses, Mößbauer spectroscopy, and EPR spectroscopy of the adjacent redox states [Fe(dcpp)(ddpd)]3+ and [Fe(dcpp)(ddpd)]+, augmented by density functional calculations. The combined effect of push–pull substitution and the strong ligand field paves the way for long‐lived charge‐transfer states in iron(II) complexes.
Multiple‐Stimulus‐Responsive Supramolecular Gels of Two Components and Dual Chiroptical Switches
Authors: Miao Wangen , Qin Long , Yang Dong , Jin Xue , Liu Minghua 
Published: November 2014

AbstractA new class of L‐glutamic gelators, LG12(CH2)nCOOH, containing different lengths of methylene spacer were synthesized. It was found that the gelation ability of these compounds themselves was very weak. However, when another compound, p‐xylylenediamine (XEA), was introduced, the gelation ability was improved greatly. In particular, LG12(CH2)10COOH showed super‐gelation ability in the presence of XEA, which could immobilize almost all of the solvents except methanol. Moreover, the formed supramolecular gels even could be molded. Interestingly, some supramolecular gels of LG12(CH2)nCOOH and XEA could respond to multiple stimuli, such as heating, shaking, sonication, and acid/base. The studies of CD spectra suggested that the supramolecular chirality induced by self‐assembled chiral gelator molecules in gels could be tuned by the length of methylene spacer. In addition, the supramolecular chirality could be regulated as on/off by heating–cooling or external NH3/HCl. This would facilitate the development of dual chiroptical switches by temperature and acid/base.