A systematic study of the phase difference between QPO harmonics in black hole X-ray binaries

We perform a systematic study of the evolution of the waveform of black hole X-ray binary low-frequency QPOs, by measuring the phase difference between their fundamental and harmonic features. This phase difference has been studied previously for small number of QPO frequencies in individual sources. Here, we present a sample study spanning fourteen sources and a wide range of QPO frequencies. With an automated pipeline, we systematically fit power spectra and calculate phase differences from archival Rossi X-ray Timing Explorer (RXTE) observations. We measure well-defined phase differences over a large range of QPO frequencies for most sources, demonstrating that a QPO for a given source and frequency has a persistent underlying waveform. This confirms the validity of recently developed spectral-timing methods performing phase resolved spectroscopy of the QPO. Furthermore, we evaluate the phase difference as a function of QPO frequency. For Type-B QPOs, we find that the phase difference stays constant with frequency for most sources. We propose a simple jet precession model to explain these constant Type-B QPO phase differences. The phase difference of the Type-C QPO is not constant but systematically evolves with QPO frequency, with the resulting relation being similar for a number of high inclination sources, but more variable for low-inclination sources. We discuss how the evolving phase difference can naturally arise in the framework of precession models for the Type-C QPO, by considering the contributions of a direct and reflected component to the QPO waveform

Transient study using LoTSS -- framework development and preliminary results

We present a search for transient radio sources on time-scales of seconds to hours at 144 MHz using the LOFAR Two-metre Sky Survey (LoTSS). This search is conducted by examining short time-scale images derived from the LoTSS data. To allow imaging of LoTSS on short time-scales, a novel imaging and filtering strategy is introduced. This includes sky model source subtraction, no cleaning or primary beam correction, a simple source finder, fast filtering schemes and source catalogue matching. This new strategy is first tested by injecting simulated transients, with a range of flux densities and durations, into the data. We find the limiting sensitivity to be 113 and 6 mJy for 8 second and 1 hour transients respectively. The new imaging and filtering strategies are applied to 58 fields of the LoTSS survey, corresponding to LoTSS-DR1 (2% of the survey). One transient source is identified in the 8 second and 2 minute snapshot images. The source shows one minute duration flare in the 8 hour observation. Our method puts the most sensitive constraints on/estimates of the transient surface density at low frequencies at time-scales of seconds to hours; $<4.0\cdot 10^{-4} \; \text{deg}^{-2}$ at 1 hour at a sensitivity of 6.3 mJy; $5.7\cdot 10^{-7} \; \text{deg}^{-2}$ at 2 minutes at a sensitivity of 30 mJy; and $3.6\cdot 10^{-8} \; \text{deg}^{-2}$ at 8 seconds at a sensitivity of 113 mJy. In the future, we plan to apply the strategies presented in this paper to all LoTSS data.Comment: submitted to MNRA

Limits on long-time-scale radio transients at 150 MHz using the TGSS ADR1 and LoTSS DR2 catalogues

We present a search for transient radio sources on timescales of 2 to 9 yr at 150 MHz. This search is conducted by comparing the first Alternative Data Release of the TIFR GMRT Sky Survey (TGSS ADR1) and the second data release of the LOFAR Two-metre Sky Survey (LoTSS DR2). The overlapping survey area covers 5570 $\rm{deg}^2$ on the sky, or 14 per cent of the total sky. We introduce a method to compare the source catalogues that involves a pair match of sources, a flux density cutoff to meet the survey completeness limit and a newly developed compactness criterion. This method is used to identify both transient candidates in the TGSS source catalogue that have no counterpart in the LoTSS catalogue and transient candidates in LoTSS without a counterpart in TGSS. We find that imaging artefacts and uncertainties and variations in the flux density scales complicate the transient search. Our method to search for transients by comparing two different surveys, while taking into account imaging artefacts around bright sources and misaligned flux scales between surveys, is universally applicable to future radio transient searches. No transient sources were identified, but we are able to place an upper limit on the transient surface density of $<5.4 \cdot 10^{-4}\ \text{deg}^{-2}$ at 150 MHz for compact sources with an integrated flux density over 100 mJy. Here we define a transient as a compact source with flux density greater than 100 mJy that appears in the catalogue of one survey without a counterpart in the other survey.Comment: 14 pages, 11 figure

Low-frequency radio observations of recurrent nova RS Ophiuchi with MeerKAT and LOFAR

We report low-frequency radio observations of the 2021 outburst of the recurrent nova RS Ophiuchi. These observations include the lowest frequency observations of this system to date. Detailed light curves are obtained by MeerKAT at 0.82 and 1.28 GHz and LOFAR at 54 and 154 MHz. These low-frequency detections allow us to put stringent constraints on the brightness temperature that clearly favour a non-thermal emission mechanism. The radio emission is interpreted and modelled as synchrotron emission from the shock interaction between the nova ejecta and the circumbinary medium. The light curve shows a plateauing behaviour after the first peak, which can be explained by either a non-uniform density of the circumbinary medium or a second emission component. Allowing for a second component in the light curve modelling captures the steep decay at late times. Furthermore, extrapolating this model to 15 years after the outburst shows that the radio emission might not fully disappear between outbursts. Further modelling of the light curves indicates a red giant mass loss rate of $\sim 5 \cdot 10^{-8}~{\rm M_\odot~yr^{-1}}$. The spectrum cannot be modelled in detail at this stage, as there are likely at least four emission components. Radio emission from stellar wind or synchrotron jets are ruled out as the possible origin of the radio emission. Finally, we suggest a strategy for future observations that would advance our understanding of the physical properties of RS Oph.Comment: submitted to MNRA

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data.

BACKGROUND: Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from the murine host. The reads of murine origin result in false positives in mutation analysis of DNA samples and obscure gene expression levels when sequencing RNA. However, currently available algorithms are limited and improvements in accuracy and ease of use are necessary. RESULTS: We developed the R-package XenofilteR, which separates mouse from human sequence reads based on the edit-distance between a sequence read and reference genome. To assess the accuracy of XenofilteR, we generated sequence data by in silico mixing of mouse and human DNA sequence data. These analyses revealed that XenofilteR removes > 99.9% of sequence reads of mouse origin while retaining human sequences. This allowed for mutation analysis of xenograft samples with accurate variant allele frequencies, and retrieved all non-synonymous somatic tumor mutations. CONCLUSIONS: XenofilteR accurately dissects RNA and DNA sequences from mouse and human origin, thereby outperforming currently available tools. XenofilteR is open source and available at https://github.com/PeeperLab/XenofilteR

Comparative effectiveness of surgery in traumatic acute subdural and intracerebral haematoma: study protocol for a prospective observational study within CENTER-TBI and Net-QuRe

INTRODUCTION: Controversy exists about the optimal treatment for patients with a traumatic acute subdural haematoma (ASDH) and an intracerebral haematoma/contusion (t-ICH). Treatment varies largely between different regions. The effect of this practice variation on patient outcome is unknown. Here, we present the protocol for a prospective multicentre observational study aimed at comparing the effectiveness of different treatment strategies in patients with ASDH and/or t-ICH. Specifically, the aims are to compare (1) an acute surgical approach to an expectant approach and (2) craniotomy to decompressive craniectomy when evacuating the haematoma. METHODS AND ANALYSIS: Patients presenting to the emergency room with an ASDH and/or an t-ICH are eligible for inclusion. Standardised prospective data on patient and injury characteristics, treatment and outcome will be collected on 1000 ASDH and 750 t-ICH patients in 60-70 centres within two multicentre prospective observational cohort studies: the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) and Neurotraumatology Quality Registry (Net-QuRe). The interventions of interest are acute surgery, defined as surgery directly after the first CT at presentation versus late or no surgery and craniotomy versus decompressive craniectomy. The primary outcome measure is the Glasgow Outcome Score-Extended at 6 months. Secondary outcome measures include in-hospital mortality, quality of life and neuropsychological tests. In the primary analysis, the effect of treatment preference (eg, proportion of patients in which the intervention under study is preferred) per hospital will be analysed with random effects ordinal regression models, adjusted for casemix and stratified by study. Such a hospital-level approach reduces confounding by the indication. Sensitivity analyses will includ

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

The Perceived Impact of Trauma-Focused Research on Forensic Psychiatric Patients With Lifetime Victimization Histories

This study examined the perceived costs, benefits, and motivations for participating in individual trauma-focused interviews among forensic psychiatric patients (N = 74). The majority of our participants were male, and 100% endorsed adverse childhood experiences (e.g., abuse, neglect) or exposure to potentially traumatic events (e.g., assault). Levels of posttraumatic avoidance (41.9%), reexperiencing (59.5%), and increased arousal (51.3%) were high. In line with previous studies, our findings suggest an overall positive research experience in this sample. In spite of extensive histories of lifetime victimization we did not find an association between victimization, posttraumatic symptomatology, and a negative research experience. Our findings suggest that participation in trauma-focused research is not only possible with, but also potentially beneficial for forensic patients