bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral hardening of cosmic ray protons and helium nuclei in supernova remnant shocks *
Authors: Lin Wen-Hui , Bao Bi-Wen , Jiang Ze-Jun , Zhang Li 
Published: April 2019

Abstract
The observed hardening of the spectra of cosmic ray protons and helium nuclei is studied within the model of nonlinear diffusive shock acceleration of supernova remnants (SNRs). In this model, the injected particles with energies below the spectral " knee” are assumed to be described by two populations with different spectral indexes around 200 GeV. The high-energy population is dominated by the particles with energies above 200 GeV released upstream of the shock of SNR, and the low-energy population is attributed to the particles with energies below 200 GeV released downstream of the shock of SNR. In this scenario, the spectral hardening of cosmic ray protons and helium nuclei observed by PAMELA, AMS-02, and CREAM experiments can be reproduced.
Constituent counting rule and the production of

at high energies *
Authors: Dong Yubing , Shen Pengnian 
Published: April 2019

Abstract
The constituent counting rule, determining the scaling behavior of the transition amplitudes in an exclusive process at high energies, is applied to probe the internal structure of the newly observed

resonance. Several selected exclusive processes at high energies for the production of

are discussed. Results of two structural scenarios for

, a hexaquark dominant compact system in the quark degrees of freedom, and a

three-body bound state in the hadronic degrees of freedom, are analyzed and compared. A rather remarkable difference between the results of these two scenarios for the mentioned processes are addressed.
Second to tenth order susceptibilities of conserved charges within a modified Nambu-Jona-Lasinio model *
Authors: Fan Wenkai , Luo Xiaofeng , Zong Hongshi 
Published: April 2019

Abstract
We discuss the sign and energy dependence of second to tenth order susceptibilities of the baryon number, charge number, and strangeness for the analysis of critical conditions in heavy ion collisions in the LHC and RHIC by applying a modified Nambu-Jona-Lasinio model. This model is fitted to the quark condensate of the lattice QCD result at finite temperature and zero baryon chemical potential. The presence of a critical point made these susceptibilities deviate considerably from a Hadron-Resonance-Gas model that shows no criticality. The sign, magnitude, and energy dependence of these higher order fluctuations hint towards the existence and location of a critical point that could be discovered in future heavy ion collision experiments.
Jet shape modification at LHC energies by JEWEL *
Authors: Wan Ren-Zhuo , Ding Lei , Gui Xi , Yang Fan , Li Shuang , Zhou Dai-Cui 
Published: April 2019

Abstract
Jet shape measurements are employed to explore the microscopic evolution mechanisms of parton-medium interaction in ultra-relativistic heavy-ion collisions. In this study, jet shape modifications are quantified in terms of the fragmentation function

, relative momentum

, density of charged particles

, jet angularity

, jet momentum dispersion

, and

for proton-proton (pp) collisions at 0.9, 2.76, 5.02, 7, and 13 TeV, as well as for lead-lead collisions at 2.76 TeV and 5.02 TeV by JEWEL. A differential jet shape parameter

is proposed and studied at a smaller jet radius

. The results indicate that the medium has the dominant effect on jet shape modification, which also has a weak dependence on the center-of-mass energy. Jet fragmentation is enhanced significantly at very low

, and fragmented jet constituents are linearly spread to larger jet-radii for

. The waveform attenuation phenomena is observed in

,

, and

distributions. The results obtained for

from

to

, where the wave-like distribution in

collision is ahead of

collisions at small jet-radii, indicates a strong medium effect.
Cloud cover and delayed herbivory relative to timing of spring onset interact to dampen climate change impacts on net ecosystem exchange in a coastal Alaskan wetland
Authors: Leffler A Joshua , Beard Karen H , Kelsey Katharine C , Choi Ryan T , Schmutz Joel A , Welker Jeffrey M 
Published: April 2019

Abstract
Rapid warming in northern ecosystems over the past four decades has resulted in earlier spring, increased precipitation, and altered timing of plant–animal interactions, such as herbivory. Advanced spring phenology can lead to longer growing seasons and increased carbon (C) uptake. Greater precipitation coincides with greater cloud cover possibly suppressing photosynthesis. Timing of herbivory relative to spring phenology influences plant biomass. None of these changes are mutually exclusive and their interactions could lead to unexpected consequences for Arctic ecosystem function. We examined the influence of advanced spring phenology, cloud cover, and timing of grazing on C exchange in the Yukon–Kuskokwim Delta of western Alaska for three years. We combined advancement of the growing season using passive-warming open-top chambers (OTC) with controlled timing of goose grazing (early, typical, and late season) and removal of grazing. We also monitored natural variation in incident sunlight to examine the C exchange consequences of these interacting forcings. We monitored net ecosystem exchange of C (NEE) hourly using an autochamber system. Data were used to construct daily light curves for each experimental plot and sunlight data coupled with a clear-sky model was used to quantify daily and seasonal NEE over a range of incident sunlight conditions. Cloudy days resulted in the largest suppression of NEE, reducing C uptake by approximately 2 g C m−2 d−1 regardless of the timing of the season or timing of grazing. Delaying grazing enhanced C uptake by approximately 3 g C m−2 d−1. Advancing spring phenology reduced C uptake by approximately 1.5 g C m−2 d−1, but only when plots were directly warmed by the OTCs; spring advancement did not have a long-term influence on NEE. Consequently, the two strongest drivers of NEE, cloud cover and grazing, can have opposing effects and thus future growing season NEE will depend on the magnitude of change in timing of grazing and incident sunlight.
Contractual issues for Building Information Modelling (BIM)-based construction projects: An exploratory case study
Authors: Huzaimi Abd Jamil Ahmad , Syazli Fathi Mohamad 
Published: April 2019

Abstract
Building Information Modelling (BIM) enables close collaboration among project stakeholders to visualize what is to be built in a simulated environment by identifying any potential design, construction or operational issues. Despite the fact of its well-documented benefits, the extensive integration of BIM throughout the project lifecycle remains sporadic. The conventional contracts used in the Malaysian construction industry were established before the development of BIM. As BIM becoming ingrain in the delivery process, the inadequacies of these existing contracts have become visible. This paper presents the results of an exploratory case study using Qualitative Content Analysis dedicated to a BIM project and discusses a procurement approach of BIM to establish the contractual context by addressing the legal and contractual impediments namely; intellectual property, liability and process related risks-allocation in a Malaysian public construction. This paper also outlines the reasons why the implementation of BIM will foster the evolution of integrated contract delivery methods.
Quantum spin Hall phase in honeycomb nanoribbons with two different atoms: edge shape effect to bulk-edge correspondence
Authors: Kondo Kenji , Ito Ren 
Published: April 2019

Abstract
In this study, we consider a quantum spin Hall (QSH) phase in both the zigzag and the armchair type of honeycomb nanoribbons with two different atoms from the viewpoint of bulk-edge correspondence. Generally, the QSH phase in honeycomb nanoribbons is determined by the topology of the bulk Hamiltonian. However, the armchair type of nanoribbons seems to become the QSH phase in a very different region compared with bulk materials. On the other hand, the zigzag type of nanoribbons seems to become the QSH phase in almost the same region as bulk materials. We study the reason why the QSH phase in nanoribbons seems to be different from that of bulk materials using the extended Kane-Mele Hamiltonian. As a result, there is a clear difference in the edge states in the QSH phase between the zigzag and the armchair type of nanoribbons. We find that the QSH phase region in nanoribbons is actually different from that of bulk materials. This is because the coherence lengths of edge wave functions of nanoribbons are extremely influenced by their edge-shapes. We can conclude that the bulk-edge correspondence does not hold for relatively narrow nanoribbons compared with their coherence lengths and that the edge shapes of nanoribbons make their coherence lengths of edge wavefunctions different, which largely influences the QSH phase.
John Wesley and the origins of Methodism
Authors: Abraham William J. 
Published: April 2019

Abstract
‘John Wesley and the origins of Methodism’ explains that John Wesley never had any intention to form a movement or church. The early life of John Wesley and his brother Charles is described. In the 1730s, his life was redirected from academia in a series of developments that led him to become an extraordinary evangelist and spiritual director. Preaching in the open air was the first of many innovations for Wesley and was pivotal in the spread of Methodism. By the early 1750s, Methodism had become an evangelical order within the Church of England. The severe challenges faced by Methodism and the spread of Methodism to North America are also described.
The decline of Methodism
Authors: Abraham William J. 
Published: April 2019

Abstract
A report, Statistics in Mission, issued in 2014 tracked the decline of Methodists in Britain over a ten-year period. It showed a 3.7 per cent year-on-year decline and a reduction of 29.35 per cent overall. This decline is part of the wider decline of Christianity in the Anglo-Saxon and Celtic world. Although not as bad, a similar story is seen in the United States. ‘The decline of Methodism’ considers the various theories for this decline—including the increased secularization in the West and the intellectual changes in British culture with the rise of science—and some of the solutions proposed by the Methodist church to resolve the problem.
Future prospects of Methodism
Authors: Abraham William J. 
Published: April 2019

Abstract
‘Future prospects of Methodism’ considers the main options currently in play for the survival of Methodism. If Methodism is to have a future, there needs to be a recovery of nerve about its origins, its message, its practices, and its mission. Equally there needs to be a fresh way of thinking about Methodism as a full-scale church in the history of Christianity. The present prospects of fresh division open up the way for a new conversation about Methodist identity that can shape what it will become in the future. One thing is sure: Methodism will survive.
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes
Authors: Liu Yating , Sargent Luke , Leung Wilson , Elgin Sarah C R , Goecks Jeremy 
Published: April 2019

Abstract

Summary
G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings.

Availability and implementation
The virtual machine images and tutorials are available on the G-OnRamp web site (http://g-onramp.org/deployments). The source code is available under an Academic Free License version 3.0 through the goeckslab GitHub repository (https://github.com/goeckslab).

Supplementary information
Supplementary data are available at Bioinformatics online.
Soil Available Water Holding Capacity Can Alter the Reproductive Performance of Mountain Pine Beetle (Coleoptera: Curculionidae) in Jack Pine (Pinales: Pinaceae) Through Phloem Nitrogen Concentration
Authors: Hussain Altaf , Classens Gail , Guevara-Rozo Sydne , Erbilgin Nadir 
Published: April 2019

AbstractMountain pine beetle (Dendroctonus ponderosae Hopkins, Coleoptera: Curculionidae, Scolytidae) has recently invaded novel jack pine (Pinus banksiana Lamb., Pinales: Pinaceae) forests in western Canada. Jack pine seems to be a suitable host for mountain pine beetle, but how growing conditions influence jack pine’s quality as a host, and hence, its susceptibility for mountain pine beetle, is unknown. Specifically, how soil nutrient concentrations and available water holding capacity (AWHC) affect jack pine quality should be investigated. Host plant quality is an important determinant of mountain pine beetle host colonization and reproduction and is usually assessed by primary (nutrients) and secondary (defense chemistry) constituents of host phloem. We evaluated mountain pine beetle host acceptance and brood production by recording the percentage of female mountain pine beetle that entered the phloem and oviposited in 30 jack pine bolts from two sites that differed in soil nutrient concentrations and AWHC. We also compared the concentrations of phloem nutrients and defense monoterpenes among the selected trees and found that trees at the Low AWHC site had higher amounts of nitrogen, phosphorus, and potassium. Monoterpene concentrations did not differ among trees at the two sites. Host acceptance by and brood production of mountain pine beetle were greater in bolts from the Low AWHC site. We conclude that AWHC of the soil may influence mountain pine beetle host acceptance and brood production through altering host plant quality, particularly nitrogen in the phloem, and will potentially influence any further range expansion of the beetle in eastern North America.
β-glucan suppresses cell death of ASC deficient macrophages invaded by periodontopathic bacteria through the caspase-11 pathway
Authors: Inoue Maki , Okinaga Toshinori , Usui Michihiko , Kawano Aki , Thongsiri Chuencheewit , Nakashima Keisuke , Ariyoshi Wataru , Nishihara Tatsuji 
Published: April 2019

ABSTRACT
β-glucan is an abundant cell wall component of fungi and yeast. Dectin-1, a β-glucan receptor, plays an important regulatory role in the natural immunity. In the present study, we investigated the effect of β-glucan on mouse macrophages that had been invaded by the periodontopathic bacterium, Aggregatibacter actinomycetemcomitans. Exposure to curdlan, a type of β-glucan, suppressed cell death and led to the accumulation of a sub-G1-phase population upon A. actinomycetemcomitans invasion under conditions of constitutive expression of dectin-1. Members of the nucleotide-binding domain leucine-rich repeat-containing (NLR) protein family, such as NLR protein 3 (NLRP3), NLR family apoptosis inhibitory protein (NAIP), and NLR family CARD domain-containing protein 4 (NLRC4), as well as an associated protein, caspase-11, were clearly detected in A. actinomycetemcomitans-invaded control RAW cells (c-RAW cells; negative control). Interestingly, NAIP expression was upregulated and caspase-11 expression was downregulated by dectin-1 activity in A. actinomycetemcomitans-invaded dectin-1 overexpressing RAW 264.7 cells (d-RAW cells), suggesting that dectin-1 in macrophages regulates cell death upon A. actinomycetemcomitans invasion. These results support a potential correlation between dectin-1 and regulation of cell death in macrophages.
CCR7-deficient mice exhibit a delayed antigen-specific mucosal IgA antibody response to an oral recombinantSalmonellastrain
Authors: Hashizume-Takizawa Tomomi , Kobayashi Ryoki , Tsuzukibashi Osamu , Saito Masanori , Kurita-Ochiai Tomoko 
Published: April 2019

ABSTRACTThe migration of antigen (Ag)-loading dendritic cells (DCs) from Peyer's patches (PPs) to the draining mesenteric lymph nodes (MLNs) via chemokine receptor 7 (CCR7) is thought to be an important step in the initiation of acquired immunity. Our previous study showed that PPs were indispensable for Ag-specific secretory (S)IgA antibody (Ab) responses against oral recombinant Salmonella (rSalmonella). In this study, we attempted to show direct PP DC migration to MLNs by employing photoconvertible protein transgenic mice and investigated the role of the CCR7 signaling pathway in mucosal IgA induction. Our results demonstrated an actual flux of DCs from PPs to MLNs. The frequency of CCR7+ CD11c+ DCs in MLNs of PP-deficient mice was reduced, suggesting that some PP DCs migrated via CCR7. Immunization of CCR7−/− mice elicited significantly lower levels of Ag-specific SIgA Ab responses, which was associated with diminished formation of the germinal center in PPs. However, increased SIgA Ab production and dissemination of rSalmonella were observed at later time points. These results suggest that, although CCR7 was required for SIgA induction at normal velocity, the CCR7-mediated pathway is not essential for the induction of Ag-specific SIgA Ab responses to rSalmonella.
Lactic acid bacteria decrease Salmonella enterica Javiana virulence and modulate host inflammation during infection of an intestinal epithelial cell line
Authors: Burkholder Kristin M , Fletcher Dylan H , Gileau Lauren , Kandolo Arnold 
Published: April 2019

ABSTRACT
Salmonella enterica Javiana is a leading cause of severe foodborne Salmonellosis. Despite its emergence as a major foodborne pathogen, little is known of how S. Javiana interacts with intestinal epithelial cells, or of potential methods for ameliorating the bacterial-host interaction. Using cell-based adhesion, invasion and lactate dehydrogenase release assays, we observed an invasive and cytotoxic effect of S. Javiana on intestinal epithelial cells. We assessed the effect of probiotic species of lactic acid bacteria (LAB) on the S. Javiana-host cell interaction, and hypothesized that LAB would reduce S. Javiana infectivity. Salmonella enterica Javiana invasion was significantly impaired in host cells pre-treated with live Lactobacillus acidophilus and Lactobacillus rhamnosus. In addition, pre-exposure of host cells to live L. acidophilus, L. rhamnosus and L. casei reduced S. Javiana-induced cytotoxicity, while heat-killed LAB cultures had no effect on S. Javiana invasion or cytotoxicity. qRT-PCR analysis revealed that S. Javiana exposed to L. acidophilus and L. rhamnosus exhibited reduced virulence gene expression. Moreover, pre-treating host cells with LAB prior to S. Javiana infection reduced host cell production of inflammatory cytokines. Data suggest a potential protective effect of L. acidophilus, L. rhamnosus and L. casei against intestinal epithelial infection and pathogen-induced damage caused by S. Javiana.
Serum Adiponectin is Related to Dementia
Authors: Benavente Kimberly S K , Palmer Raymond F , Royall Donald R 
Published: April 2019

Abstract

Background
The adipokine adiponectin (APN)’s role in Alzheimer’s disease (AD) is controversial. Some studies suggest APN is neuroprotective while others propose it has harmful effects. We have used Multiple Indicators Multiple Causes (MIMIC) models to evaluate the effects of serum protein biomarkers on cognitive performance in the Texas Alzheimer’s Research and Care Consortium (TARCC) (Royall DR, Bishnoi RJ, Palmer RF. Serum IGF-BP2 strongly moderates age’s effect on cognition: a MIMIC analysis. Neurobiol Aging. 2015;36:2232–2240; Bishnoi RJ, Palmer RF, Royall DR. Vitamin D binding protein as a serum biomarker of Alzheimer’s disease. J Alzheimers Dis. 2015;43:37–45; Bishnoi RJ, Palmer RF, Royall DR. Serum interleukin (IL)-15 as a biomarker of Alzheimer’s disease. PLoS One. 2015;10:e0117282).

Methods
MIMIC models were constructed and replicated in randomly selected 50% splits of TARCC’s data (Group 1 N = 1,691; Group 2 N = 1,690) and used to evaluate the relationship between serum APN levels and cognition. Our approach has been to divide general intelligence (Spearman’s g) (Spearman C. The Abilities of Man: Their Nature and Measurement. 1932) into two latent variables, δ (ie, a dementia-specific phenotype representing the disabling fraction of cognitive variance) and g prime (g′) (ie, the residual non-disabling fraction). Only effects on δ are likely to be dementing.

Results
Serum APN was significantly related to δ scores (r = .10, p = .015). APN had no significant effect on g′ (r = −.25, p = .66), nor did it have any independent direct effects on cognitive performance. These results were replicated across random subsets (ΔCHISQ = 2.8(7), p &gt; .90).

Conclusions
APN’s effect on cognition is mediated through intelligence (ie, δ), likely to be disabling, and therefore to mediate one or more dementing processes. We have previously shown APN to partially mediate age’s-specific effect on δ (Royall DR, Al-Rubaye S, Bishnoi R, Palmer RF. Serum protein mediators of dementia and aging proper. Aging (Albany NY). 2016;8:3241–3254). However, because the current model is age adjusted, APN must mediate one or more additional age-independent dementing process(es), possibly AD.
Attachment Beyond the Adhesive System: The Contribution of Claws to Gecko Clinging and Locomotion
Authors: Naylor Emily R , Higham Timothy E 
Published: April 2019

AbstractAttachment is imperative for many biological functions, such as holding position and climbing, but can be challenged by natural conditions. Adhesive toe pads and claws have evolved in multiple terrestrial lineages as important dynamic attachment mechanisms, and some clades (e.g., geckos) exhibit both features. The functional relationship of these features that comprise a complex attachment system is not well-understood, particularly within lizards (i.e., if pads and claws are redundant or multifunctional). Geckos exhibit highly adept frictional adhesive toe pads that continue to fuel biological inquiry and inspiration. However, gecko claws (the ancestral lizard clinging condition) have received little attention in terms of their functional or evolutionary significance. We assessed claw function in Thecadactylus rapicauda using assays of clinging performance and locomotor trials on different surfaces (artificial and natural) and inclines with claws intact, then partially removed. Area root mean square height (Sq), a metric of 3D surface roughness, was later quantified for all test surfaces, including acrylic, sandpaper, and two types of leaves (smooth and hairy). Maximum clinging force significantly declined on all non-acrylic surfaces after claw removal, indicating a substantial contribution to static clinging on rough and soft surfaces. With and without claws, clinging force exhibited a negative relationship with Sq. However, claw removal had relatively little impact on locomotor function on surfaces of different roughness at low inclines (≤30°). High static and dynamic safety factor estimates support these observations and demonstrate the species’ robust frictional adhesive system. However, maximum station-holding capacity significantly declined on the rough test surface after partial claw removal, showing that geckos rely on their claws to maintain purchase on rough, steeply inclined surfaces. Our results point to a context-dependent complex attachment system within geckos, in which pads dominate on relatively smooth surfaces and claws on relatively rough surfaces, but also that these features function redundantly, possibly synergistically, on surfaces that allow attachment of both the setae and the claw (as in some insects). Our study provides important novel perspectives on gecko attachment, which we hope will spur future functional studies, new evolutionary hypotheses, and biomimetic innovation, along with collaboration and integration of perspectives across disciplines.