bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics
Authors: Chong Rowena , Shi Mang , Grueber Catherine E , Holmes Edward C , Hogg Carolyn , Belov Katherine , Barrs Vanessa R 
Published: October 2018

AbstractBackgroundThe Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about the viruses present in devils, and whether any of these are of potential conservation relevance for this endangered species.MethodsUsing both metagenomics based on virus-like particle (VLP) enrichment and sequence-independent amplification (VLP metagenomics), and meta-transcriptomics based on bulk RNA sequencing, we characterised and compared the faecal viromes of captive and wild Tasmanian devils.ResultsA total of 54 devil faecal samples collected from captive (n = 2) and wild (n = 4) populations were processed for virome characterisation using both approaches. We detected many novel, highly divergent viruses, including vertebrate viruses, bacteriophage and other dietary associated plant and insect viruses. In total, 18 new vertebrate viruses, including novel sapelovirus, astroviruses, bocaviruses, papillomaviruses and gammaherpesvirus were identified, as well as known mammalian pathogens including rabbit haemorrhagic disease virus 2 (RHDV2). Captive devils showed significantly lower levels of viral diversity than wild devils. Comparison of the two methodological approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics mainly identifying RNA viruses, and VLP metagenomics largely identifying DNA viruses.ConclusionThis study has greatly expanded our knowledge of eukaryotic viruses in the Tasmanian devil and provides important baseline information that will contribute to the conservation and captive management of this endangered species. In addition, our results showed that a combination of VLP metagenomics and meta-transcriptomics may be a more comprehensive approach to virome characterisation than either method alone.
An intrinsic neural eye tracker in primary visual cortex
Authors: Morris Adam P. , Krekelberg Bart 
Published: October 2018

SummaryHumans and other primates rely on eye movements to explore visual scenes and to track moving objects. As a result, the image that is projected onto the retina – and propagated throughout the visual cortical hierarchy – is almost constantly changing and makes little sense without taking into account the momentary direction of gaze. How is this achieved in the visual system? Here we show that in primary visual cortex (V1), the earliest stage of cortical vision, neural representations carry an embedded “eye tracker” that signals the direction of gaze associated with each image. Using chronically implanted multi-electrode arrays, we recorded the activity of neurons in V1 during tasks requiring fast (exploratory) and slow (pursuit) eye movements. Neurons were stimulated with flickering, full-field luminance noise at all times. As in previous studies 1-4, we observed neurons that were sensitive to gaze direction during fixation, despite comparable stimulation of their receptive fields. We trained a decoder to translate neural activity into metric estimates of (stationary) gaze direction. This decoded signal not only tracked the eye accurately during fixation, but also during fast and slow eye movements, even though the decoder had not been exposed to data from these behavioural states. Moreover, this signal lagged the real eye by approximately the time it took for new visual information to travel from the retina to cortex. Using simulations, we show that this V1 eye position signal could be used to take into account the sensory consequences of eye movements and map the fleeting positions of objects on the retina onto their stable position in the world.
Genetic control of variability in subcortical and intracranial volumes
Authors: Córdova-Palomera Aldo , van der Meer Dennis , Kaufmann Tobias , Bettella Francesco , Wang Yunpeng , Alnæs Dag , Doan Nhat Trung , Agartz Ingrid , Bertolino Alessandro , Buitelaar Jan K. , Coynel David , Djurovic Srdjan , Dørum Erlend S. , Espeseth Thomas , Fazio Leonardo , Franke Barbara , Frei Oleksandr , Håberg Asta , Le Hellard Stephanie , Jönsson Erik G. , Kolskår Knut K. , Lund Martina J. , Moberget Torgeir , Nordvik Jan E. , Nyberg Lars , Papassotiropoulos Andreas , Pergola Giulio , Quervain Dominique de , Rampino Antonio , Richard Genevieve , Rokicki Jaroslav , Sanders Anne-Marthe , Schwarz Emanuel , Smeland Olav B. , Steen Vidar M. , Starrfelt Jostein , Sønderby Ida E. , Ulrichsen Kristine M. , Andreassen Ole A. , Westlye Lars T. 
Published: October 2018

AbstractSensitivity to external demands is essential for adaptation to dynamic environments, but comes at the cost of increased risk of adverse outcomes when facing poor environmental conditions. Here, we apply a novel methodology to perform genome-wide association analysis of mean and variance in nine key brain features (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus, intracranial volume and cortical thickness), integrating genetic and neuroanatomical data from a large lifespan sample (n=25,575 individuals; 8 to 89 years, mean age 51.9 years). We identify genetic loci associated with phenotypic variability in cortical thickness, thalamus, pallidum, and intracranial volumes. The variance-controlling loci included genes with a documented role in brain and mental health and were not associated with the mean anatomical volumes. This proof-of-principle of the hypothesis of a genetic regulation of brain volume variability contributes to establishing the genetic basis of phenotypic variance (i.e., heritability), allows identifying different degrees of brain robustness across individuals, and opens new research avenues in the search for mechanisms controlling brain and mental health.
MaxQuant.Live enables global targeting of more than 25,000 peptides
Authors: Wichmann Christoph , Meier Florian , Winter Sebastian Virreira , Brunner Andreas-David , Cox Jürgen , Mann Matthias 
Published: October 2018

ABSTRACTMass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. While achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on pre-scheduled mass-to-charge and retention time windows. Here we set out to merge these two concepts by a global targeting approach in which an arbitrary number of precursors of interest are detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses. We made use of a fast application programming interface to a quadrupole Orbitrap instrument and real-time recalibration in mass, retention time and intensity dimensions to predict precursor identity. MaxQuant.Live is freely available (www.maxquant.live) and has a graphical user interface to specify many pre-defined data acquisition strategies. Acquisition speed is as fast as with the vendor software and the power of our approach is demonstrated with the acquisition of breakdown curves for hundreds of precursors of interest. We also uncover precursors that are not even visible in MS1 scans, using elution time prediction based on the auto-adjusted retention time alone. Finally, we successfully recognized and targeted more than 25,000 peptides in single LC-MS runs. Global targeting combines the advantages of two classical approaches in MS-based proteomics, while greatly expanding the analytical toolbox.
A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking
Authors: Wood N Ezgi , Doncic Andreas 
Published: October 2018

AbstractLive cell time-lapse microscopy, a widely-used technique to study gene expression and protein dynamics in single cells, relies on segmentation and tracking of individual cells for data generation. The potential of the data that can be extracted from this technique is limited by the inability to accurately segment a large number of cells from such microscopy images and track them over long periods of time. Existing segmentation and tracking algorithms either require additional dyes or markers specific to segmentation or they are highly specific to one imaging condition and cell morphology and/or necessitate manual correction. Here we introduce a fully automated, fast and robust segmentation and tracking algorithm for budding yeast that overcomes these limitations. Full automatization is achieved through a novel automated seeding method, which first generates coarse seeds, then automatically fine-tunes cell boundaries using these seeds and automatically corrects segmentation mistakes. Our algorithm can accurately segment and track individual yeast cells without any specific dye or biomarker. Moreover, we show how existing channels devoted to a biological process of interest can be used to improve the segmentation. The algorithm is versatile in that it accurately segments not only cycling cells with smooth elliptical shapes, but also cells with arbitrary morphologies (e.g. sporulating and pheromone treated cells). In addition, the algorithm is largely independent of the specific imaging method (bright-field/phase) and objective used (40X/63X). We validate our algorithm’s performance on 9 cases each entailing a different imaging condition, objective magnification and/or cell morphology. Taken together, our algorithm presents a powerful segmentation and tracking tool that can be adapted to numerous budding yeast single-cell studies.
The sequence dependent search mechanism of EcoRI
Authors: Piatt S.C. , Loparo J.J. , Price A.C. 
Published: October 2018

ABSTRACTOne-dimensional search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of one-dimensional diffusion can help resolve the competing demands of fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies. In this work, we report observations of one-dimensional search by QD labeled EcoRI. Our data supports the view that proteins search DNA via rotation coupled sliding over a corrugated energy landscape. We observed that while EcoRI primarily slides along DNA at low salt concentrations, at higher concentrations its diffusion is a combination of sliding and hopping. We also observed long-lived pauses at genomic star sites which differ by a single nucleotide from the target sequence. To reconcile these observations with prior biochemical and structural data, we propose a model of search in which the protein slides over a sequence independent energy landscape during fast search, but rapidly interconverts with a “hemi-specific” binding mode in which a half site is probed. This half site interaction stabilizes the transition to a fully specific mode of binding which can then lead to target recognition.
Hypomorphic mutation of the mouse Huntington’s disease gene orthologue
Authors: Murthy Vidya , Tebaldi Toma , Yoshida Toshimi , Erdin Serkan , Calzonetti Teresa , Vijayvargia Ravi , Tripathi Takshashila , Kerschbamer Emanuela , Seong Ihn Sik , Quattrone Alessandro , Talkowski Michael E. , Gusella James F. , Georgopoulos Katia , MacDonald Marcy E. , Biagioli Marta 
Published: October 2018

AbstractRare individuals with hypomorphic inactivating mutations in the Huntington’s Disease (HD) gene (HTT), identified by CAG repeat expansion in the eponymous neurodegenerative disorder, exhibit variable abnormalities that implyHTTessential roles during organ development. Here we report phenotypes produced when increasingly severe hypomorphic mutations inHtt, the murineHTTorthologue (inHdhneoQ20,HdhneoQ50,HdhneoQ111mice), were placed over a null allele (Hdhex4/5). The most severe hypomorphic allele failed to rescue null lethality at gastrulation, while the intermediate alleles yielded perinatal lethality and a variety of fetal abnormalities affecting body size, skin, skeletal and ear formation, and transient defects in hematopoiesis. Comparative molecular analysis of wild-type andHtt-null retinoic acid-differentiated cells revealed gene network dysregulation associated with organ development and proposed polycomb repressive complexes and miRNAs as molecular mediators. Together these findings demonstrate that the HD gene acts both pre- and post-gastrulation and possibly suggest pleiotropic consequences ofHTT-lowering therapeutic strategies.Author SummaryTheHTTgene product mutated in Huntington’s Disease (HD) has essential roles during normal organism development, however, still not fully predictable are the functional consequences of its partial inactivation. Our genetic study provides a comprehensive effects’ description of progressively stronger suppression ofHttgene, the murineHTTcounterpart. The most severeHttreduction leads to embryo lethality, while intermediateHttdosages yield a variety of developmental abnormalities affecting body size, skin, skeletal and ear formation, and hematopoiesis. Complementing molecular analysis in differentiating cells depleted of a functionalHttgene further elucidates genes’ networks dysregulated during organ development and proposes chromatin regulators and short non-coding RNAs as key molecular mediators. Together these findings demonstrate that the HD gene acts both at early and later stages of development, thus possibly suggesting long-term consequences associated to the newest HD therapeutic strategies aimed at lowering theHTTgene product.
MxB restricts HIV-1 by targeting the tri-hexamer interface of the viral capsid
Authors: Smaga Sarah Sierra , Xu Chaoyi , Summers Brady James , Digianantonio Katherine Marie , Perilla Juan Roberto , Xiong Yong 
Published: October 2018

AbstractMyxovirus resistance protein B (MxB) is an interferon-inducible restriction factor of HIV-1 that blocks nuclear import of the viral genome. Evidence suggests that MxB recognizes higher-order interfaces of the HIV capsid lattice, but the mechanistic details of this interaction are not known. Previous studies have mapped the restriction activity of MxB to its N-terminus encompassing a triple arginine motif11RRR13. Here we demonstrate a direct and specific interaction between the MxB N-terminus and helical assemblies of HIV-1 capsid protein (CA) using highly purified recombinant proteins. We performed thorough mutagenesis to establish the detailed molecular requirements for the CA interaction with MxB. The results map MxB binding to the interface of three CA hexamers, specifically interactions between positively charged MxB N-terminal residues and negatively charged CA residues. Our crystal structures show that the CA mutations affecting MxB interaction and restriction do not alter the conformation of capsid assembly. In addition, 30 microsecond long all-atom molecular dynamics (MD) simulations of the complex between the MxB N-terminus and the HIV CA tri-hexamer interface show persistent MxB binding and identify a MxB-binding pocket surrounded by three CA hexamers. These results establish the molecular details of the binding of a lattice-sensing host factor onto HIV capsid, and provide insight into how MxB recognizes HIV capsid for the restriction of HIV-1 infection.Author summaryThe human antiviral protein MxB is a restriction factor that fights HIV infection. Previous experiments have demonstrated that MxB targets the HIV capsid, a protein shell that protects the viral genome. To make the conical shaped capsid, HIV CA proteins are organized into a lattice composed of hexamer and pentamer building blocks, providing many interfaces for host proteins to recognize. Through extensive biochemical and biophysical studies and molecular dynamics simulations, we show that MxB is targeting the HIV capsid by recognizing the region created at the intersection of three CA hexamers. We are further able to map this interaction to a few CA residues, located in a negatively-charged well at the interface between the three CA hexamers. This work provides detailed residue-level mapping of the targeted capsid interface and how MxB interacts. This information could inspire the development of capsid-targeting therapies for HIV.
Cold spraying and laser cladding as an alternative to electroplating processes
Authors: Sienicki Jaroslaw , Zórawski Wojciech , Dworak Adam , Koruba Piotr , Jurewicz Piotr , Reiner Jacek 
Published: October 2018

Purpose
The purpose of this paper is to propose cold spraying and laser cladding processes as alternatives to cadmium and chromium electroplating, respectively. There are many substances or chemicals within the coating technology that can be identified as substances of very high concern because of their carcinogenic or mutagenic nature. Cadmium and chromium undoubtedly belong to these items and are the basic constituents of electrolytic coating processes. Finding an alternative and adapting to the existing restrictions of the usage of such hazardous products stands for many to be or not to be in the market.

Design/methodology/approach
The research work was focused on down selecting the appropriate materials, producing the coating samples, testing their properties and optimizing process parameters by statistical method. On the one hand, the high-pressure cold spray system and spraying of the titanium coating on the landing gear component, and on the other hand, the high-energy laser cladding facility and the wear resistant cobalt-based coating deposited onto the shock absorber piston. Substrates of these two applications were made of the same material, 4330 – high-strength low-carbon steel.

Findings
Meeting the requirements of Registration, Evaluation, Authorization and Restriction of Chemicals implies undertaking research and implementation work to identify alternative processes. The work provides the technical characteristics of new coatings justifying application readiness of the researched processes.

Originality/value
Taguchi’s design of experiment method was combined with the measurements and analysis of specified coating properties for the optimization of the cold spray process parameters. There is also laser cladding process development presented as a fast rate technology generating coatings with the unique properties.
The effect of aerofoil camber on cycloidal propellers
Authors: Zhang Hailang , Hu Yu , Wang Gengqi 
Published: October 2018

Purpose
This paper aims to investigate the impact of aerofoil camber on the performance of micro-air-vehicle-scale cycloidal propellers.

Design/methodology/approach
First, experiments were conducted to validate the numerical methodology. After that, three turbulent models were compared to select the most accurate one. Then, 2D numerical simulation was carried out on 11 aerofoils with different cambers, including five cambered aerofoils, one symmetrical aerofoil and five inverse cambered aerofoils. The inverse cambered aerofoils are symmetrical about the chord line to the corresponding cambered ones.

Findings
The cycloidal propeller with large cambered aerofoil gives the lowest hovering efficiency, but with symmetrical aerofoil or small inverse cambered aerofoil shows the highest. Also, blades with large cambered aerofoil display high performance at the upper part of its trajectory, while with symmetrical aerofoil or the inverse cambered aerofoil have their best at the lower part. In addition, intensified downwash can be observed in the rotor cage for all cases. When a blade runs through the top-left part of its circle path, all cases display the feature of deep dynamic stall. When the blade travels through the nadir of its path, the actual angle of attack is close to zero due to the strong downwash. Furthermore, there exits intensified blade-vortex interaction induced by the preceding blade for large cambered aerofoils at the lower-right part of its trajectory.

Practical implications
This paper develops a new cycloidal propeller which is more efficient than the one already present.

Originality/value
This paper discovers that the aerofoil camber is a vital design parameter in the performance of cycloidal propeller, and the authors expect that the rotor with deformable aerofoil on camber would achieve much higher efficiency.
MLS based local approximation in numerical manifold method
Authors: Chen Yuanqiang , Zheng H. , Li Wei , Lin Shan 
Published: October 2018

Purpose
The purpose of this paper is to propose a new three-node triangular element in the framework of the numerical manifold method (NMM), which is designated by Trig3-MLScns.

Design/methodology/approach
The formulation uses the improved parametric shape functions of classical triangular elements (Trig3-0) to construct the partition of unity (PU) and the moving least square (MLS) interpolation method to construct the local approximation function.

Findings
Compared with the classical three-node element (Trig3-0), the Trig3-MLScns element has a higher order of approximations, much better accuracy and continuous nodal stress. Moreover, the linear dependence problem associated with many PU-based methods with high-order approximations is eliminated in the present element. A number of numerical examples indicate the high accuracy and robustness of the Trig3-MLScns element.

Originality/value
The proposed element inherits the individual merits of the NMM and the MLS.