bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local variations of the Stellar Velocity Ellipsoid-I: the disc of galaxies in the Auriga simulations
Authors: Walo-Martín Daniel , Pérez Isabel , Grand Robert J J , Falcón-Barroso Jesús , Pinna Francesca , Martig Marie 
Published: June 2021

ABSTRACT
The connection between the Stellar Velocity Ellipsoid (SVE) and the dynamical evolution of galaxies has been a matter of debate in the last years and there is no clear consensus whether different heating agents (e.g. spiral arms, giant molecular clouds, bars and mergers) leave clear detectable signatures in the present day kinematics. Most of these results are based on a single and global SVE and have not taken into account that these agents do not necessarily equally affect all regions of the stellar disc. We study the two-dimensional (2D) spatial distribution of the SVE across the stellar discs of Auriga galaxies, a set of high resolution magnetohydrodynamical cosmological zoom-in simulations, to unveil the connection between local and global kinematic properties in the disc region. We find very similar, global, σz/σr = 0.80 ± 0.08 values for galaxies of different Hubble types. This shows that the global properties of the SVE at z = 0 are not a good indicator of the heating and cooling events experienced by galaxies. We also find that similar σz/σr radial profiles are obtained through different combinations of σz and σr trends: at a local level, the vertical and radial components can evolve differently, leading to similar σz/σr profiles at z = 0. By contrast, the 2D spatial distribution of the SVE varies a lot more from galaxy to galaxy. Present day features in the SVE spatial distribution may be associated with specific interactions such as fly-by encounters or the accretion of low mass satellites even in the cases when the global SVE is not affected. The stellar populations decomposition reveals that young stellar populations present colder and less isotropic SVEs and more complex 2D distributions than their older and hotter counterparts.
Properties of the multiphase outflows in local (ultra)luminous infrared galaxies
Authors: Fluetsch A , Maiolino R , Carniani S , Arribas S , Belfiore F , Bellocchi E , Cazzoli S , Cicone C , Cresci G , Fabian A C , Gallagher R , Ishibashi W , Mannucci F , Marconi A , Perna M , Sturm E , Venturi G 
Published: June 2021

ABSTRACT
Galactic outflows are known to consist of several gas phases; however, the connection between these phases has been investigated little and only in a few objects. In this paper, we analyse Multi Unit Spectroscopic Explorer (MUSE)/Very Large Telescope (VLT) data of 26 local (U)LIRGs and study their ionized and neutral atomic phases. We also include objects from the literature to obtain a sample of 31 galaxies with spatially resolved multiphase outflow information. We find that the ionized phase of the outflows has on average an electron density three times higher than the disc (ne,disc ∼ 145 cm−3 versus ne,outflow ∼ 500 cm−3), suggesting that cloud compression in the outflow is more important than cloud dissipation. We find that the difference in extinction between outflow and disc correlates with the outflow gas mass. Together with the analysis of the outflow velocities, this suggests that at least some of the outflows are associated with the ejection of dusty clouds from the disc. This may support models where radiation pressure on dust contributes to driving galactic outflows. The presence of dust in outflows is relevant for potential formation of molecules inside them. We combine our data with millimetre data to investigate the molecular phase. We find that the molecular phase accounts for more than 60 ${{\ \rm per\ cent}}$ of the total mass outflow rate in most objects and this fraction is higher in active galactic nuclei (AGN)-dominated systems. The neutral atomic phase contributes of the order of 10 ${{\ \rm per\ cent}}$, while the ionized phase is negligible. The ionized-to-molecular mass outflow rate declines slightly with AGN luminosity, although with a large scatter.
High-resolution ALMA and HST images of q1 Eri: an asymmetric debris disc with an eccentric Jupiter
Authors: Lovell J B , Marino S , Wyatt M C , Kennedy G M , MacGregor M A , Stapelfeldt K , Dent B , Krist J , Matrà L , Kral Q , Panić O , Pearce T D , Wilner D 
Published: June 2021

ABSTRACT
We present Atacama Large Millimetre/sub-Millimetre Array (ALMA) 1.3 and 0.86 mm observations of the nearby (17.34 pc) F9V star q1 Eri (HD 10647, HR 506). This system, with age ∼1.4 Gyr, hosts a ∼2 au radial velocity planet and a debris disc with the highest fractional luminosity of the closest 300 FGK type stars. The ALMA images, with resolution ∼0${_{.}^{\prime\prime}}$5, reveal a broad (34–134 au) belt of millimetre emission inclined by 76.7 ± 1.0 degrees with maximum brightness at 81.6 ± 0.5 au. The images reveal an asymmetry, with higher flux near the south-west ansa, which is also closer to the star. Scattered light observed with the Hubble Space Telescope is also asymmetric, being more radially extended to the north-east. We fit the millimetre emission with parametric models and place constraints on the disc morphology, radius, width, dust mass, and scale height. We find that the south-west ansa asymmetry is best fitted by an extended clump on the inner edge of the disc, consistent with perturbations from a planet with mass $8\, M_{\oplus } {-} 11\, M_{\rm Jup}$ at ∼60 au that may have migrated outwards, similar to Neptune in our Solar system. If the measured vertical aspect ratio of h = 0.04 ± 0.01 is due to dynamical interactions in the disc, then this requires perturbers with sizes &gt;1200 km. We find tentative evidence for a 0.86 mm excess within 10 au, $70{\pm }22\, \mu$Jy, that may be due to an inner planetesimal belt. We find no evidence for CO gas, but set an upper bound on the CO gas mass of 4 × 10−6 M⊕ ($3\sigma$), consistent with cometary abundances in the Solar system.
A force proportional to velocity squared derived from spacetime algebra
Authors: Hansen Steen H 
Published: June 2021

ABSTRACT
The underlying geometry of spacetime algebra allows one to derive a force by contracting the relativistic generalization of angular momentum, M, with the mass-current, mω, where w is a proper 4-vector velocity. By applying this force to a cosmological object, a repulsive inverse distance-square law is found, which is proportional to the velocity dispersion squared of that structure. It is speculated if this finding may be relevant to the recent suggestion, that such a force may accelerate the expanding universe with no need for a cosmological constant.
Impact of the interplay between stemness features, p53 and pol iota on replication pathway choices
Authors: Ihle Michaela , Biber Stephanie , Schroeder Insa S , Blattner Christine , Deniz Miriam , Damia Giovanna , Gottifredi Vanesa , Wiesmüller Lisa 
Published: June 2021

AbstractUsing human embryonic, adult and cancer stem cells/stem cell-like cells (SCs), we demonstrate that DNA replication speed differs in SCs and their differentiated counterparts. While SCs decelerate DNA replication, differentiated cells synthesize DNA faster and accumulate DNA damage. Notably, both replication phenotypes depend on p53 and polymerase iota (POLι). By exploring protein interactions and newly synthesized DNA, we show that SCs promote complex formation of p53 and POLι at replication sites. Intriguingly, in SCs the translocase ZRANB3 is recruited to POLι and required for slow-down of DNA replication. The known role of ZRANB3 in fork reversal suggests that the p53–POLι complex mediates slow but safe bypass of replication barriers in SCs. In differentiated cells, POLι localizes more transiently to sites of DNA synthesis and no longer interacts with p53 facilitating fast POLι-dependent DNA replication. In this alternative scenario, POLι associates with the p53 target p21, which antagonizes PCNA poly-ubiquitination and, thereby potentially disfavors the recruitment of translocases. Altogether, we provide evidence for diametrically opposed DNA replication phenotypes in SCs and their differentiated counterparts putting DNA replication-based strategies in the spotlight for the creation of therapeutic opportunities targeting SCs.
Tracing contacts to evaluate the transmission of COVID-19 from highly exposed individuals in public transportation
Authors: Ponte Caio , Carmona Humberto A. , Oliveira Erneson A. , Caminha Carlos , Lima Neto Antonio S. , Andrade José S. , Furtado Vasco 
Published: June 2021

AbstractWe investigate, through a data-driven contact tracing model, the transmission of COVID-19 inside buses during distinct phases of the pandemic in a large Brazilian city. From this microscopic approach, we recover the networks of close contacts within consecutive time windows. A longitudinal comparison is then performed by upscaling the traced contacts with the transmission computed from a mean-field compartmental model for the entire city. Our results show that the effective reproduction numbers inside the buses, Rebus, and in the city, Recity, followed a compatible behavior during the first wave of the local outbreak. Moreover, by distinguishing the close contacts of healthcare workers in the buses, we discovered that their transmission, Rehealth, during the same period, was systematically higher than Rebus. This result reinforces the need for special public transportation policies for highly exposed groups of people.
Development of low-cost serological immunoassay to detect antiviral antibodies to Sars-Cov-2 Spike protein
Authors: Peroni Luis Antonio , Toscaro Jessica , Canateli Camila , Lima Gabriel , Pagliarone Ana , Cardoso Elaine , Viana Renata , Borges Jessica Bassani , Lin-Wang Hui Tzu , Abboud Cely S. , Gun Carlos , Franchini Kleber , Bajgelman Marcio 
Published: June 2021

AbstractSeroconversion to SARS-CoV-2 has been widely studied to evaluate infection spreading for epidemiological purpose, or even in studies of protective immunity in convalescent or vaccinated individuals. The viral particle has an envelope harboring the spike glycoprotein, which can be used as an antigen for assay development, to detect antiviral antibodies to SARS-CoV-2. Since several vaccines encode a spike subunit, the full length spike-based immunoassay should be a universal tool to evaluate seroconversion. In this manuscript, we propose a low-cost ELISA that can be used to detect antiviral IgG to SARS-CoV-2 in human serum.
Extended Invariant Information Clustering is Effective for Leave-One-Site-Out Cross-Validation in Resting State Functional Connectivity Modelling
Authors: Okamoto Naoki , Akama Hiroyuki 
Published: June 2021

AbstractHerein, we propose a new deep neural network model based on invariant information clustering (IIC), proposed by Ji et al., to improve the modeling performance of the leave-one-site-out cross-validation (LOSO-CV) for a multi-source dataset. Our Extended IIC (EIIC) is a type of contrastive learning; however, unlike the original IIC, it is characterized by transfer learning with labeled data pairs, but without the need for a data augmentation technique. Each site in LOSO-CV is left out in turn from the remaining sites used for training and receives a value for modeling evaluation. We applied the EIIC to the resting state functional connectivity magnetic resonance imaging dataset of the Autism Brain Imaging Data Exchange. The challenging nature of brain analysis for autism spectrum disorder (ASD) can be attributed to the variability of subjects, particularly the rapid change in the neural system of children as the target ASD age group. However, EIIC demonstrated higher LOSO-CV classification accuracy for the majority of scanning locations than previously used methods. Particularly, with the adjustment of a mini-batch size, EIIC outperformed other classifiers with an accuracy >0.8 for the sites with highest mean age of the subjects. Considering its effectiveness, our proposed method might be promising for harmonization in other domains, owing to its simplicity and intrinsic flexibility. We are currently submitting this manuscript to Frontiers in Neuroinformatics.
The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour
Authors: Oliveira A. Sofia F. , Shoemark Deborah K. , Ibarra Amaurys Avila , Davidson Andrew D. , Berger Imre , Schaffitzel Christiane , Mulholland Adrian J. 
Published: June 2021

AbstractThe SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells and mediates membrane fusion. Recently, a fatty acid binding site was identified in the spike (Toelzer et al. Science 2020). The presence of linoleic acid at this site modulates binding of the spike to the human ACE2 receptor, stabilizing a locked conformation of the protein. Here, dynamical-nonequilibrium molecular dynamics simulations reveal that this fatty acid site is coupled to functionally relevant regions of the spike, some of them far from the fatty acid binding pocket. Removal of a ligand from the fatty acid binding site significantly affects the dynamics of distant, functionally important regions of the spike, including the receptor-binding motif, furin cleavage site and fusion-peptide-adjacent regions. The results also show significant differences in behaviour between clinical variants of the spike: e.g. the D614G mutation shows a significantly different conformational response for some structural motifs relevant for binding and fusion. The simulations identify structural networks through which changes at the fatty acid binding site are transmitted within the protein. These communication networks significantly involve positions that are prone to mutation, indicating that observed genetic variation in the spike may alter its response to linoleate binding and associated allosteric communication.
Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial
Authors:   RECOVERY Collaborative Group, Horby Peter W , Pessoa-Amorim Guilherme , Staplin Natalie , Emberson Jonathan R , Campbell Mark , Spata Enti , Peto Leon , Brunskill Nigel J , Tiberi Simon , Chew Victor , Brown Thomas , Tahir Hasan , Ebert Beate , Chadwick David , Whitehouse Tony , Sarkar Rahuldeb , Graham Clive , Baillie J Kenneth , Basnyat Buddha , Buch Maya H , Chappell Lucy C , Day Jeremy , Faust Saul N , Hamers Raph L , Jaki Thomas , Juszczak Edmund , Jeffery Katie , Lim Wei Shen , Montgomery Alan , Mumford Andrew , Rowan Kathryn , Thwaites Guy , Mafham Marion , Haynes Richard , Landray Martin J 
Published: June 2021

SUMMARYBackgroundAspirin has been proposed as a treatment for COVID-19 on the basis of its antithrombotic properties.MethodsIn this randomised, controlled, open-label platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care plus 150mg aspirin once daily until discharge or usual standard of care alone using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).FindingsBetween 01 November 2020 and 21 March 2021, 7351 patients were randomly allocated to receive aspirin and 7541 patients to receive usual care alone. Overall, 1222 (17%) patients allocated to aspirin and 1299 (17%) patients allocated to usual care died within 28 days (rate ratio 0·96; 95% confidence interval [CI] 0·89-1·04; p=0·35). Consistent results were seen in all pre-specified subgroups of patients. Patients allocated to aspirin had a slightly shorter duration of hospitalisation (median 8 vs. 9 days) and a higher proportion were discharged from hospital alive within 28 days (75% vs. 74%; rate ratio 1·06; 95% CI 1·02-1·10; p=0·0062). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs. 22%; risk ratio 0·96; 95% CI 0·90-1·03; p=0·23). Aspirin use was associated with an absolute reduction in thrombotic events of 0.6% (SE 0.4%) and an absolute increase in major bleeding events of 0.6% (SE 0.2%).InterpretationIn patients hospitalised with COVID-19, aspirin was not associated with reductions in 28-day mortality or in the risk of progressing to invasive mechanical ventilation or death but was associated with a small increase in the rate of being discharged alive within 28 days.FundingUK Research and Innovation (Medical Research Council), National Institute of Health Research (Grant ref: MC_PC_19056), and the Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.
Association between Preventive Measures against Workplace Infection and Preventive Behavior against Personal Infection
Authors: Kawasumi Mika , Nagata Tomohisa , Ando Hajime , Hino Ayako , Tateishi Seiichiro , Tsuji Mayumi , Matsuda Shinya , Fujino Yoshihisa , Mori Koji ,   for the CORoNaWork project
Published: June 2021

AbstractObjectivesTo prevent the spread of coronavirus disease 2019 (COVID-19) infection, it is necessary for each individual to adopt infection prevention behavior. We investigated the effect of infection control measures implemented in the workplace on personal infection prevention behavior.MethodsWe conducted a self-administered questionnaire survey through the Internet from December 22 to 25, 2020, during which period COVID-19 was spreading. Among respondents aged 20 to 65 years (n=27,036), a total of 21,915 workers were included in the analysis after excluding self-employed workers (n=2,202), workers in small/home offices (n=377), and agriculture, forestry, and fisheries workers (n=212), etc., whose personal infection prevention behavior was almost the same as infection control measures taken in the workplace.ResultsThe results showed that as the number of infection control measures in the workplace increased, implementation of infection prevention behavior by individuals also significantly increased. However, the relationship differed depending on the type of personal infection prevention behavior. Specifically, infection control measures against COVID-19 in the workplace may affect personal infection prevention behavior.ConclusionImplementation of infection control measures in the workplace appears to deepen personal understanding of infection prevention behaviors, and increases awareness of the importance of individual infection prevention behavior and its implementation by all individuals. These findings may be applicable not only to COVID-19 measures but also to responses to other emerging infections and seasonal influenza.
The missing pathway in current visuospatial processing models
Authors: Beyh Ahmad , Dell’Acqua Flavio , Cancemi Daniele , De Santiago Requejo Francisco , ffytche Dominic , Catani Marco 
Published: June 2021

SummaryVisuospatial learning depends on the parahippocampal place area (PPA), a functionally heterogenous area which current visuospatial processing models place downstream from parietal cortex and only from area V4 of early visual cortex (EVC). However, evidence for anatomical connections between the PPA and other EVC areas is inconsistent, and these connections are not discussed in current models. Through a data-driven analysis based on diffusion MRI tractography, we present evidence that the PPA sits at the confluence of two white matter systems. The first conveys information from the retrosplenial complex to the anterior PPA and runs within the cingulum bundle. The second system connects all peripheral EVC areas to the posterior PPA and corresponds to the medial occipital longitudinal tract (MOLT), a novel white matter pathway distinct from the cingulum. Based on further functional connectivity analysis and meta-analytic data, we propose that the MOLT supports early stage encoding of visuospatial information by allowing direct reciprocal exchange between the PPA and EVC.
TheStreptochaetagenome and the evolution of the grasses
Authors: Seetharam Arun , Yu Yunqing , Belanger Sébastien , Clark Lynn G. , Meyers Blake C. , Kellogg Elizabeth A. , Hufford Matthew B. 
Published: June 2021

AbstractIn this work, we sequenced and annotated the genome ofStreptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size, capturing most of the gene space.Streptochaetais similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However,Streptochaeta(and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology ofStreptochaetamay thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacteria Mucilaginibacter paludis
Authors: Li Wenqiang , Liu Yang , Wang Fei , Ma Lixin 
Published: June 2021

ABSTRACTArgonaute (Ago) proteins are programmable nuclease found in both eukaryotes and prokaryotes. Prokaryotic Argonaute proteins (pAgos) share a high degree of structural homology with eukaryotic Argonaute proteins (eAgos) and eAgos are considered to evolve from pAgos. However, the majority of studied pAgos prefer to cleave DNA targets, and eAgos exclusively cleave RNA targets. Here, we characterize a novel pAgo, MbpAgo, from psychrotolerant bacteria Mucilaginibacter paludis that can be programmed with DNA guides and prefers to cleave RNA targets rather than DNA targets. MbpAgo can be active at a wide range of temperatures (4-65°C). In comparison with previously studied pAgos, MbpAgo is able to utilize 16-nt long 5’phosphorylated and 5’hydroxylated DNA guides for efficient and precise cleavage and displays no obvious preference for the 5’end nucleotide of a guide. Furthermore, the cleavage efficiency can be regulated by mismatches in the central and 3’supplementary regions of the guide. MbpAgo can efficiently cleave highly-structured RNA targets using both 5’phosphorylated and 5’hydroxylated DNA guides in the presence of Mg2+ or Mn2+. In conclusion, we have demonstrated that MbpAgo is a unique programmable nuclease that has a strong preference for RNA targets, with great potential applications in the field of nucleic acid biotechnology.