Hybrid phase-space simulation method for interacting Bose fields

We introduce an approximate phase-space technique to simulate the quantum dynamics of interacting bosons. With the future goal of treating Bose-Einstein condensate systems, the method is designed for systems with a natural separation into highly occupied (condensed) modes and lightly occupied modes. The method self-consistently uses the Wigner representation to treat highly occupied modes and the positive-P representation for lightly occupied modes. In this method, truncation of higher-derivative terms from the Fokker-Planck equation is usually necessary. However, at least in the cases investigated here, the resulting systematic error, over a finite time, vanishes in the limit of large Wigner occupation numbers. We tested the method on a system of two interacting anharmonic oscillators, with high and low occupations, respectively. The Hybrid method successfully predicted atomic quadratures to a useful simulation time 60 times longer than that of the positive-P method. The truncated Wigner method also performed well in this test. For the prediction of the correlation in a quantum nondemolition measurement scheme, for this same system, the Hybrid method gave excellent agreement with the exact result, while the truncated Wigner method showed a large systematic error.Comment: 13 pages; 6 figures; references added; figures correcte

Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia Glade was an exception to the generally high support we observed; the topology of this Glade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.Peer reviewe

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced

Next-Generation Comprehensive Data-Driven Models of Solar Eruptive Events

Solar flares and coronal mass ejections are interrelated phenomena that together are known as solar eruptive events. These are the main drivers of space weather and understanding their origins is a primary goal of Heliophysics. In this white paper, we advocate for the allocation of sufficient resources to bring together experts in observations and modeling to construct and test next generation data-driven models of solar eruptive events. We identify the key components necessary for constructing comprehensive end-to-end models including global scale 3D MHD resolving magnetic field evolution and reconnection, small scale simulations of particle acceleration in reconnection exhausts, kinetic scale transport of flare-accelerated particles into the lower solar atmosphere, and the radiative and hydrodynamics responses of the solar atmosphere to flare heating. Using this modeling framework, long-standing questions regarding how solar eruptive events release energy, accelerate particles, and heat plasma can be explored. To address open questions in solar flare physics, we recommend that NASA and NSF provide sufficient research and analysis funds to bring together a large body of researchers and numerical tools to tackle the end-to-end modeling framework that we outline. Current dedicated theory and modeling funding programs are relatively small scale and infrequent; funding agencies must recognize that modern space physics demands the use of both observations and modeling to make rapid progress.Comment: White paper submitted to the Decadal Survey for Solar and Space Physics (Heliophysics) 2024-2033; 9 pages, 4 figure

Hopes and Fears: Community cohesion and the ‘White working class’ in one of the ‘failed spaces’ of multiculturalism

Since 2001, community cohesion has been an English policy concern, with accompanying media discourse portraying a supposed failure by Muslims to integrate. Latterly, academia has foregrounded White majority attitudes towards ethnic diversity, particularly those of the ‘White working class’. Whilst questioning this categorisation, we present data on attitudes towards diversity from low income, mainly White areas within Dewsbury, West Yorkshire, a town portrayed in media discourse as one of the ‘failed spaces’ of multiculturalism. Drawing on mixed methods research, we present and discuss data that provide a complex message, seemingly confirming pessimistic analyses around ethnic diversity and predominantly White neighbourhoods but also highlighting an appetite within the same communities for greater and more productive inter-ethnic contact. Furthermore, anxieties about diversity and integration have largely failed to coalesce into broad support for organised anti-minority politics manifest in groups such as the English Defence League

Combined analysis of weak lensing and X-ray blind surveys

We present a joint weak lensing and X-ray analysis of 4 deg$^2$ from the CFHTLS and XMM-LSS surveys. Our weak lensing analysis is the first analysis of a real survey using shapelets, a new generation weak lensing analysis method. We create projected mass maps of the images, and extract 6 weak-lensing-detected clusters of galaxies. We show that their counts can be used to constrain the power spectrum normalisation $\sigma_8 =0.92_{-0.30}^{+0.26}$ for $\Omega_m=0.24$. We show that despite the large scatter generally observed in the M-T relation derived from lensing masses, tight constraints on both its slope and normalisation $M_*$ can be obtained with a moderate number of sources provided that the covered mass range is large enough. Adding clusters from Bardeau et al. (2007) to our sample, we measure $M_* = 2.71_{-0.61}^{+0.79} 10^{14} h^{-1} M_\odot$. Although they are dominated by shot noise and sample variance, our measurements are consistent with currently favoured values, and set the stage for future surveys. We thus investigate the dependence of those estimates on survey size, depth, and integration time, for joint weak lensing and X-ray surveys. We show that deep surveys should be dedicated to the study of the physics of clusters and groups of galaxies. For a given exposure time, wide surveys provide a larger number of detected clusters and are therefore preferred for the measurement of cosmological parameters such as $\sigma_8$ and $M_*$. We show that a wide survey of a few hundred square degrees is needed to improve upon current measurements of these parameters. More ambitious surveys covering 7000 deg$^2$ will provide the 1% accuracy in the estimation of the power spectrum and the M-T relation normalisations.Comment: MNRAS in press Matches accepted version. References update

Urinary Metal Levels and Coronary Artery Calcification: Longitudinal Evidence in the Multi-Ethnic Study of Atherosclerosis (MESA)

Objective: Growing evidence indicates that exposure to metals are risk factors for cardiovascular disease (CVD). We hypothesized that higher urinary levels of metals with prior evidence of an association with CVD, including non-essential (cadmium , tungsten, and uranium) and essential (cobalt, copper, and zinc) metals are associated with baseline and rate of change of coronary artery calcium (CAC) progression, a subclinical marker of atherosclerotic CVD. Methods: We analyzed data from 6,418 participants in the Multi-Ethnic Study of Atherosclerosis (MESA) with spot urinary metal levels at baseline (2000-2002) and 1-4 repeated measures of spatially weighted coronary calcium score (SWCS) over a ten-year period. SWCS is a unitless measure of CAC highly correlated to the Agatston score but with numerical values assigned to individuals with Agatston score=0. We used linear mixed effect models to assess the association of baseline urinary metal levels with baseline SWCS, annual change in SWCS, and SWCS over ten years of follow-up. Urinary metals (adjusted to μg/g creatinine) and SWCS were log transformed. Models were progressively adjusted for baseline sociodemographic factors, estimated glomerular filtration rate, lifestyle factors, and clinical factors. Results: At baseline, the median and interquartile range (25th, 75th) of SWCS was 6.3 (0.7, 58.2). For urinary cadmium, the fully adjusted geometric mean ratio (GMR) (95%Cl) of SWCS comparing the highest to the lowest quartile was 1.51 (1.32, 1.74) at baseline and 1.75 (1.47, 2.07) at ten years of follow-up. For urinary tungsten, uranium, and cobalt the corresponding GMRs at ten years of follow-up were 1.45 (1.23, 1.71), 1.39 (1.17, 1.64), and 1.47 (1.25, 1.74), respectively. For copper and zinc, the association was attenuated with adjustment for clinical risk factors; GMRs at ten years of follow-up before and after adjustment for clinical risk factors were 1.55 (1.30, 1.84) and 1.33 (1.12, 1.58), respectively, for copper and 1.85 (1.56, 2.19) and 1.57 (1.33, 1.85) for zinc. Conclusion: Higher levels of cadmium, tungsten, uranium, cobalt, copper, and zinc, as measured in urine, were associated with subclinical CVD at baseline and at follow-up. These findings support the hypothesis that metals are pro-atherogenic factors.The Multi-Ethnic Study of Atherosclerosis (MESA) is supported by contracts 75N92020D00001, HHSN268201500003I, N01-HC-95159, 75N92020D00005, N01-HC-95160, 75N92020D00002, N01-HC-95161, 75N92020D00003, N01-HC-95162, 75N92020D00006, N01-HC-95163, 75N92020D00004, N01-HC-95164, 75N92020D00007, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168 and N01-HC-95169 from the National Heart, Lung, and Blood Institute, and by grants UL1-TR-000040, UL1-TR-001079, and UL1-TR-001420 from the National Center for Advancing Translational Sciences (NCATS). This publication was developed under the Science to Achieve Results (STAR) research assistance agreements, No. RD831697 (MESA Air) and RD-83830001 (MESA Air Next Stage), awarded by the U.S Environmental Protection Agency (EPA). It has not been formally reviewed by the EPA. The views expressed in this document are solely those of the authors and the EPA does not endorse any products or commercial services mentioned in this publication. Dr. Maria Tellez-Plaza was supported by grants PI15/00071 and PI22/00029 from the Strategic Action for Health Research, Instituto de Salud Carlos III and the Spanish Ministry of Science and Innovation, and co-funded with European Funds for Regional Development (FEDER). The opinions and views expressed in this article are those of the authors and do not necessarily represent the official position of the Instituto de Salud Carlos III (Spain). Work in the authors? laboratories is also supported in part by NIH grants P42ES023716, P42ES010349, P42ES033719, P30ES009089, T32ES007322, R01ES029967, R01HL155576. The authors thank the other investigators, the staff, and the participants of the MESA study for their valuable contributions. A full list of participating MESA investigators and institutions can be found at http://www.mesa-nhlbi.org. This paper has been reviewed and approved by the MESA Publications and Presentations Committee.N

Lectin-like bacteriocins from pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor

Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins

Gas and Dust Associated with the Strange, Isolated, Star BP Piscium

We have carried out a multiwavelength observational campaign demonstrating some of the remarkable properties of the infrared-bright variable star BP Psc. Surrounded by a compact dusty, gaseous disk, this little-studied late-G (or early-K) type star emits about 75% of its detected energy flux at infrared wavelengths. Evidence for accretion of gas in conjunction with narrow bi-polar jets and Herbig-Haro objects is apparently consistent with classification of BP Psc as a pre-main sequence star, as postulated in most previous studies. If young, then BP Psc would be one of the nearest and oldest known classical T Tauri stars. However, such an evolutionary classification encounters various problems that are absent or much less severe if BP Psc is instead a luminosity class III post-main sequence star. In this case, it would be the first known example of a first ascent giant surrounded by a massive molecular disk with accompanying rapid gas accretion and prominent jets and HH objects. In this model, the genesis of the massive dusty gaseous disk could be a consequence of the envelopment of a low mass companion star. Properties in the disk may be conducive to the current formation of planets, a gigayear or more after the formation of BP Psc itself.Comment: Accepted for Astrophysical Journal New version with minor changes: includes fixing a typo on the 3rd line of the paragraph that follows Equa 4 and adding a new reference (Nordhaus and Blackman 2006

The internal brakes on violent escalation:a typology

Most groups do less violence than they are capable of. Yet while there is now an extensive literature on the escalation of or radicalisation towards violence, particularly by ‘extremist’ groups or actors, and while processes of de-escalation or de-radicalisation have also received significant attention, processes of non- or limited escalation have largely gone below the analytical radar. This article contributes to current efforts to address this limitation in our understanding of the dynamics of political aggression by developing a descriptive typology of the ‘internal brakes’ on violent escalation: the mechanisms through which members of the groups themselves contribute to establish and maintain limits upon their own violence. We identify five underlying logics on which the internal brakes operate: strategic, moral, ego maintenance, outgroup definition, and organisational. The typology is developed and tested using three very different case studies: the transnational and UK jihadi scene from 2005 to 2016; the British extreme right during the 1990s, and the animal liberation movement in the UK from the mid-1970s until the early 2000s