Aspects of the numerical simulation of binary black hole spacetimes

The focus of this thesis is the use of numerical simulations of black hole spacetimes in gravitational wave astronomy. The history of the field over the past century is briefly sketched, tracing the journey from general relativity through to the production of full 3D simulations of the inspiral and merger of a black hole binary. This is followed by an exploration of the current state of the art of numerical black hole binary simulations as used by the LIGO-Virgo-KAGRA Collaboration, first with the presentation of a catalogue of such simulations, then through an investigation into the consistency of simulations produced by three prominent numerical relativity codes. Significant disagreement is observed in their gravitational wave phases which may prove problematic for future ground-based gravitational wave astronomy. Finally the practical obstacles inherent to the simulation of high mass ratio binaries, of particular relevance to upcoming space-based gravitational wave detectors, is discussed and a novel solution proposed with tests on a preliminary implementation of this conducted for static and boosted black holes, and for the head-on collision of two black holes. A reduction in resolution of three orders of magnitude is achieved in these exploratory simulations, equivalent to a speed increase of 60,000% in the static black hole case. While this demonstrates its potential for further development, significant questions remain over how accurately the true solution is recovered or whether it is only the phenomenology that is approximated

Effectiveness of financial incentives to improve adherence to maintenance treatment with antipsychotics: cluster randomised controlled trial

Objective: To test whether offering financial incentives to patients with psychotic disorders is effective in improving adherence to maintenance treatment with antipsychotics. Design: Cluster randomised controlled trial. Setting: Community mental health teams in secondary psychiatric care in the United Kingdom. Participants: Patients with a diagnosis of schizophrenia, schizoaffective disorder, or bipolar disorder, who were prescribed long acting antipsychotic (depot) injections but had received 75% or less of the prescribed injections. We randomly allocated 73 teams with a total of 141 patients. Primary outcome data were available for 35 intervention teams with 75 patients (96% of randomised) and for 31 control teams with 56 patients (89% of randomised). Interventions: Participants in the intervention group were offered £15 (€17; $22) for each depot injection over a 12 month period. Participants in the control condition received treatment as usual. Main outcome measure: The primary outcome was the percentage of prescribed depot injections given during the 12 month intervention period. Results 73 teams with 141 consenting patients were randomised, and outcomes were assessed for 131 patients (93%).⇓ Average baseline adherence was 69% in the intervention group and 67% in the control group. During the 12 month trial period adherence was 85% in the intervention group and 71% in the control group. The adjusted effect estimate was 11.5% (95% confidence interval 3.9% to 19.0%, P=0.003). A secondary outcome was an adherence of ≥95%, which was achieved in 28% of the intervention group and 5% of the control group (adjusted odds ratio 8.21, 95% confidence interval 2.00 to 33.67, P=0.003). Although differences in clinician rated clinical improvement between the groups failed to reach statistical significance, patients in the intervention group had more favourable subjective quality of life ratings (β=0.71, 95% confidence interval 0.26 to 1.15, P=0.002). The number of admissions to hospital and adverse events were low in both groups and did not show substantial differences. Conclusion: Offering modest financial incentives to patients with psychotic disorders is an effective method for improving adherence to maintenance treatment with antipsychotics

Single-molecule imaging of Bacteroides fragilis AddAB reveals the highly processive translocation of a single motor helicase

The AddAB helicase and nuclease complex is used for repairing double-strand DNA breaks in the many bacteria that do not possess RecBCD. Here, we show that AddAB, from the Gram-negative opportunistic pathogen Bacteroides fragilis, can rescue the ultraviolet sensitivity of an Escherichia coli recBCD mutant and that addAB is required for survival of B. fragilis following DNA damage. Using single-molecule observations we demonstrate that AddAB can translocate along DNA at up to 250 bp per second and can unwind an average of 14 000 bp, with some complexes capable of unwinding 40 000 bp. These results demonstrate the importance of processivity for facilitating encounters with recognition sequences that modify enzyme function during homologous recombination

Cost-effectiveness of financial incentives to promote adherence to depot antipsychotic medication: economic evaluation of a cluster-randomised controlled trial

Background: Offering a modest financial incentive to people with psychosis can promote adherence to depot antipsychotic medication, but the cost-effectiveness of this approach has not been examined. Methods: Economic evaluation within a pragmatic cluster-randomised controlled trial. 141 patients under the care of 73 teams (clusters) were randomised to intervention or control; 138 patients with diagnoses of schizophrenia, schizo-affective disorder or bipolar disorder participated. Intervention participants received £15 per depot injection over 12 months, additional to usual acute, mental and community primary health services. The control group received usual health services. Main outcome measures: incremental cost per 20% increase in adherence to depot antipsychotic medication; incremental cost of ‘good’ adherence (defined as taking at least 95% of the prescribed number of depot medications over the intervention period). Findings: Economic and outcome data for baseline and 12-month follow-up were available for 117 participants. The adjusted difference in adherence between groups was 12.2% (73.4% control vs. 85.6% intervention); the adjusted costs difference was £598 (95% CI -£4 533, £5 730). The extra cost per patient to increase adherence to depot medications by 20% was £982 (95% CI -£8 020, £14 000). The extra cost per patient of achieving 'good' adherence was £2 950 (CI -£19 400, £27 800). Probability of cost-effectiveness exceeded 97.5%at willingness-to-pay values of £14 000 for a 20% increase in adherence and £27 800 for good adherence. Interpretation: Offering a modest financial incentive to people with psychosis is cost-effective in promoting adherence to depot antipsychotic medication. Direct healthcare costs (including costs of the financial incentive) are unlikely to be increased by this intervention. Trial Registration: ISRCTN.com 7776928

Engineering a reagentless biosensor for single-stranded DNA to measure real-time helicase activity in Bacillus

Single-stranded DNA-binding protein(SSB)is a well characterized ubiquitous and essential bacterial protein involved in almost all aspects of DNA metabolism. Using the Bacillus subtilis SSB we have generated areagentless SSB biosensor that can be used as a helicase probe in B. subtilis and closely related gram positive bacteria. We have demonstrated the utility of the probe in a DNA unwinding reaction using a helicase from Bacillus and for the first time,characterized the B. subtilis SSB's DNA binding mode switching and stoichiometry.The importance of SSB in DNA metabolism is not limited to simply binding and protecting ssDNA during DNA replication, as previously thought. It interacts with an array of partner proteins to coordinate many different aspects of DNA metabolism. In most cases its interactions with partner proteins is species-specific and for this reason, knowing how to produce and use cognate reagentless SSB biosensors indifferent bacteria is critical.Here we explain how to produce a B. subtilis SSB probe that exhibits 9-fold fluorescence increase upon binding to single stranded DNA and can be used in all related grampositive firmicutes which employ drastically different DNA replication and repair systems than the widely studied Escherichiacoli. The materials to produce the B. subtilis SSB probe a recommercially available, so the methodology described here is widely available unlike previously published methods for the E. coli SSB

Bacillus subtilis polynucleotide phosphorylase 3′-to-5′ DNase activity is involved in DNA repair

In the presence of Mn2+, an activity in a preparation of purified Bacillus subtilis RecN degrades single-stranded (ss) DNA with a 3′ → 5′ polarity. This activity is not associated with RecN itself, because RecN purified from cells lacking polynucleotide phosphorylase (PNPase) does not show the exonuclease activity. We show here that, in the presence of Mn2+ and low-level inorganic phosphate (Pi), PNPase degrades ssDNA. The limited end-processing of DNA is regulated by ATP and is inactive in the presence of Mg2+ or high-level Pi. In contrast, the RNase activity of PNPase requires Mg2+ and Pi, suggesting that PNPase degradation of RNA and ssDNA occur by mutually exclusive mechanisms. A null pnpA mutation (ΔpnpA) is not epistatic with ΔrecA, but is epistatic with ΔrecN and Δku, which by themselves are non-epistatic. The addA5, ΔrecO, ΔrecQ (ΔrecJ), ΔrecU and ΔrecG mutations (representative of different epistatic groups), in the context of ΔpnpA, demonstrate gain- or loss-of-function by inactivation of repair-by-recombination, depending on acute or chronic exposure to the damaging agent and the nature of the DNA lesion. Our data suggest that PNPase is involved in various nucleic acid metabolic pathways, and its limited ssDNA exonuclease activity plays an important role in RecA-dependent and RecA-independent repair pathways

The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε

Replication fork stalling and accumulation of single-stranded DNA trigger the S phase checkpoint, a signalling cascade that, in budding yeast, leads to the activation of the Rad53 kinase. Rad53 is essential in maintaining cell viability, but its targets of regulation are still partially unknown. Here we show that Rad53 drives the hyper-SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε, principally following replication forks stalling induced by nucleotide depletion. Pol2 is the main target of SUMOylation within the replisome and its modification requires the SUMO-ligase Mms21, a subunit of the Smc5/6 complex. Moreover, the Smc5/6 complex co-purifies with Pol ε, independently of other replisome components. Finally, we map Pol2 SUMOylation to a single site within the N-terminal catalytic domain and identify a SUMO-interacting motif at the C-terminus of Pol2. These data suggest that the S phase checkpoint regulate Pol ε during replication stress through Pol2 SUMOylation and SUMO-binding abilit

Search for gravitational-lensing signatures in the full third observing run of the LIGO-Virgo network

Gravitational lensing by massive objects along the line of sight to the source causes distortions of gravitational wave-signals; such distortions may reveal information about fundamental physics, cosmology and astrophysics. In this work, we have extended the search for lensing signatures to all binary black hole events from the third observing run of the LIGO--Virgo network. We search for repeated signals from strong lensing by 1) performing targeted searches for subthreshold signals, 2) calculating the degree of overlap amongst the intrinsic parameters and sky location of pairs of signals, 3) comparing the similarities of the spectrograms amongst pairs of signals, and 4) performing dual-signal Bayesian analysis that takes into account selection effects and astrophysical knowledge. We also search for distortions to the gravitational waveform caused by 1) frequency-independent phase shifts in strongly lensed images, and 2) frequency-dependent modulation of the amplitude and phase due to point masses. None of these searches yields significant evidence for lensing. Finally, we use the non-detection of gravitational-wave lensing to constrain the lensing rate based on the latest merger-rate estimates and the fraction of dark matter composed of compact objects

A revision of the genus Ima Tindale (Mantodea: Nanomantidae: Fulciniinae) with the description of a new genus

Ima fusca is one of a number of unusual and infrequently collected Australian mantises about which relatively little is known. Long considered a single species, morphological studies instead revealed the presence of a second cryptic species. We here describe this species as Ima corymbia sp. nov. and redescribe both Ima and Ima fusca in detail. Additionally, we describe a unique, robust species allied to Ima that was discovered with the aid of citizen science, Inimia nat gen. et sp. nov. In light of this discovery, we provide keys to both the Australian Fulciniini genera and to the species of Ima. Finally, we provide detailed behavioural and ecological records for all three species, including the peculiar host plant specificity of Ima spp. We document and discuss this specificity in depth and suggest several possible reasons for its occurrence

Revision of the genus Calofulcinia Giglio-Tos (Mantodea: Nanomantidae: Fulciniinae) in Australia

The genus Calofulcinia comprises several species of small, cryptic mantis, three of which have been described from Australia. The genus is infrequently recorded and is thus very poorly known, and even basic questions of species delimitation and distribution have remained virtually unknown since the descriptions of these taxa. We here redescribe and figure the three known Australian species of Calofulcinia in full and provide a detailed key to Australian species. We record significant range extensions for all three species, and provide the first detailed behavioural and ecological records for the genus. In addition, we group the Australian species into a Robust Group (C. paraoxypila) and a Gracile Group (C. australis and C. oxynota), we detail the occurrence of colour polymorphism within the genus, and finally we discuss the apparent microhabitat specificity of Calofulcinia spp. (mosses and lichens) and their preference for cool, moist environments with reference to our changing climate