Measuring the Edwards-Anderson order parameter of the Bose glass : a quantum gas microscope approach

We thank D Cassettari, A Daley, S Denny, J Keeling, P Kirton and A Trombettoni for insightful discussions and assistance. Computations were performed on the EPSRC CDT Computer Cluster and the University of St Andrews School of Physics & Astronomy computer cluster. SJT acknowledges studentship funding from EPSRC under grant no. EP/G03673X/1. GDB acknowledges support from the Leverhulme Trust RPG-2013-074.With the advent of spatially resolved fluorescence imaging in quantum gas microscopes, it is now possible to directly image glassy phases and probe the local effects of disorder in a highly controllable setup. Here we present numerical calculations using a spatially resolved local mean-field theory, show that it captures the essential physics of the disordered system and use it to simulate the density distributions seen in single-shot fluorescence microscopy. From these simulated images we extract local properties of the phases which are measurable by a quantum gas microscope and show that unambiguous detection of the Bose glass is possible. In particular, we show that experimental determination of the Edwards-Anderson order parameter is possible in a strongly correlated quantum system using existing experiments. We also suggest modifications to the experiments which will allow further properties of the Bose glass to be measured.PostprintPeer reviewe

Can quantum gas microscopes directly image exotic glassy phases?

With the advent of spatially resolved fluorescence imaging in quantum gas microscopes (see e.g. [1]), it is now possible to directly image glassy phases and probe the local effects of disorder in a highly controllable setup. Here we present numerical calculations using a spatially resolved local mean-field theory, show that it captures the essential physics of the disordered system, and use it to simulate the density distributions seen in single-shot fluorescence microscopy [2]. From these simulated images we extract local properties of the phases which are measurable by a quantum gas microscope and show that unambiguous detection of the Bose glass is possible. In particular, we show that experimental determination of the Edwards-Anderson order parameter is possible in a strongly correlated quantum system using existing experiments. We also suggest modifications to the experiments by using spatial light modulators (see [3] and references therein) to tailor the lattice, which will allow further properties of the Bose glass to be measured. References: [1] E Haller, et al., "Single-atom imaging of fermions in a quantum-gas microscope" Nature Physics 11, 738 (2015) [2] S J Thomson, et al., "Measuring the Edwards-Anderson order parameter of the Bose glass: A quantum gas microscope approach" Phys. Rev. A 94, 051601(R) (2016) [3] F Buccheri, et al., "Holographic optical traps for atom-based topological Kondo devices" New J. Phys. 18, 075012 (2016)PostprintNon peer reviewe

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high- quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open- source software pipeline, ‘ResPipe’

Changes in gene expression in space and time orchestrate environmentally mediated shaping of root architecture

Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana, at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response nonredundancy. Using causative gene network inference to compare the genes regulated in different cell types and during responses to nitrogen and a biotic interaction we found that common transcriptional modules often regulate the same gene families, but control different individual members of these families, specific to response and cell type. This reinforces that the activity of a gene cannot be defined simply as molecular function; rather, it is a consequence of spatial location, expression timing and environmental responsiveness

Prevalence, risk factors, and treatments for post-COVID breathlessness:a systematic review and meta-analysis

Persistent breathlessness >28 days after acute COVID-19 infection has been identified as a highly debilitating post-COVID symptom. However, the prevalence, risk factors, mechanisms and treatments for post-COVID breathlessness remain poorly understood. We systematically searched PubMed and Embase for relevant studies published from 1 January 2020 to 1 November 2021 (PROSPERO registration number: CRD42021285733) and included 119 eligible papers. Random-effects meta-analysis of 42 872 patients with COVID-19 reported in 102 papers found an overall prevalence of post-COVID breathlessness of 26% (95% CI 23-29) when measuring the presence/absence of the symptom, and 41% (95% CI 34-48) when using Medical Research Council (MRC)/modified MRC dyspnoea scale. The pooled prevalence decreased significantly from 1-6 months to 7-12 months post-infection. Post-COVID breathlessness was more common in those with severe/critical acute infection, those who were hospitalised and females, and was less likely to be reported by patients in Asia than those in Europe or North America. Multiple pathophysiological mechanisms have been proposed (including deconditioning, restrictive/obstructive airflow limitation, systemic inflammation, impaired mental health), but the body of evidence remains inconclusive. Seven cohort studies and one randomised controlled trial suggested rehabilitation exercises may reduce post-COVID breathlessness. There is an urgent need for mechanistic research and development of interventions for the prevention and treatment of post-COVID breathlessness

Predictive rules of efflux inhibition and avoidance in Pseudomonas aeruginosa

Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance.Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa. We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of anti-bacterial agents suitable for treatment of P. aeruginosa infections

Automatic vetting of planet candidates from ground based surveys : machine learning with NGTS

State of the art exoplanet transit surveys are producing ever increasing quantities of data. To make the best use of this resource, in detecting interesting planetary systems or in determining accurate planetary population statistics, requires new automated methods. Here we describe a machine learning algorithm that forms an integral part of the pipeline for the NGTS transit survey, demonstrating the efficacy of machine learning in selecting planetary candidates from multi-night ground based survey data. Our method uses a combination of random forests and self-organising-maps to rank planetary candidates, achieving an AUC score of 97.6% in ranking 12368 injected planets against 27496 false positives in the NGTS data. We build on past examples by using injected transit signals to form a training set, a necessary development for applying similar methods to upcoming surveys. We also make the autovet code used to implement the algorithm publicly accessible. autovet is designed to perform machine learned vetting of planetary candidates, and can utilise a variety of methods. The apparent robustness of machine learning techniques, whether on space-based or the qualitatively different ground-based data, highlights their importance to future surveys such as TESS and PLATO and the need to better understand their advantages and pitfalls in an exoplanetary context

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

Active ageing, pensions and retirement in the UK

The ageing population has led to increasing concerns about pensions and their future sustainability. Much of the dominant policy discourse around ageing and pension provision over the last decade has focussed on postponing retirement and prolonging employment. These measures are central to productive notions of ‘active ageing’. Initially the paper briefly sets out the pension developments in the UK. Then it introduces active ageing and active ageing policy, exploring its implications for UK pension provision. It demonstrates that a more comprehensive active ageing framework, which incorporates a life-course perspective, has the potential to assist the UK to respond to the challenges of an ageing population. In doing so it needs to highlight older people as an economic and social resource, and reduce barriers to older people’s participation in society

A genomic epidemiological study shows prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage

Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four Enterobacterales genera, primarily Escherichia coli, were purified from livestock (cattle, pigs, and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long and short read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although E. coli isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep, with cattle isolates being intermediates. Approximately 28% of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90% of sequenced isolates harboured diverse plasmids, only 11% of plasmids (n=58/522) identified contained AMR genes, with 91% of AMR plasmids being from pig, 9% from cattle and none from sheep isolates; these results indicated pigs were a principle reservoir of AMR genes harboured by plasmids likely involved in their horizontal transfer. Significant associations were observed between AMU (mg/kg) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than other livestock species. Therefore, our results show that AMR prevalence in livestock is not only impacted by recent AMU on-farm but also livestock related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmissio