bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of intertidal habitat on seasonal lipid composition changes in blue mussels,Mytilus edulisL., from the White Sea
Authors: Fokina N.N. , Ruokolainen T.R. , Nemova N.N. 
Published: June 2018

ABSTRACTThe lipid composition of blue musselsMytilus edulisL. living under different environmental conditions (in the intertidal zone and in aquaculture) was studied to detect origin-related differences in seasonal modifications of lipids, and their fatty acid composition in gills and digestive glands. In early May, the gills and digestive glands of intertidal mussels contained higher amounts of total lipids, chiefly phospholipids and sterols, which appear to perform a protective function as maintenance of membrane integrity. Seasonal modifications in lipid composition of both intertidal and aquaculture mussels were related to environmental factors (mainly low temperature), reproductive processes and food availability. We show that seasonal changes in membrane lipid composition of both intertidal and aquaculture mussels reflect the process of membrane lipid remodelling (namely changes in phosphatidylethanolamine proportion and in the fatty acid composition of phospholipids) required for homeoviscous adaptation in low-temperature conditions. In particular, the unsaturation index and chain fluidity index of phospholipids increased in gills and digestive glands of mussels collected in early May and in November. Similar seasonal changes in the triacylglycerol levels and its fatty acid composition were observed in gills and digestive glands of both intertidal and aquaculture mussels collected in late May and August.
Photon beam attenuation characteristics of three commercial radiation therapy treatment couch-tops
Authors: Wajid Hamza , Fleck Andre , Darko Johnson , Osei Ernest 
Published: June 2018

AbstractAimThe purpose of the study was to investigate the detailed angularly dependent attenuation characteristics of three different commercial couch-tops: Varian IGRT, Qfix kVue Standard and Qfix kVue Dose Max couch-tops used in radiation therapy.Materials and methodsThe attenuation of photon beams by the treatment couch-tops was measured using a farmer chamber inserted at the centre of a 16 cm diameter cylindrical acrylic phantom for five different photon energies: 6 MV, 6FFF MV, 10 MV, 10FFF MV and 15 MV photon beams. The Varian IGRT couch-top has three different thicknesses thus attenuation measurements were done at the three different longitudinal locations. Measurements were made with the sliding support rails of the Qfix kVue Standard and Qfix kVue Dose Max couch-tops at both ‘rails-in’ and ‘rails-out’ positions. All measurements were taken for several projections through 360° movement of the gantry and for two different field sizes; 5×5 cm2 and 10×10 cm2.Results and findingsThe results indicate that the maximum attenuation of the Varian IGRT couch-top at the thin, medium and thick portions are 5·1, 5·7 and 8·9%, respectively, the Qfix kVue Standard couch with the rails-in and rails-out are 11·2 and 13·7%, respectively, and Qfix kVue Dose Max couch-top with rails-in and rails-out are 9·7 and 13·8%, respectively. The results from this study can be used to account for the couch-top attenuation during radiation treatment planning of patients treated with these couch-tops.
A Bayesian Method for Incorporating Self‐Similarity Into Earthquake Slip Inversions
Authors: Amey R. M. J. , Hooper A. , Walters R. J. 
Published: June 2018

AbstractDistributions of coseismic slip help illuminate many properties of earthquakes, including fault geometry, stress changes, frictional properties, and potential future hazard. Slip inversions take observations and calculate slip at depth, but there are a number of commonly adopted assumptions such as minimizing the second spatial derivative of slip (the Laplacian) that have little physical basis and potentially bias the result. In light of growing evidence that fault slip shows fractal properties, we suggest that this information should be incorporated into slip inversions as a form of regularization, instead of Laplacian smoothing. We have developed a Bayesian approach to efficiently solve for slip incorporating von Karman regularization. In synthetic tests, our approach retrieves fractal slip better than Laplacian regularization, as expected, but even performs comparably, or better, when the input slip is not fractal. We apply this to the 2014 Mw 6.0 Napa Valley earthquake on a two‐segment fault using Interferometric Synthetic Aperture Radar (InSAR) and Global Positioning System (GPS) data. We find the von Karman and Laplacian inversions give similar slip magnitude but in different locations, and the von Karman solution has much tighter confidence bounds on slip than the Laplacian solution. Differences in earthquake slip due to the regularization technique could have important implications for the interpretation and modeling of stress changes on the causative and neighboring faults. We therefore recommend that choice of regularization method should be routinely made explicit and justified and that von Karman regularization is a better default than Laplacian.
Assessing the Challenges of Surface‐Level Aerosol Mass Estimates From Remote Sensing During the SEAC4RS and SEARCH Campaigns: Baseline Surface Observations and Remote Sensing in the Southeastern United States
Authors: Kaku K. C. , Reid J. S. , Hand J. L. , Edgerton E. S. , Holben B. N. , Zhang J. , Holz R. E. 
Published: June 2018

AbstractThe Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) campaign conducted in the southeast United States (SEUS) during the summer of 2013 provided a singular opportunity to study local aerosol chemistry and investigate aerosol radiative properties and PM2.5 relationships, focusing on the complexities involved in simplifying the relationship into a linear regression. We utilize three Southeastern Aerosol Research and Characterization network sites and one Environmental Protection Agency Chemical Speciation Network station that afforded simultaneous Aerosol Robotic Network (AERONET) aerosol optical depth (AOD) and aerosol mass, chemistry, and light scattering monitoring. Prediction of AERONET AOD using linear regression of daily‐mean PM2.5 during the SEAC4RS campaign yielded r2 of 0.36–0.53 and highly variable slopes across four sites. There were further reductions in PM2.5 predictive skill using Moderate Resolution Imaging Spectroradiometer (MODIS) and Multi‐angle Imaging SpetroRadiometer (MISR) AOD data, which have shorter correlation lengths and times relative to surface PM2.5. Long‐term trends in aerosol chemistry and optical properties in the SEUS are also investigated and compared to SEAC4RS period data, establishing that the SEUS experienced significant reduction in aerosol mass, corresponding with changes in both aerosol chemistry and optical properties. These changes have substantial impact on the PM2.5‐AOD linear regression relationship and reinforce the need for long‐term aerosol observation stations in addition to concentrated field campaigns.
Global Longitudinal Behavior of IRI Bottomside Profile Parameters From FORMOSAT‐3/COSMIC Ionospheric Occultations
Authors: Panda Sampad Kumar , Haralambous Haris , Kavutarapu Venkatesh 
Published: June 2018

AbstractThe bottomside thickness and shape (B0 and B1) are the critical key elements for depicting a realistic electron density profile in the International Reference Ionosphere (IRI) model. We investigated their longitudinal variability using a large database of FORMOSAT‐3/COSMIC (Constellation Observing System for Meteorology, Ionosphere, and Climate) electron density profiles covering the period 2006–2015 from which these parameters are derived using a simple analytic Chapman least squares fitting. The parameters are then compared with the IRI‐2012 submodels, that is, Bil‐2000, Gul‐1987, and ABT‐2009 during different seasons and solar activity. Besides apparent adherence of B0 to the equatorial region, the opposite occurrence pattern of maximum B0 to that of NmF2 is realized, manifesting semiannual distribution and hemispheric asymmetry. Unlike NmF2, the presence of single anomaly crest in B0 in all seasons except March equinox and their leading local time stamps are among the key observations. In spite of regular representation of IRI submodels during equinox, the performance of Gul‐1987 seems to be inferior during solstice with respect to geomagnetic field and equatorial electrodynamics, thereby depicting an erroneous distribution of B0. The striking wave‐like feature in B0 longitudinal variability is also revealed indicating its possible connection with the nonmigrating diurnal/semidiurnal tides. Moreover, the solar activity effect on B0 appears to be relatively higher over the Asian and Pacific longitudes (60–150°E). Although speculations are made over B1 variability, its complete longitudinal characteristics are indistinguishable in our results, except the subordinate magnitude as compared to IRI estimations. The important findings from this study may reinforce the understanding of bottomside variability and future improvements in IRI.
Harnessing synthetic lethality to predict the response to cancer treatment
Authors: Lee Joo Sang , Das Avinash , Jerby-Arnon Livnat , Arafeh Rand , Auslander Noam , Davidson Matthew , McGarry Lynn , James Daniel , Amzallag Arnaud , Park Seung Gu , Cheng Kuoyuan , Robinson Welles , Atias Dikla , Stossel Chani , Buzhor Ella , Stein Gidi , Waterfall Joshua J. , Meltzer Paul S. , Golan Talia , Hannenhalli Sridhar , Gottlieb Eyal , Benes Cyril H. , Samuels Yardena , Shanks Emma , Ruppin Eytan 
Published: June 2018

AbstractWhile synthetic lethality (SL) holds promise in developing effective cancer therapies, SL candidates found via experimental screens often have limited translational value. Here we present a data-driven approach, ISLE (identification of clinically relevant synthetic lethality), that mines TCGA cohort to identify the most likely clinically relevant SL interactions (cSLi) from a given candidate set of lab-screened SLi. We first validate ISLE via a benchmark of large-scale drug response screens and by predicting drug efficacy in mouse xenograft models. We then experimentally test a select set of predicted cSLi via new screening experiments, validating their predicted context-specific sensitivity in hypoxic vs normoxic conditions and demonstrating cSLi’s utility in predicting synergistic drug combinations. We show that cSLi can successfully predict patients’ drug treatment response and provide patient stratification signatures. ISLE thus complements existing actionable mutation-based methods for precision cancer therapy, offering an opportunity to expand its scope to the whole genome.
Stable complete methane oxidation over palladium based zeolite catalysts
Authors: Petrov Andrey W. , Ferri Davide , Krumeich Frank , Nachtegaal Maarten , van Bokhoven Jeroen A. , Kröcher Oliver 
Published: June 2018

AbstractIncreasing the use of natural gas engines is an important step to reduce the carbon footprint of mobility and power generation sectors. To avoid emissions of unburnt methane and the associated severe greenhouse effect of lean-burn engines, the stability of methane oxidation catalysts against steam-induced sintering at low temperatures (<500 °C) needs to be improved. Here we demonstrate how the combination of catalyst development and improved process control yields a highly efficient solution for complete methane oxidation. We design a material based on palladium and hierarchical zeolite with fully sodium-exchanged acid sites, which improves the support stability and prevents steam-induced palladium sintering under reaction conditions by confining the metal within the zeolite. Repeated short reducing pulses enable the use of a highly active transient state of the catalyst, which in combination with its high stability provides excellent performance without deactivation for over 90 h in the presence of steam.
Continuous biomarker monitoring by particle mobility sensing with single molecule resolution
Authors: Visser Emiel W. A. , Yan Junhong , van IJzendoorn Leo J. , Prins Menno W. J. 
Published: June 2018

AbstractHealthcare is in demand of technologies for real-time sensing in order to continuously guard the state of patients. Here we present biomarker-monitoring based on the sensing of particle mobility, a concept wherein particles are coupled to a substrate via a flexible molecular tether, with both the particles and substrate provided with affinity molecules for effectuating specific and reversible interactions. Single-molecular binding and unbinding events modulate the Brownian particle motion and the state changes are recorded using optical scattering microscopy. The technology is demonstrated with DNA and protein as model biomarkers, in buffer and in blood plasma, showing sensitivity to picomolar and nanomolar concentrations. The sensing principle is direct and self-contained, without consuming or producing any reactants. With its basis in reversible interactions and single-molecule resolution, we envisage that the presented technology will enable biosensors for continuous biomarker monitoring with high sensitivity, specificity, and accuracy.
Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster
Authors: Iyer Janani , Singh Mayanglambam Dhruba , Jensen Matthew , Patel Payal , Pizzo Lucilla , Huber Emily , Koerselman Haley , Weiner Alexis T. , Lepanto Paola , Vadodaria Komal , Kubina Alexis , Wang Qingyu , Talbert Abigail , Yennawar Sneha , Badano Jose , Manak J. Robert , Rolls Melissa M. , Krishnan Arjun , Girirajan Santhosh 
Published: June 2018

AbstractAs opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of individual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interactions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes.
Prioritizing network communities
Authors: Zitnik Marinka , Sosič Rok , Leskovec Jure 
Published: June 2018

AbstractUncovering modular structure in networks is fundamental for systems in biology, physics, and engineering. Community detection identifies candidate modules as hypotheses, which then need to be validated through experiments, such as mutagenesis in a biological laboratory. Only a few communities can typically be validated, and it is thus important to prioritize which communities to select for downstream experimentation. Here we develop CRank, a mathematically principled approach for prioritizing network communities. CRank efficiently evaluates robustness and magnitude of structural features of each community and then combines these features into the community prioritization. CRank can be used with any community detection method. It needs only information provided by the network structure and does not require any additional metadata or labels. However, when available, CRank can incorporate domain-specific information to further boost performance. Experiments on many large networks show that CRank effectively prioritizes communities, yielding a nearly 50-fold improvement in community prioritization.
Prevalence of Parkinson’s disease across North America
Authors: Marras C. , Beck J. C. , Bower J. H. , Roberts E. , Ritz B , Ross G. W. , Abbott R. D. , Savica R. , Van Den Eeden S. K. , Willis A. W. , Tanner CM ,   on behalf of the Parkinson’s Foundation P4 Group
Published: June 2018

AbstractEstimates of the prevalence of Parkinson’s disease in North America have varied widely and many estimates are based on small numbers of cases and from small regional subpopulations. We sought to estimate the prevalence of Parkinson’s disease in North America by combining data from a multi-study sampling strategy in diverse geographic regions and/or data sources. Five separate cohort studies in California (2), Minnesota (1), Hawaii USA (1), and Ontario, Canada (1) estimated the prevalence of PD from health-care records (3), active ascertainment through facilities, large group, and neurology practices (1), and longitudinal follow-up of a population cohort (1). US Medicare program data provided complementary estimates for the corresponding regions. Using our age- and sex-specific meta-estimates from California, Minnesota, and Ontario and the US population structure from 2010, we estimate the overall prevalence of PD among those aged ≥45 years to be 572 per 100,000 (95% confidence interval 537–614) that there were 680,000 individuals in the US aged ≥45 years with PD in 2010 and that that number will rise to approximately 930,000 in 2020 and 1,238,000 in 2030 based on the US Census Bureau population projections. Regional variations in prevalence were also observed in both the project results and the Medicare-based calculations with which they were compared. The estimates generated by the Hawaiian study were lower across age categories. These estimates can guide health-care planning but should be considered minimum estimates. Some heterogeneity exists that remains to be understood.
Uhlmann curvature in dissipative phase transitions
Authors: Carollo Angelo , Spagnolo Bernardo , Valenti Davide 
Published: June 2018

AbstractA novel approach based on the Uhlmann curvature is introduced for the investigation of non-equilibrium steady-state quantum phase transitions (NESS-QPTs). Equilibrium phase transitions fall invariably into two markedly non-overlapping categories: classical phase transitions and quantum phase transitions. NESS-QPTs offer a unique arena where such a distinction fades off. We propose a method to reveal and quantitatively assess the quantum character of such critical phenomena. We apply this tool to a paradigmatic class of lattice fermion systems with local reservoirs, characterised by Gaussian non-equilibrium steady states. The relations between the behaviour of the Uhlmann curvature, the divergence of the correlation length, the character of the criticality and the dissipative gap are demonstrated. We argue that this tool can shade light upon the nature of non equilibrium steady state criticality in particular with regard to the role played by quantum vs classical fluctuations.
HrpE, the major component of the Xanthomonas type three protein secretion pilus, elicits plant immunity responses
Authors: Gottig Natalia , Vranych Cecilia V. , Sgro Germán G. , Piazza Ainelén , Ottado Jorgelina 
Published: June 2018

AbstractLike several pathogenic bacteria, Xanthomonas infect host plants through the secretion of effector proteins by the Hrp pilus of the Type Three Protein Secretion System (T3SS). HrpE protein was identified as the major structural component of this pilus. Here, using the Xanthomonas citri subsp. citri (Xcc) HrpE as a model, a novel role for this protein as an elicitor of plant defense responses was found. HrpE triggers defense responses in host and non-host plants revealed by the development of plant lesions, callose deposition, hydrogen peroxide production and increase in the expression levels of genes related to plant defense responses. Moreover, pre-infiltration of citrus or tomato leaves with HrpE impairs later Xanthomonas infections. Particularly, HrpE C-terminal region, conserved among Xanthomonas species, was sufficient to elicit these responses. HrpE was able to interact with plant Glycine-Rich Proteins from citrus (CsGRP) and Arabidopsis (AtGRP-3). Moreover, an Arabidopsis atgrp-3 knockout mutant lost the capacity to respond to HrpE. This work demonstrate that plants can recognize the conserved C-terminal region of the T3SS pilus HrpE protein as a danger signal to defend themselves against Xanthomonas, triggering defense responses that may be mediated by GRPs.
The adiponectin promoter activator NP-1 induces high levels of circulating TNFα and weight loss in obese (fa/fa) Zucker rats
Authors: Decara Juan , Serrano Antonia , Pavón Francisco Javier , Rivera Patricia , Arco Rocio , Gavito Ana , Vargas Antonio , Navarro Juan A. , Tovar Ruben , Lopez-Gambero Antonio J. , Martínez Ana , Suárez Juan , Rodríguez de Fonseca Fernando , Baixeras Elena 
Published: June 2018

AbstractChronic NP-1 administration reduces body weight and hepatic steatosis despite induction of tolerance in adiponectin gene transcription with respect to the acute actions of this drug. This study explored the hypothesis that NP-1 could exert these effects through mechanisms independent of adiponectin. To this aim, we took advantage of the Zucker (fa/fa) rat model, which exhibits obesity, fatty liver and elevated leptin and adiponectin levels. Body weight and food intake were reduced after chronic NP-1 treatment. Plasma TNFα concentrations were elevated but no increase in adiponectin was found. Even so, NP-1 ameliorated fatty liver and corrected dyslipidemia by mechanisms probably associated with reduced feeding, transcription of Cpt1 and down-regulation of Hmgcr-CoA expression. In brown fat tissue NP-1 increased Dnmt1 (inhibitor of Adipoq) while it reduced Ucp1 expression and heat production, which excludes thermogenesis as a mechanism of the NP-1 slimming effect. The anti-obesity action of chronic NP-1 administration might be mediated by TNFα, which is known to have anorectic actions in the hypothalamus and to regulate both Dmnt1 and Ucp1 expression in adipose tissues. This finding opens up the possibility of using NP-1-mediated TNFα-induced weight loss as an innovative treatment of complicated obesity under strict pharmacologic control.
Increased nuclear DNA damage precedes mitochondrial dysfunction in peripheral blood mononuclear cells from Huntington’s disease patients
Authors: Askeland Georgina , Dosoudilova Zaneta , Rodinova Marie , Klempir Jiri , Liskova Irena , Kuśnierczyk Anna , Bjørås Magnar , Nesse Gaute , Klungland Arne , Hansikova Hana , Eide Lars 
Published: June 2018

AbstractHuntington’s disease (HD) is a progressive neurodegenerative disorder primarily affecting the basal ganglia and is caused by expanded CAG repeats in the huntingtin gene. Except for CAG sizing, mitochondrial and nuclear DNA (mtDNA and nDNA) parameters have not yet proven to be representative biomarkers for disease and future therapy. Here, we identified a general suppression of genes associated with aerobic metabolism in peripheral blood mononuclear cells (PBMCs) from HD patients compared to controls. In HD, the complex II subunit SDHB was lowered although not sufficiently to affect complex II activity. Nevertheless, we found decreased level of factors associated with mitochondrial biogenesis and an associated dampening of the mitochondrial DNA damage frequency in HD, implying an early defect in mitochondrial activity. In contrast to mtDNA, nDNA from HD patients was four-fold more modified than controls and demonstrated that nDNA integrity is severely reduced in HD. Interestingly, the level of nDNA damage correlated inversely with the total functional capacity (TFC) score; an established functional score of HD. Our data show that PBMCs are a promising source to monitor HD progression and highlights nDNA damage and diverging mitochondrial and nuclear genome responses representing early cellular impairments in HD.