Albatross:a scalable simulation-based inference pipeline for analysing stellar streams in the Milky Way

Stellar streams are potentially a very sensitive observational probe of galactic astrophysics, as well as the dark matter population in the Milky Way. On the other hand, performing a detailed, high-fidelity statistical analysis of these objects is challenging for a number of key reasons. First, the modelling of streams across their (potentially billions of years old) dynamical age is complex and computationally costly. Secondly, their detection and classification in large surveys such as Gaia renders a robust statistical description regarding e.g. the stellar membership probabilities, challenging. As a result, the majority of current analyses must resort to simplified models that use only subsets or summaries of the high quality data. In this work, we develop a new analysis framework that takes advantage of advances in simulation-based inference techniques to perform complete analysis on complex stream models. To facilitate this, we develop a new, modular dynamical modelling code sstrax for stellar streams that is highly accelerated using jax. We test our analysis pipeline on a mock observation that resembles the GD1 stream, and demonstrate that we can perform robust inference on all relevant parts of the stream model simultaneously. Finally, we present some outlook as to how this approach can be developed further to perform more complete and accurate statistical analyses of current and future data

Sequential simulation-based inference for gravitational wave signals

The current and upcoming generations of gravitational wave experiments represent an exciting step forward in terms of detector sensitivity and performance. For example, key upgrades at the LIGO, Virgo and KAGRA facilities will see the next observing run (O4) probe a spatial volume around four times larger than the previous run (O3), and design implementations for, e.g., the Einstein Telescope, Cosmic Explorer, and LISA experiments are taking shape to explore a wider frequency range and probe cosmic distances. In this context, however, a number of very real data analysis problems face the gravitational wave community. For example, it will be critical to develop tools and strategies to analyze (among other scenarios) signals that arrive coincidentally in detectors, longer signals that are in the presence of nonstationary noise or other shorter transients, as well as noisy, potentially correlated, coherent stochastic backgrounds. With these challenges in mind, we develop peregrine, a new sequential simulation-based inference approach designed to study broad classes of gravitational wave signal. In this work, we describe the method and implementation, before demonstrating its accuracy and robustness through direct comparison with established likelihood-based methods. Specifically, we show that we are able to fully reconstruct the posterior distributions for every parameter of a spinning, precessing compact binary coalescence using one of the most physically detailed and computationally expensive waveform approximants (SEOBNRv4PHM). Crucially, we are able to do this using only 2% of the waveform evaluations that are required in, e.g., nested sampling approaches. Finally, we provide some outlook as to how this level of simulation efficiency and flexibility in the statistical analysis could allow peregrine to tackle these current and future gravitational wave data analysis problems

Crustal structure of the conjugate Equatorial Atlantic Margins, derived by gravity anomaly inversion

Abstract The crustal structure of the Equatorial Atlantic conjugate margins (South America and West Africa) has been investigated using 3D gravity anomaly inversion, which allows for (1) the elevated geothermal gradient of the lithosphere following rifting and break-up and (2) magmatic addition to the crust during rifting and break-up. It is therefore particularly suitable for the analysis of rifted margins and their associated ocean basins. Maps of crustal thickness and conjugate-margin stretching, derived from gravity anomaly inversion, are used to illustrate how the Equatorial Atlantic opened as a set of stepped rift-transform segments, rather than as a simple orthogonal rifted margin. The influence of the transform faults and associated oceanic fracture zones is particularly clear when the results of the gravity anomaly inversion are combined with a shaded-relief display of the free-air gravity anomaly. A set of crustal cross-sections has been extracted from the results of the gravity inversion along both equatorial margins. These illustrate the crustal structure of both rifted-margin segments and transform-margin segments. The maps and cross-sections are used to delineate crustal type on the margins as (1) inboard, entirely continental, (2) outboard, entirely oceanic and (3) the ocean–continent transition in between where mixed continental and magmatic crust is likely to be present. For a given parameterization of melt generation the amount of magmatic addition within the ocean–continent transition is predicted by the gravity inversion. One of the strengths of the gravity-inversion technique is that these predictions can be made in the absence of any other directly acquired data. On both margins anomalously thick crust is resolved close to a number of oceanic fracture zones. On the South American margin we believe that this thick crust is probably the result of post-break-up magmatism within what was originally normal-thickness oceanic crust. On the West African margin, however, three possible origins are discussed: (1) continental crust extended oceanwards along the fracture zones; (2) oceanic crust magmatically thickened at the fracture zones; and (3) oceanic crust thickened by transpression along the fracture zones. Gravity inversion alone cannot discriminate between these possibilities. The cross-sections also show that, while ‘normal thickness’ oceanic crust (c. 7 km) predominates regionally, local areas of thinner (c. 5 km) and thicker (c. 10 km) oceanic crust are also present along both margins. Finally, using maps of crustal thickness and thinning factor as input to plate reconstructions, the regional palaeogeography of the Equatorial Atlantic during and after break-up is displayed at 10 Ma increments.</jats:p

Nuclear rupture at sites of high curvature compromises retention of DNA repair factors.

The nucleus is physically linked to the cytoskeleton, adhesions, and extracellular matrix-all of which sustain forces, but their relationships to DNA damage are obscure. We show that nuclear rupture with cytoplasmic mislocalization of multiple DNA repair factors correlates with high nuclear curvature imposed by an external probe or by cell attachment to either aligned collagen fibers or stiff matrix. Mislocalization is greatly enhanced by lamin A depletion, requires hours for nuclear reentry, and correlates with an increase in pan-nucleoplasmic foci of the DNA damage marker γH2AX. Excess DNA damage is rescued in ruptured nuclei by cooverexpression of multiple DNA repair factors as well as by soft matrix or inhibition of actomyosin tension. Increased contractility has the opposite effect, and stiff tumors with low lamin A indeed exhibit increased nuclear curvature, more frequent nuclear rupture, and excess DNA damage. Additional stresses likely play a role, but the data suggest high curvature promotes nuclear rupture, which compromises retention of DNA repair factors and favors sustained damage

Qualification of academic facilities for small-scale automated manufacture of autologous cell-based products

Academic centres, hospitals and small companies, as typical development settings for UK regenerative medicine assets, are significant contributors to the development of autologous cell-based therapies. Often lacking the appropriate funding, quality assurance heritage or specialist regulatory expertise, qualifying aseptic cell processing facilities for Good Manufacturing Practice (GMP) compliance is a significant challenge. The qualification of a new Cell Therapy Manufacturing Facility (CTMF) with automated processing capability, the first of its kind in a UK academic setting, provides a unique demonstrator for the qualification of small-scale, automated facilities for GMP compliant manufacture of autologous cell-based products in these settings. This paper shares our experiences in qualifying the CTMF, focussing on our approach to streamlining the qualification effort, the challenges, project delays and inefficiencies we encountered and the subsequent lessons learned

Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline

Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality

New constraints on the mass of fermionic dark matter from dwarf spheroidal galaxies

Theoretical Physic

Repurposing a photosynthetic antenna protein as a super-resolution microscopy label

Techniques such as Stochastic Optical Reconstruction Microscopy (STORM) and Structured Illumination Microscopy (SIM) have increased the achievable resolution of optical imaging, but few fluorescent proteins are suitable for super-resolution microscopy, particularly in the far-red and near-infrared emission range. Here we demonstrate the applicability of CpcA, a subunit of the photosynthetic antenna complex in cyanobacteria, for STORM and SIM imaging. The periodicity and width of fabricated nanoarrays of CpcA, with a covalently attached phycoerythrobilin (PEB) or phycocyanobilin (PCB) chromophore, matched the lines in reconstructed STORM images. SIM and STORM reconstructions of Escherichia coli cells harbouring CpcA-labelled cytochrome bd 1 ubiquinol oxidase in the cytoplasmic membrane show that CpcA-PEB and CpcA-PCB are suitable for super-resolution imaging in vivo. The stability, ease of production, small size and brightness of CpcA-PEB and CpcA-PCB demonstrate the potential of this largely unexplored protein family as novel probes for super-resolution microscopy