The genome sequence of the Orange-tipped sea squirt, Corella eumyota Traustedt, 1882

We present a genome assembly from an individual specimen of Corella eumyota (the Orange-tipped sea squirt; Chordata; Ascidiacea; Phlebobranchia; Corellidae). The genome sequence is 129.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.53 kilobases in length.

The genome sequence of the ruby bryozoan, Bugula neritina (Linnaeus, 1758)

We present a genome assembly from a specimen of Bugula neritina (the ruby bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence has total length of 216.00 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,264 protein-coding genes.

The genome sequence of the sand star, Astropecten irregularis (Pennant, 1777)

We present a genome assembly from an individual Astropecten irregularis (the sand star; Echinodermata; Asteroidea; Paxillosida; Astropectinidae). The genome sequence spans 475.80 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.34 kilobases in length.

The genome sequence of a segmented worm, Terebella lapidaria Linnaeus, 1767

We present a genome assembly from an individual Terebella lapidaria (segmented worm; Annelida; Polychaeta; Terebellida; Terebellidae). The genome sequence spans 765.20 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.97 kilobases in length.

Outcomes of UK military personnel treated with ice cold water immersion for exertional heat stroke

INTRODUCTION

Despite mitigation efforts, exertional heat stroke (EHS) is known to occur in military personnel during training and operations. It has significant potential to cause preventable morbidity and mortality. International consensus from sports medicine organisations supports treating EHS with early rapid cooling by immersing the casualty in cold water. However, evidence remains sparse and the practice is not yet widespread in the UK.

METHODS

Following changes to enable on-site ice cold water immersion (ICWI) at the Royal Marines Commando Training Centre, Lympstone, UK, we prospectively gathered data on 35 patients treated with ICWI over a 3-year period. These data included the incidence of adverse events (e.g. death, cardiac arrest or critical care admission) as the primary outcome. Basic anthropometric data, cooling rates achieved and biochemical and haematological test results on days 0-5 were also gathered and analysed.

RESULTS

Despite being a cohort of patients in whom we might expect significant morbidity and mortality based on the severity of EHS at presentation, none experienced a serious adverse event. In this cohort with rapid initiation of effective cooling, biochemical derangement appeared less severe than that reported in previous studies. Higher body mass index (BMI) was associated with a lower cooling rate across a range of values previously reported as potentially of clinical significance.

CONCLUSIONS

This case series supports recent updates to UK military guidance that ICWI should be more widely adopted for the treatment of EHS. Clinicians should be aware of likely patterns of blood test abnormalities in the days following EHS. Further work should seek to establish the impact of lower rates of cooling and develop strategies to optimise cooling in patients with higher BMI.

Heterogeneity in maternal mRNAs within clutches of eggs in response to thermal stress during the embryonic stage

BACKGROUND

The origin of variation is of central interest in evolutionary biology. Maternal mRNAs govern early embryogenesis in many animal species, and we investigated the possibility that heterogeneity in maternal mRNA provisioning of eggs can be modulated by environmental stimuli.

RESULTS

We employed two sibling species of the ascidian Ciona, called here types A and B, that are adapted to different temperature regimes and can be hybridized. Previous study showed that hybrids using type B eggs had higher susceptibility to thermal stress than hybrids using type A eggs. We conducted transcriptome analyses of multiple single eggs from crosses using eggs of the different species to compare the effects of maternal thermal stress on heterogeneity in egg provisioning, and followed the effects across generations. We found overall decreases of heterogeneity of egg maternal mRNAs associated with maternal thermal stress. When the eggs produced by the F1 AB generation were crossed with type B sperm and the progeny ('ABB' generation) reared unstressed until maturation, the overall heterogeneity of the eggs produced was greater in a clutch from an individual with a heat-stressed mother compared to one from a non-heat-stressed mother. By examining individual genes, we found no consistent overall effect of thermal stress on heterogeneity of expression in genes involved in developmental buffering. In contrast, heterogeneity of expression in signaling molecules was directly affected by thermal stress.

CONCLUSIONS

Due to the absence of batch replicates and variation in the number of reads obtained, our conclusions are very limited. However, contrary to the predictions of bet-hedging, the results suggest that maternal thermal stress at the embryo stage is associated with reduced heterogeneity of maternal mRNA provision in the eggs subsequently produced by the stressed individual, but there is then a large increase in heterogeneity in eggs of the next generation, although itself unstressed. Despite its limitations, our study presents a proof of concept, identifying a model system, experimental approach and analytical techniques capable of providing a significant advance in understanding the impact of maternal environment on developmental heterogeneity.

The genome sequence of a solitary sea squirt, Ascidia mentula (Müller, 1776)

We present a genome assembly from an individual Ascidia mentula (the (a solitary sea squirt); Chordata; Ascidiacea; Phlebobranchia; Ascidiidae). The genome sequence is 197.0 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.46 kilobases in length.

A comparison of the efficacy of trastuzumab deruxtecan in advanced HER2-positive breast cancer: active brain metastasis versus progressive extracranial disease alone

BACKGROUND

Trastuzumab deruxtecan (T-DXd) has demonstrated efficacy in patients with brain metastasis (BM), a group historically with poor outcomes. The prevalence of BMs in patients commencing T-DXd is currently unknown. No direct comparisons have been made of the activity of T-DXd in patients with active BM versus those with extracranial progression alone. This real-world study explored the prevalence of BMs in patients commencing T-DXd, the efficacy of T-DXd in active BM versus extracranial progression alone and the safety of T-DXd.

PATIENTS AND METHODS

Patients with human epidermal growth factor receptor 2-positive advanced breast cancer treated with T-DXd between June 2021 and February 2023 at our specialist cancer hospital were identified and notes reviewed. Clinicopathological information, prior treatment, the presence or absence of central nervous system (CNS) disease, outcomes and treatment-emergent adverse events (TEAEs) were recorded.

RESULTS

Twenty-nine female patients, with a median age of 52 years (interquartile range 44-62 years), were identified; the prevalence of BM was 41%. Median number of lines of prior therapy was 2 (range 2-6). At a median follow-up of 13.8 months, median progression-free survival (PFS) for the overall population was 13.9 months [95% confidence interval (CI) 12.4 months-not estimable (NE)], 16.1 months (95% CI 15.1 months-NE) for active BMs and 12.4 months (95% CI 8.3 months-NE) for progressive extracranial disease alone. The 12-month overall survival (OS) rate was 74% (95% CI 59% to 95%) in the overall population, and 83% (95% CI 58% to 100%) and 66% (95% CI 45% to 96%) for active BMs and extracranial disease only, respectively. Most common TEAEs were fatigue, alopecia, and constipation. In nine patients (31%, including two deaths), pneumonitis occurred.

CONCLUSION

In this real-world population, we demonstrate T-DXd to be effective in patients with active BMs and those with progressive extracranial disease alone. PFS and OS were numerically longer in those with active BMs. These data demonstrate that patients with active BM treated with T-DXd have at least comparable outcomes to those with extracranial disease alone. The high rate of pneumonitis warrants further consideration.

The genome sequence of the light-bulb sea squirt, Clavelina lepadiformis (Müller, 1776)

We present a genome assembly from an individual Clavelina lepadiformis (the light-bulb sea squirt; Chordata; Ascidiacea; Aplousobranchia; Clavelinidae). The genome sequence is 210.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.48 kilobases in length.

The genome sequence of the brown sea anemone, Metridium senile (Linnaeus, 1761)

We present a genome assembly from an individual Metridium senile (the brown sea anemone; Cnidaria; Anthozoa; Actiniaria; Metridiidae). The genome sequence is 390.9 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.44 kilobases in length.

Sample size determination for external pilot cluster randomised trials with binary feasibility outcomes: a tutorial

Justifying sample size for a pilot trial is a reporting requirement, but few pilot trials report a clear rationale for their chosen sample size. Unlike full-scale trials, pilot trials should not be designed to test effectiveness, and so, conventional sample size justification approaches do not apply. Rather, pilot trials typically specify a range of primary and secondary feasibility objectives. Often, these objectives relate to estimation of parameters that inform the sample size justification for the full-scale trial, many of which are binary. These binary outcomes are referred to as "feasibility outcomes" and include expected prevalence of the primary trial outcome, primary outcome availability, or recruitment or retention proportions.For pilot cluster trials, sample size calculations depend on the number of clusters, the cluster sizes, the anticipated intra-cluster correlation coefficient for the feasibility outcome and the anticipated proportion for that outcome. Of key importance is the intra-cluster correlation coefficient for the feasibility outcome. It has been suggested that correlations for feasibility outcomes are larger than for clinical outcomes measuring effectiveness. Yet, there is a dearth of information on realised values for these correlations.In this tutorial, we demonstrate how to justify sample size in external pilot cluster trials where the objective is to estimate a binary feasibility outcome. We provide sample size calculation formulae for a variety of scenarios, make available an R Shiny app for implementation, and compile a report of intra-cluster correlations for feasibility outcomes from a convenience sample. We demonstrate that unless correlations are very low, external pilot cluster trials can be made more efficient by including more clusters and fewer observations per cluster.

First Observation of the β3αp Decay of ^{13}O via β-Delayed Charged-Particle Spectroscopy

The β-delayed proton decay of ^{13}O has previously been studied, but the direct observation of β-delayed 3αp decay has not been reported. Rare 3αp events from the decay of excited states in ^{13}N^{⋆} provide a sensitive probe of cluster configurations in ^{13}N. To measure the low-energy products following β-delayed 3αp decay, the Texas Active Target (TexAT) time projection chamber was employed using the one-at-a-time β-delayed charged-particle spectroscopy technique at the Cyclotron Institute, Texas A&M University. A total of 1.9×10^{5} ^{13}O implantations were made inside the TexAT time projection chamber. A total of 149 3αp events were observed, yielding a β-delayed 3αp branching ratio of 0.078(6)%. Four previously unknown α-decaying excited states were observed in ^{13}N at 11.3, 12.4, 13.1, and 13.7 MeV decaying via the 3α+p channel.

The genome sequence of the sea mat, Membranipora membranacea (Linnaeus, 1767)

We present a genome assembly from an adult colony of Membranipora membranacea (the sea mat; Bryozoa; Gymnolaemata; Cheilostomatida; Membraniporidae). The genome sequence is 339 megabases in span. Most of the assembly (99.95%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.7 kilobases in length.

The genome sequence of an erect bryozoan, Bugulina stolonifera (Ryland, 1960)

We present a genome assembly from a Bugulina stolonifera colony (an erect bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence is 235 megabases in span. Most of the assembly (99.85%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 14.4 kilobases long.

The genome sequence of the scale worm, Lepidonotus clava (Montagu, 1808)

We present a genome assembly from an individual Lepidonotus clava (scale worm; Annelida; Polychaeta; Phyllodocida; Polynoidae). The genome sequence is 1,044 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.6 kilobases in length.

Antenatal preventative pelvic floor muscle exercise intervention led by midwives to reduce postnatal urinary incontinence (APPEAL): protocol for a feasibility and pilot cluster randomised controlled trial

Background

Antenatal pelvic floor muscle exercises (PFME) in women without prior urinary incontinence (UI) are effective in reducing postnatal UI; however, UK midwives often do not provide advice and information to women on undertaking PFME, with evidence that among women who do receive advice, many do not perform PFME.

Methods

The primary aim of this feasibility and pilot cluster randomised controlled trial is to provide a potential assessment of the feasibility of undertaking a future definitive trial of a midwifery-led antenatal intervention to support women to perform PFME in pregnancy and reduce UI postnatally.

Community midwifery teams in participating NHS sites comprise trial clusters (n = 17). Midwives in teams randomised to the intervention will be trained on how to teach PFME to women and how to support them in undertaking PFME in pregnancy. Women whose community midwifery teams are allocated to control will receive standard antenatal care only.

All pregnant women who give birth over a pre-selected sample month who receive antenatal care from participating community midwifery teams (clusters) will be sent a questionnaire at 10–12 weeks postpartum (around 1400–1500 women). Process evaluation data will include interviews with midwives to assess if the intervention could be implemented as planned. Interviews with women in both trial arms will explore their experiences of support from midwives to perform PFME during pregnancy. Data will be stored securely at the Universities of Birmingham and Exeter.

Results will be disseminated through publications aimed at maternity service users, clinicians, and academics and inform a potential definitive trial of effectiveness. The West Midlands–Edgbaston Research Ethics Committee approved the study protocol.

Discussion

Trial outcomes will determine if criteria to progress to a definitive cluster trial are met. These include women’s questionnaire return rates, prevalence of UI, and other health outcomes as reported by women at 10–12 weeks postpartum. Progress to a definitive trial however is likely to be prevented in the UK context by new perinatal pelvic health service, although this may be possible elsewhere.

Trial registration

10.1186/ISRCTN10833250. Registered 09/03/2020

HeartCV: a tool for transferrable, automated measurement of heart rate and heart rate variability in transparent animals

Heart function is a key component of whole-organismal physiology. Bioimaging is commonly, but not exclusively, used for quantifying heart function in transparent individuals, including early developmental stages of aquatic animals, many of which are transparent. However, a central limitation of many imaging-related methods is the lack of transferability between species, life-history stages and experimental approaches. Furthermore, locating the heart in mobile individuals remains challenging. Here, we present HeartCV: an open-source Python package for automated measurement of heart rate and heart rate variability that integrates automated localization and is transferrable across a wide range of species. We demonstrate the efficacy of HeartCV by comparing its outputs with measurements made manually for a number of very different species with contrasting heart morphologies. Lastly, we demonstrate the applicability of the software to different experimental approaches and to different dataset types, such as those corresponding to longitudinal studies.

Co-expression network analysis of environmental canalization in the ascidian Ciona

BACKGROUND

Canalization, or buffering, is defined as developmental stability in the face of genetic and/or environmental perturbations. Understanding how canalization works is important in predicting how species survive environmental change, as well as deciphering how development can be altered in the evolutionary process. However, how developmental gene expression is linked to buffering remains unclear. We addressed this by co-expression network analysis, comparing gene expression changes caused by heat stress during development at a whole-embryonic scale in reciprocal hybrid crosses of sibling species of the ascidian Ciona that are adapted to different thermal environments.

RESULTS

Since our previous work showed that developmental buffering in this group is maternally inherited, we first identified maternal developmental buffering genes (MDBGs) in which the expression level in embryos is both correlated to the level of environmental canalization and also differentially expressed depending on the species' gender roles in hybrid crosses. We found only 15 MDBGs, all of which showed high correlation coefficient values for expression with a large number of other genes, and 14 of these belonged to a single co-expression module. We then calculated correlation coefficients of expression between MDBGs and transcription factors in the central nervous system (CNS) developmental gene network that had previously been identified experimentally. We found that, compared to the correlation coefficients between MDBGs, which had an average of 0.96, the MDBGs are loosely linked to the CNS developmental genes (average correlation coefficient 0.45). Further, we investigated the correlation of each developmental to MDBGs, showing that only four out of 62 CNS developmental genes showed correlation coefficient > 0.9, comparable to the values between MDBGs, and three of these four genes were signaling molecules: BMP2/4, Wnt7, and Delta-like.

CONCLUSIONS

We show that the developmental pathway is not centrally located within the buffering network. We found that out of 62 genes in the developmental gene network, only four genes showed correlation coefficients as high as between MDBGs. We propose that loose links to MDBGs stabilize spatiotemporally dynamic development.

Neutron-upscattering enhancement of the triple-alpha process

The neutron inelastic scattering of carbon-12, populating the Hoyle state, is a reaction of interest for the triple-alpha process. The inverse process (neutron upscattering) can enhance the Hoyle state’s decay rate to the bound states of ¹²C, effectively increasing the overall triple-alpha reaction rate. The cross section of this reaction is impossible to measure experimentally but has been determined here at astrophysically-relevant energies using detailed balance. Using a highly-collimated monoenergetic beam, here we measure neutrons incident on the Texas Active Target Time Projection Chamber (TexAT TPC) filled with CO₂ gas, we measure the 3α-particles (arising from the decay of the Hoyle state following inelastic scattering) and a cross section is extracted. Here we show the neutron-upscattering enhancement is observed to be much smaller than previously expected. The importance of the neutron-upscattering enhancement may therefore not be significant aside from in very particular astrophysical sites (e.g. neutron star mergers).

The triple-alpha process plays a role in nucleosynthesis, in the formation of ¹²C. Here, the authors discuss the rate and role of the neutron upscattering phenomenon on the triple-alpha process in a multi-step process.

The genome sequence of Aplidium turbinatum (Savigny 1816), a colonial sea squirt

We present a genome assembly from an individual Aplidium turbinatum (Chordata; Ascidiacea; Aplousobranchia; Polyclinidae). The genome sequence is 605 megabases in span. The majority of the assembly (99.98%) is scaffolded into 18 chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 18.4 kilobases in length.

The genome sequence of the orange-striped anemone, Diadumene lineata (Verrill, 1869)

We present a genome assembly from an individual Diadumene lineata (the orange-striped anemone; Cnidaria; Anthozoa; Actiniaria; Diadumenidae). The genome sequence is 313 megabases in span. The majority of the assembly (96.03%) is scaffolded into 16 chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 17.6 kilobases in length.