bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategic design of a Mussel-inspired in situ reduced Ag/Au-Nanoparticle Coated Magnesium Alloy for enhanced viability, antibacterial property and decelerated corrosion rates for degradable implant Applications
Authors: Rezk Abdelrahman I. , Ramachandra Kurup Sasikala Arathyram , Nejad Amin Ghavami , Mousa Hamouda M. , Oh Young Min , Park Chan Hee , Kim Cheol Sang 
Published: January 2019

AbstractMagnesium (Mg) and its alloys have attracted much attention as a promising candidate for degradable implant applications however the rapid corrosion of magnesium inside the human body greatly limits its use as an implant material. Therefore, coating the alloy surface with a multifunctional film is a promising way to overcome the drawbacks. Here we propose for the first time a multifunction layer coating to enhance the cell viability, antibacterial property and decelerated corrosion rates to act as a novel material to be used for degradable implant Applications. For that, the magnesium alloy (AZ31) was first treated with hydrofluoric acid (HF) and then dopamine tris Hydrochloric acid (tris-HCL) solution. The reducing catechol groups in the polydopamine (PD) layer subsequently immobilize silver/gold ions in situ to form uniformly dispersed Ag/Au nanoparticles on the coating layer. The successful formation of Ag/Au nanoparticles on the HF-PD AZ31 alloy was confirmed using XPS and XRD, and the morphology of all the coated samples were investigated using SEM images. The alloy with HF-PDA exhibit enhanced cell attachment and proliferation. Moreover, the nanoparticle immobilized HF-PD alloy exhibited dramatic corrosion resistance enhancement with superior antibacterial properties and accountable biocompatibility. Thus the result suggest that HF-PD Ag/Au alloy has great potential in the application of degradable implant and the surface modification method is of great significance to determine its properties.
Prototype foamy virus intasome aggregation is mediated by outer protein domains and prevented by protocatechuic acid
Authors: Jones Nathan D. , Mackler Randi M. , Lopez Miguel A. , Baltierra-Jasso Laura E. , Altman Matthew P. , Senavirathne Gayan , Yoder Kristine E. 
Published: January 2019

AbstractThe integrase (IN) enzyme of retrovirus prototype foamy virus (PFV) consists of four domains: amino terminal extension (NED), amino terminus (NTD), catalytic core (CCD), and carboxyl terminus domains (CTD). A tetramer of PFV IN with two viral DNA ends forms the functional intasome. Two inner monomers are catalytically active while the CCDs of the two outer monomers appear to play only structural roles. The NED, NTD, and CTD of the outer monomers are disordered in intasome structures. Truncation mutants reveal that integration to a supercoiled plasmid increases without the outer monomer CTDs present. Deletion of the outer CTDs enhances the lifetime of the intasome compared to full length (FL) IN or deletion of the outer monomer NTDs. High ionic strength buffer or several additives, particularly protocatechuic acid (PCA), enhance the integration of FL intasomes by preventing aggregation. These data confirm previous studies suggesting the disordered outer domains of PFV intasomes are not required for intasome assembly or integration. Instead, the outer CTDs contribute to aggregation of PFV intasomes which may be inhibited by high ionic strength buffer or the small molecule PCA.
Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod
Authors: Kirubakaran Tina Graceline , Andersen Øivind , De Rosa Maria Cristina , Andersstuen Terese , Hallan Kristina , Kent Matthew Peter , Lien Sigbjørn 
Published: January 2019

AbstractThe genetic mechanisms determining sex in teleost fishes are highly variable and the master sex determining gene has only been identified in few species. Here we characterize a male-specific region of 9 kb on linkage group 11 in Atlantic cod (Gadus morhua) harboring a single gene namedzkYfor zinc knuckle on the Y chromosome. Diagnostic PCR test of phenotypically sexed males and females confirm the sex-specific nature of the Y-sequence. We identified twelve highly similar autosomal gene copies ofzkY, of which eight code for proteins containing the zinc knuckle motif. 3D modeling suggests that the amino acid changes observed in six copies might influence the putative RNA-binding specificity. Cod zkY and the autosomal proteins zk1 and zk2 possess an identical zinc knuckle structure, but only the Y-specific genezkYwas expressed at high levels in the developing larvae before the onset of sex differentiation. Collectively these data suggestzkYas a candidate master masculinization gene in Atlantic cod. PCR amplification of Y-sequences in Arctic cod (Arctogadus glacialis) and Greenland cod (Gadus macrocephalus ogac) suggests that the male-specific region emerged in codfishes more than 7.5 million years ago.
Phase partitioning during fragmentation revealed by QEMSCAN Particle Mineralogical Analysis of volcanic ash
Authors: Hornby A. J. , Lavallée Y. , Kendrick J. E. , Rollinson G. , Butcher A. R. , Clesham S. , Kueppers U. , Cimarelli C. , Chigna G. 
Published: January 2019

AbstractVolcanic ash particle properties depend upon their genetic fragmentation processes. Here, we introduce QEMSCAN Particle Mineralogical Analysis (PMA) to quantify the phase distribution in ash samples collected during activity at Santiaguito, Guatemala and assess the fragmentation mechanisms. Volcanic ash from a vulcanian explosion and from a pyroclastic density current resulting from a dome collapse were selected. The ash particles resulting from both fragmentation modes are dense and blocky, typical of open-vent dome volcanoes and have a componentry consistent with their andesitic composition. We use image analysis to compare the fraction of each phase at particle boundaries compared to the total particle fraction. Our results show that the explosion-derived ash has an even distribution of plagioclase and glass, but boundaries enriched in pyroxene and amphibole. In contrast, the ash generated during dome collapse has an increased fraction of glass and decreased fraction of plagioclase at particle boundaries, suggesting that fractures preferentially propagate through glass during abrasion and milling in pyroclastic flows. This study presents QEMSCAN PMA as a new resource to identify generation mechanisms of volcanic ash, which is pertinent to volcanology, aviation, respiratory health and environmental hazards, and highlights the need for further experimental constraints on the fragmentation mechanism fingerprint.
Modernization of Golgi staining techniques for high-resolution, 3-dimensional imaging of individual neurons
Authors: Vints Katlijn , Vandael Dorien , Baatsen Pieter , Pavie Benjamin , Vernaillen Frank , Corthout Nikky , Rybakin Vasily , Munck Sebastian , Gounko Natalia V. 
Published: January 2019

AbstractAnalysis of neuronal arborization and connections is a powerful tool in fundamental and clinical neuroscience. Changes in neuronal morphology are central to brain development and plasticity and are associated with numerous diseases. Golgi staining is a classical technique based on a deposition of metal precipitate in a random set of neurons. Despite their versatility, Golgi methods have limitations that largely precluded their use in advanced microscopy. We combined Golgi staining with fluorescent labeling and tissue clearing techniques in an Alzheimer’s disease model. We further applied 3D electron microscopy to visualize entire Golgi-stained neurons, while preserving ultrastructural details of stained cells, optimized Golgi staining for use with block-face scanning electron microscopy, and developed an algorithm for semi-automated neuronal tracing of cells displaying complex staining patterns. Our method will find use in fundamental neuroscience and the study of neuronal morphology in disease.
Ghrelin octanoylation by ghrelin O-acyltransferase: Unique protein biochemistry underlying metabolic signaling
Authors: Hougland James L. 
Published: January 2019

Abstract
Ghrelin is a small peptide hormone that requires a unique post-translational modification, serine octanoylation, to bind and activate the GHS-R1a receptor. Ghrelin signaling is implicated in a variety of neurological and physiological processes, but is most well known for its roles in controlling hunger and metabolic regulation. Ghrelin octanoylation is catalyzed by ghrelin O-acyltransferase (GOAT), a member of the membrane-bound O-acyltransferase (MBOAT) enzyme family. From the status of ghrelin as the only substrate for GOAT in the human genome to the source and requirement for the octanoyl acyl donor, the ghrelin–GOAT system is defined by multiple unique aspects within both protein biochemistry and endocrinology. In this review, we examine recent advances in our understanding of the interactions and mechanisms leading to ghrelin modification by GOAT, discuss the potential sources for the octanoyl acyl donor required for ghrelin's activation, and summarize the current landscape of molecules targeting ghrelin octanoylation through GOAT inhibition.
Toward development of ecosystem asset accounts at the national level
Authors: Vačkářů Dava , Grammatikopoulou Ioanna 
Published: January 2019

ABSTRACT
Ecosystem accounting has become one of the key components in the revision of international statistical standards. Expansion of the System of Environmental-Economic Accounting for ecosystem services follows the rapid progress of science in this area as well as expanding applications to sustainability challenges. In this contribution, we discuss approaches to accounting of ecosystem assets as a natural capital basis that is critical for ecosystem service delivery. Based on examples from the Czech Republic, a Central European country, we illustrate the construction of ecosystem extent accounts based on the methodology of Land and Ecosystem Accounting. This analysis is complemented by monetary ecosystem asset accounting through quantification of the present value of future ecosystem service flows. Ecosystem condition is represented by the Mean Species Abundance indicator, which gauges the direction of ecosystem naturalness. Based on the demonstration of approaches to ecosystem asset accounting, we discuss selected aspects of ecosystem condition measurements, valuation, and policy implications of ecosystem asset accounting at the national level.
PSiTE: a Phylogeny guided Simulator for Tumor Evolution
Authors: Yang Hechuan , Lu Bingxin , Lai Lan Huong , Lim Abner Herbert , Alvarez Jacob Josiah Santiago , Zhai Weiwei 
Published: January 2019

Abstract

Summary
Simulating realistic clonal dynamics of tumors is an important topic in cancer genomics. Here, we present Phylogeny guided Simulator for Tumor Evolution, a tool that can simulate different types of tumor samples including single sector, multi-sector bulk tumor as well as single-cell tumor data under a wide range of evolutionary trajectories. Phylogeny guided Simulator for Tumor Evolution provides an efficient tool for understanding clonal evolution of cancer.

Availability and implementation
PSiTE is implemented in Python and is available at https://github.com/hchyang/PSiTE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Variation in Host Plant Usage and Diet Breadth Predict Sibling Preference and Performance in the Neotropical Tortoise Beetle Chelymorpha alternans (Coleoptera: Chrysomelidae: Cassidinae)
Authors: Morrison Colin R , Aubert Clément , Windsor Donald M 
Published: January 2019

AbstractSpecialized interactions between insects and the plants that they consume are one of the most ubiquitous and consequential ecological associations on the plant. Decades of investigation suggest that a narrow diet favors an individual phytophagous insect’s performance relative to a dietary generalist. However, this body of research has tended to approach questions of diet breadth and host usage from the perspective of temperate plant–insect associations. Relationships between diet breadth, host usage, and variation in tropical insect preference and performance remain largely uninvestigated. Here we characterize how variation in diet breadth and host usage affect oviposition preference, development, survival, and gain in mass of a Neotropical tortoise beetle Chelymorpha alternans Boheman 1854 (Coleoptera: Chrysomelidae), using a split-brood, sibling experimental design. Host performance was measured after splitting broods among four no-choice host diets. Groups consuming single hosts varied among themselves in developmental time and survival from larva to adult. Performance did not vary among groups consuming multiple and single hosts. Oviposition preference was measured in choice and no-choice tests. Females displayed preference for the original host in both experiments. Developmental time and survival of offspring sourced from the no-choice experiment was measured for two complete generations to explore correlations with female oviposition preference. Preference for the original host correlated with high survivorship and an intermediate developmental time. Survivorship and time to develop were also high on an alternative host that was less preferred. Departures from predictions of prevailing preference–performance hypotheses suggest that host usage presents C. alternans with fitness trade-offs.
Stage-dependent differential effects of interleukin-1 isoforms on experimental atherosclerosis
Authors: Vromman Amélie , Ruvkun Victoria , Shvartz Eugenia , Wojtkiewicz Gregory , Santos Masson Gustavo , Tesmenitsky Yevgenia , Folco Eduardo , Gram Hermann , Nahrendorf Matthias , Swirski Filip K , Sukhova Galina K , Libby Peter 
Published: January 2019

Abstract

Aims
Targeting interleukin-1 (IL-1) represents a novel therapeutic approach to atherosclerosis. CANTOS demonstrated the benefits of IL-1β neutralization in patients post-myocardial infarction with residual inflammatory risk. Yet, some mouse data have shown a prominent role of IL-1α rather than IL-1β in atherosclerosis, or even a deleterious effect of IL-1 on outward arterial remodelling in atherosclerosis-susceptible mice. To shed light on these disparate results, this study investigated the effect of neutralizing IL-1α or/and IL-1β isoforms starting either early in atherogenesis or later in ApoE–/– mice with established atheroma.

Methods and results
The neutralization of IL-1α or of both IL-1 isoforms impaired outward remodelling during early atherogenesis as assessed by micro-computed tomographic and histologic assessment. In contrast, the neutralization of IL-1β did not impair outward remodelling either during early atherogenesis or in mice with established lesions. Interleukin-1β inhibition promoted a slant of blood monocytes towards a less inflammatory state during atherogenesis, reduced the size of established atheromata, and increased plasma levels of IL-10 without limiting outward remodelling of brachiocephalic arteries.

Conclusion
This study established a pivotal role for IL-1α in the remodelling of arteries during early experimental atherogenesis, whereas IL-1β drives inflammation during atherogenesis and the evolution of advanced atheroma in mice.
Predicting Control Beliefs in Older Adults: A Micro-Longitudinal Study
Authors: Zhang Shenghao , Gamaldo Alyssa A , Neupert Shevaun D , Allaire Jason C 
Published: January 2019

Abstract

Objectives
The present study examined potential sources of intra- and inter-individual differences in older adults’ control beliefs using a micro-longitudinal design.

Method
Older adults (n = 205) ranging in age from 60 to 94 (M = 72.70, SD = 6.72) completed 8 in-person testing sessions within 3 weeks which included assessments of control beliefs (Locus of Control and Perceived Competence), physical health (physical symptoms and sleep self-efficacy), stressors, emotional well-being (Positive Affect and Negative Affect), and cognition (basic cognition tests, everyday cognition, and memory failures).

Results
Multilevel models indicated that on days when older adults had higher sleep self-efficacy, more positive affect, and less negative affect, they also had more internal locus of control and higher perceived competence. Having stressors on the previous occasion was associated with lower internal locus of control on the subsequent occasion. Physical symptoms, everyday cognition, and memory failures could be predictive of locus of control for some older adults.

Discussion
Our findings showed the differentiated antecedents of locus of control and perceived competence, the unique role of sleep self-efficacy, positive affect, and negative affect in understanding antecedents of both, as well as the need to study well-being and cognition antecedents of control beliefs in future studies.
A critical comparison of technologies for a plant genome sequencing project
Authors: Paajanen Pirita , Kettleborough George , López-Girona Elena , Giolai Michael , Heavens Darren , Baker David , Lister Ashleigh , Cugliandolo Fiorella , Wilde Gail , Hein Ingo , Macaulay Iain , Bryan Glenn J , Clark Matthew D 
Published: January 2019

Abstract

Background
A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read–only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates.

Results
Here, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs.

Conclusions
The field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.
Geographic patterns of plant–herbivore interactions are driven by soil fertility
Authors: Lynn Joshua S , Fridley Jason D 
Published: January 2019

AbstractAimsGeographic patterns of the intensity of plant herbivory in relation to climate factors have garnered little general support and appear to be species specific. However, plant–herbivore interactions are also driven by resource availability, such as soil nutrient content, and it remains unclear whether broad-scale variation in soil factors is reflected in herbivore consumption rates across species’ ranges. Additionally, we know little of how intraspecific variation in tissue quality associates with edaphic and climatic factors, and how this variation controls herbivore consumption. The resource availability hypothesis (RAH) predicts that plant individuals growing in low-resource environments will have lower leaf nutritional quality and more constitutive defenses, which will result in lower rates of leaf consumption.MethodsWe collected leaves from the old-field dominant species, Solidago altissima L., from 20 sites across 10 degrees of latitude in the Eastern USA to determine the percentage leaf area consumed by insect folivores. We obtained soil and climate data for each site, as well as plant functional and defensive traits, including specific leaf area (SLA), leaf carbon:nitrogen (C:N), and trichome density.Important FindingsAlthough we found no significant latitudinal trend of leaf consumption rate, there was strong evidence that leaf herbivory decreased with leaf C:N and trichome density, which themselves decreased with soil N, supporting our hypothesis that the RAH applies for intraspecific variation across spatial gradients. Additionally, high precipitation seasonality and soil nitrogen predicted decreased herbivory. The results suggest that spatial variation in herbivory can be driven by factors other than herbivore communities and climatic gradients, and that bottom-up processes, where plant traits and soil fertility control leaf consumption, must be incorporated into spatial predictions of herbivory.
The peculiar velocity field up to z ∼ 0.05 by forward-modelling Cosmicflows-3 data
Authors: Graziani R , Courtois H M , Lavaux G , Hoffman Y , Tully R B , Copin Y , Pomarède D 
Published: January 2019

Abstract
A hierarchical Bayesian model is applied to the Cosmicflows-3 catalogue of galaxy distances in order to derive the peculiar velocity field and distribution of matter within z ∼ 0.054. The model assumes the ΛCDM model within the linear regime and includes the fit of the galaxy distances together with the underlying density field. By forward modelling the data, the method is able to mitigate biases inherent to peculiar velocity analyses, such as the Homogeneous Malmquist bias or the lognormal distribution of peculiar velocities. The statistical uncertainty on the recovered velocity field is about 150 km s−1 depending on the location, and we study systematics coming from the selection function and calibration of distance indicators. The resulting velocity field and related density fields recover the cosmography of the Local Universe which is presented in an unprecedented volume of our Universe 10 times larger than previously reached. This methodology opens the doors to reconstruction of initial conditions for larger and more accurate constrained cosmological simulations. This work is also preparatory to larger peculiar velocity data sets coming from Wallaby, TAIPAN, or LSST.
Testing a model for subphotospheric dissipation in GRBs: fits to Fermi data constrain the dissipation scenario
Authors: Ahlgren Björn , Larsson Josefin , Ahlberg Erik , Lundman Christoffer , Ryde Felix , Pe’er Asaf 
Published: January 2019

ABSTRACT
It has been suggested that the prompt emission in gamma-ray bursts (GRBs) could be described by radiation from the photosphere in a hot fireball. Such models must be tested by directly fitting them to data. In this work we use data from the Fermi Gamma-ray Space Telescope and consider a specific photospheric model, in which the kinetic energy of a low-magnetization outflow is dissipated locally by internal shocks below the photosphere. We construct a table model with a physically motivated parameter space and fit it to time-resolved spectra of the 36 brightest Fermi GRBs with a known redshift. We find that about two-thirds of the examined spectra cannot be described by the model, as it typically underpredicts the observed flux. However, since the sample is strongly biased towards bright GRBs, we argue that this fraction will be significantly lowered when considering the full population. From the successful fits we find that the model can reproduce the full range of spectral slopes present in the sample. For these cases we also find that the dissipation consistently occurs at a radius of ∼1012 cm and that only a few per cent efficiency is required. Furthermore, we find a positive correlation between the fireball luminosity and the Lorentz factor. Such a correlation has been previously reported by independent methods. We conclude that if GRB spectra are due to photospheric emission, the dissipation cannot only be the specific scenario we consider here.