bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 gag recruits PACSIN2 to promote virus spreading
Authors: Popov Sergei , Popova Elena , Inoue Michio , Wu Yuanfei , Göttlinger Heinrich 
Published: June 2018

Significance
The structural Gag proteins of HIV-1 and other retroviruses contain regions that hijack a cellular membrane fission machinery to facilitate virus release. We now show that these Gag regions additionally recruit a host protein called PACSIN2, which has been shown to remodel cellular membranes and the actin cytoskeleton. Our data indicate that PACSIN2 is recruited indirectly by binding to a small regulatory protein called ubiquitin that becomes attached to Gag. Knockdown and reconstitution experiments revealed a critical role of PACSIN2 in HIV-1 spreading, although it was not required for a single cycle of replication. Overall, our study indicates that PACSIN2 promotes the cell-to-cell spreading of HIV-1, which constitutes the predominant mode of transmission but is poorly understood.
Critical role of integrin CD11c in splenic dendritic cell capture of missing-self CD47 cells to induce adaptive immunity
Authors: Wu Jiaxi , Wu Huaizhu , An Jinping , Ballantyne Christie M. , Cyster Jason G. 
Published: June 2018

SignificanceThe cell surface protein CD47 functions as a self-recognition molecule on mammalian cells, sending a negative “don’t eat me” signal to macrophages and dendritic cells. When CD47 is missing from cells in circulation, they are promptly taken up by and cause activation of dendritic cells in the spleen, and this, in turn, leads to stimulation of the adaptive immune system. The positive recognition system used by dendritic cells to capture CD47-deficient cells has been unknown. Here we show that the integrin CD11c, a classical marker of dendritic cells, and cytoskeletal protein talin are critically involved in binding and uptake of missing-self CD47 cells. These findings may advance efforts to use CD47 blockade therapies for treatment of cancer.
Direct observation and rational design of nucleation behavior in addressable self-assembly
Authors: Sajfutdinow Martin , Jacobs William M. , Reinhardt Aleks , Schneider Christoph , Smith David M. 
Published: June 2018

Significance
Current efforts aimed at constructing complex supramolecular structures often suffer from low yields or require long assembly protocols. We address these problems by demonstrating a facile strategy for optimizing the nucleation step of a multicomponent self-assembly reaction. By tracking the formation of multisubunit clusters in situ, our experiments show that modifying the critical nucleus required to initiate structure growth can broaden the range of conditions over which self-assembly occurs and, consequently, can dramatically improve the final yield of correctly formed structures. Since varying the design of only a small portion of the target structure optimizes its yield, this strategy provides a practical route to improve the speed and accuracy of self-assembly in biomolecular, colloidal, and nanoparticle systems.
Microstructure and bonding mechanisms in cold spray coatings
Authors: Walker Michael 
Published: June 2018

Cold spray additive manufacturing is a solid state deposition process with applications in surface coatings, manufacture of near net shape parts and component repairs. The technology can be used to spray a wide range of metallic powders onto varying substrates to produce the desired properties for application. This is a review of the progress in cold spray technology with particular interest in the bonding behaviour and deformation microstructure. Comparisons between cold spray and other thermal spray technologies such as plasma, wire arc, flame and high velocity oxyfuel spraying are discussed. The key advantage of cold spray over thermal spray is the reduced heat input and absence of melting. This drastically changes the mechanisms in which coatings are formed and bonded to the substrate, thus material properties and particle velocity have a large influence on the mechanical and microstructural properties of the coating. Fundamental understanding of the cold spray process is the key to its rapid uptake into the industry. This review was submitted as part of the 2018 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Mapping Culture in the Habsburg Empire: Fashioning a Costume Book in the Court of Charles V
Authors: Bond Katherine 
Published: June 2018

AbstractThis article introduces two manuscript editions of a richly illustrated costume album dated ca. 1548–49. Commissioned by Christoph von Sternsee (d. 1560), the captain of Charles V’s German guard, and composed using visual material sourced from Dutch master Jan Cornelisz Vermeyen (ca. 1500–59), the costume album records the diversity of subjects, customs, and costumes that the guard witnessed across imperial Habsburg Europe. Shaped by Sternsee’s personal experiences of travel, war, and empire, his costume album paints a vivid picture of imperial propaganda and personal ambition, demonstrating the significant role that Habsburg networks and relationships had upon the period’s visual culture.
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with CHMI, September 2017
Authors: Viallon Joële , Idrees Faraz , Moussay Philippe , Wielgosz Robert , Šilhavý Jan , Vokoun Miroslav 
Published: June 2018

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of the Czech Republic maintained by the Czech Hydrometeorological Institute (CHMI) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range from 0 nmol/mol to 500 nmol/moll.
KEY WORDS FOR SEARCH
Ozone, Standard Reference Photometer

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Safe or Not? Consumer Responses to Recalls with Traceability
Authors: Toledo Chantal , Villas-Boas Sofia Berto 
Published: June 2018

AbstractProduct traceability is advocated as a way to target non‐compliant products in recalls and protect the sales of compliant products. Using a large scanner‐level dataset from a national grocery chain and a difference‐in‐differences approach, we test whether consumers in California reduced egg purchases after three consecutive egg recalls during the 2010 Salmonella outbreak. In a setting where contaminated eggs could be traced to the box level, leaving no contaminated eggs in stores, we find a 7% to 9% reduction in egg sales following the recalls. The effect lasted at least three months. We find no evidence of overall substitution toward “greener” types of eggs, such as organic eggs. Finally, although the national grocery chain had contaminated eggs only in Northern California, we find reductions in egg sales in Southern Californian stores as well. Our results show that, even with traceability, consumers’ responses to recalls can negatively affect the sales of compliant products.
Animal Sourced Foods and Child Stunting
Authors: Headey Derek , Hirvonen Kalle , Hoddinott John 
Published: June 2018

AbstractStunting affects 160 million pre‐school children globally with adverse life‐long consequences. While work within nutritional science suggests that stunting in early childhood is associated with low intakes of animal‐sourced foods (ASFs), this topic has received little attention from economists. We attempt to redress this omission through an analysis of 130,432 children aged 6–23 months from 49 countries. We document distinctive patterns of ASF consumption among children in different regions. We find evidence of strong associations between stunting and a generic ASF consumption indicator, as well as dairy, meat/fish, and egg consumption indicators, and evidence that consuming multiple ASFs is more advantageous than any single ASF. We explore why ASF consumption is low but also so variable across countries. Non‐tradable ASFs (fresh milk, eggs) are a very expensive source of calories in low‐income countries and caloric prices of these foods are strongly associated with children's consumption patterns. Other demand‐side factors are also important, but the strong influence of prices implies an important role for agricultural policies—in production, marketing and trade—to improve the accessibility and affordability of ASFs in poorer countries.
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics
Authors: Klukowski Piotr , Schubert Mario 
Published: June 2018

Abstract

Motivation
A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide remains a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate.

Results
We present here an efficient search algorithm, GlycoNMRSearch, which matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus, searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics.

Availability and implementation
The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.nmrhub.eu.

Supplementary information
Supplementary data are available at Bioinformatics online.
iMetaLab 1.0: a web platform for metaproteomics data analysis
Authors: Liao Bo , Ning Zhibin , Cheng Kai , Zhang Xu , Li Leyuan , Mayne Janice , Figeys Daniel 
Published: June 2018

Abstract

Summary
The human gut microbiota, a complex, dynamic and biodiverse community, has been increasingly shown to influence many aspects of health and disease. Metaproteomic analysis has proven to be a powerful approach to study the functionality of the microbiota. However, the processing and analyses of metaproteomic mass spectrometry data remains a daunting task in metaproteomics data analysis. We developed iMetaLab, a web based platform to provide a user-friendly and comprehensive data analysis pipeline with a focus on lowering the technical barrier for metaproteomics data analysis.

Availability and implementation
iMetaLab is freely available through at http://imetalab.ca.

Supplementary information
Supplementary data are available at Bioinformatics online.
Informal Support, Health, and Burden Among Parents of Adult Children With Autism
Authors: Marsack Christina N , Hopp Faith P 
Published: June 2018

AbstractBackground and ObjectivesMany adults with autism spectrum disorders require lifelong reliance on caregiver support. As these caregivers age and experience health challenges, social support can be critical. This study seeks to understand if caregiver health moderates the relationship between informal social support and caregiver burden.Research Design and MethodsA total of 320 parents (age 50+ years) of adult children diagnosed with ASD were recruited from autism organizations and support groups and completed a web-based survey. Separate moderation analyses were used to determine if caregiver health was moderating the relationship between informal social support and composite caregiver burden, as well as the separate domains of developmental, time dependence, emotional burden, and impact of caregiving on finances. For each analysis, perceptions of available informal social support were the independent variable, composite and domains of caregiver burden were dependent variables, and parents’ self-reported general health was the moderating variable.ResultsCaregiver health had a statistically significant moderating effect when predicting the relationships between informal social support and composite caregiver burden, as well as time dependence burden and impact of caregiving on finances.Discussion and ImplicationsIncreased attention should be focused on supporting the current and future needs of both aging caregivers and their adult children with ASD. Future research on the dynamics of social support, health, and burden is also urgently needed to address the growing number of aging caregivers of adults diagnosed with ASD.
A reference genome of the European beech (Fagus sylvatica L.)
Authors: Mishra Bagdevi , Gupta Deepak K , Pfenninger Markus , Hickler Thomas , Langer Ewald , Nam Bora , Paule Juraj , Sharma Rahul , Ulaszewski Bartosz , Warmbier Joanna , Burczyk Jaroslaw , Thines Marco 
Published: June 2018

Abstract

Background
The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.

Findings
Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.

Conclusions
The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
Pathogenic variant in EPHB4 results in central conducting lymphatic anomaly
Authors: Li Dong , Wenger Tara L , Seiler Christoph , March Michael E , Gutierrez-Uzquiza Alvaro , Kao Charlly , Bhoj Elizabeth , Tian Lifeng , Rosenbach Misha , Liu Yichuan , Robinson Nora , Behr Mechenzie , Chiavacci Rosetta , Hou Cuiping , Wang Tiancheng , Bakay Marina , Pellegrino da Silva Renata , Perkins Jonathan A , Sleiman Patrick , Levine Michael A , Hicks Patricia J , Itkin Maxim , Dori Yoav , Hakonarson Hakon 
Published: June 2018

Abstract
Central conducting lymphatic anomaly (CCLA) is one of the complex lymphatic anomalies characterized by dilated lymphatic channels, lymphatic channel dysmotility and distal obstruction affecting lymphatic drainage. We performed whole exome sequencing (WES) of DNA from a four-generation pedigree and examined the consequences of the variant by transfection of mammalian cells and morpholino and rescue studies in zebrafish. WES revealed a heterozygous mutation in EPHB4 (RefSeq NM_004444.4; c.2334 + 1G&gt;C) and RNA-Seq demonstrated that the EPHB4 mutation destroys the normal donor site, which leads to the use of a cryptic splice donor that results in retention of the intervening 12-bp intron sequence. Transient co-expression of the wild-type and mutant EPHB4 proteins showed reduced phosphorylation of tyrosine, consistent with a loss-of-function effect. Zebrafish ephb4a morpholino resulted in vessel misbranching and deformities in the lymphatic vessel development, indicative of possible differentiation defects in lymphatic vessels, mimicking the lymphatic presentations of the patients. Immunoblot analysis using zebrafish lysates demonstrated over-activation of mTORC1 as a consequence of reduced EPHB4 signaling. Strikingly, drugs that inhibit mTOR signaling or RAS-MAPK signaling effectively rescued the misbranching phenotype in a comparable manner. Moreover, knock-in of EPHB4 mutation in HEK293T cells also induced mTORC1 activity. Our data demonstrate the pathogenicity of the identified EPHB4 mutation as a novel cause of CCLA and suggesting that ERK inhibitors may have therapeutic benefits in such patients with complex lymphatic anomalies.
Morita Equivalences of Vector Bundles
Authors: del Hoyo Matias , Ortiz Cristian 
Published: June 2018

Abstract
We study vector bundles over Lie groupoids, known as VB-groupoids, and their induced geometric objects over differentiable stacks. We establish a fundamental theorem that characterizes VB-Morita maps in terms of fiber and basic data, and use it to prove the Morita invariance of VB-cohomology, with implications to deformation cohomology of Lie groupoids and of classic geometries. We discuss applications of our theory to Poisson geometry, providing a new insight over Marsden–Weinstein reduction and the integration of Dirac structures. We conclude by proving that the derived category of VB-groupoids is a Morita invariant, which leads to a notion of VB-stacks, and solves (an instance of) an open question on representations up to homotopy.
Uplift, climate and biotic changes at the Eocene–Oligocene transition in south-eastern Tibet
Authors: Su Tao , Spicer Robert A , Li Shi-Hu , Xu He , Huang Jian , Sherlock Sarah , Huang Yong-Jiang , Li Shu-Feng , Wang Li , Jia Lin-Bo , Deng Wei-Yu-Dong , Liu Jia , Deng Cheng-Long , Zhang Shi-Tao , Valdes Paul J , Zhou Zhe-Kun 
Published: June 2018

AbstractThe uplift history of south-eastern Tibet is crucial to understanding processes driving the tectonic evolution of the Tibetan Plateau and surrounding areas. Underpinning existing palaeoaltimetric studies has been regional mapping based in large part on biostratigraphy that assumes a Neogene modernization of the highly diverse, but threatened, Asian biota. Here, with new radiometric dating and newly collected plant-fossil archives, we quantify the surface height of part of the south-eastern margin of Tibet in the latest Eocene (∼34 Ma) to be ∼3 km and rising, possibly attaining its present elevation (3.9 km) in the early Oligocene. We also find that the Eocene–Oligocene transition in south-eastern Tibet witnessed leaf-size diminution and a floral composition change from sub-tropical/warm temperate to cool temperate, likely reflective of both uplift and secular climate change, and that, by the latest Eocene, floral modernization on Tibet had already taken place, implying modernization was deeply rooted in the Palaeogene.
Endoscopic Endonasal Focal Transclival-Medial Condylectomy Approach for Resection of a Foramen Magnum Meningioma: 2-Dimensional Operative Video
Authors: Revuelta Barbero Juan M , Montaser Alaa S , Shahein Mostafa , Beer-Furlan André , Otto Bradley A , Carrau Ricardo L , Prevedello Daniel M 
Published: June 2018

Abstract
The endoscopic endonasal approach (EEA) provides direct access to foramen magnum meningiomas; however, it often requires extensive exposure including septal flap elevation with septum removal, complete sphenoidotomy, and panclivectomy.
We present a case of a 54-yr-old-female with an incidental foramen magnum lesion followed up with serial imaging who presented 10 mo later with progressive neck discomfort and episodes of dizziness, with confirmed tumor progression and further brainstem compression. A focal transclival EEA with medial condylectomy was performed preserving the upper two-thirds of the clivus, the nasal septum, and the sphenoid sinus. Gross total removal of a meningioma WHO Grade-1 was achieved with dura resection on the majority of the tumor (Simpson 2). Closure was achieved with a random pedicled inverted V nasaopharyngeal flap. There were no complications, all symptoms improved, and no recurrence was seen in 12 mo of follow-up.
IRB approval was neither required nor saught for this single case report. The patient gave informed consent.
Topological three-dimensional dissipative optical solitons
Authors: Veretenov N. A. , Fedorov S. V. , Rosanov N. N. 
Published: June 2018

This article presents a review of recent investigations of topological three-dimensional (3D) dissipative optical solitons in homogeneous laser media with fast nonlinearity of amplification and absorption. The solitons are found numerically, with their formation, by embedding two-dimensional laser solitons or their complexes in 3D space after their rotation around a vortex straight line with their simultaneous twist. After a transient, the ‘hula-hoop’ solitons can form with a number of closed and unclosed infinite vortex lines, i.e. the solitons are tangles in topological notation. They are attractors and are characterized by extreme stability. The solitons presented here can be realized in lasers with fast saturable absorption and are promising for information applications. The tangle solitons of the type described present an example of self-organization that can be found not only in optics but also in various distributed dissipative systems of different types.
This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.