Biomechanical coupling facilitates spinal neural tube closure in mouse embryos.

Neural tube (NT) formation in the spinal region of the mammalian embryo involves a wave of "zippering" that passes down the elongating spinal axis, uniting the neural fold tips in the dorsal midline. Failure of this closure process leads to open spina bifida, a common cause of severe neurologic disability in humans. Here, we combined a tissue-level strain-mapping workflow with laser ablation of live-imaged mouse embryos to investigate the biomechanics of mammalian spinal closure. Ablation of the zippering point at the embryonic dorsal midline causes far-reaching, rapid separation of the elevating neural folds. Strain analysis revealed tissue expansion around the zippering point after ablation, but predominant tissue constriction in the caudal and ventral neural plate zone. This zone is biomechanically coupled to the zippering point by a supracellular F-actin network, which includes an actin cable running along the neural fold tips. Pharmacologic inhibition of F-actin or laser ablation of the cable causes neural fold separation. At the most advanced somite stages, when completion of spinal closure is imminent, the cable forms a continuous ring around the neuropore, and simultaneously, a new caudal-to-rostral zippering point arises. Laser ablation of this new closure initiation point causes neural fold separation, demonstrating its biomechanical activity. Failure of spinal closure in pre-spina bifida Zic2Ku mutant embryos is associated with altered tissue biomechanics, as indicated by greater neuropore widening after ablation. Thus, this study identifies biomechanical coupling of the entire region of active spinal neurulation in the mouse embryo as a prerequisite for successful NT closure.

A spatio-temporal network for video semantic segmentation in surgical videos.

PURPOSE: Semantic segmentation in surgical videos has applications in intra-operative guidance, post-operative analytics and surgical education. Models need to provide accurate predictions since temporally inconsistent identification of anatomy can hinder patient safety. We propose a novel architecture for modelling temporal relationships in videos to address these issues. METHODS: We developed a temporal segmentation model that includes a static encoder and a spatio-temporal decoder. The encoder processes individual frames whilst the decoder learns spatio-temporal relationships from frame sequences. The decoder can be used with any suitable encoder to improve temporal consistency. RESULTS: Model performance was evaluated on the CholecSeg8k dataset and a private dataset of robotic Partial Nephrectomy procedures. Mean Intersection over Union improved by 1.30% and 4.27% respectively for each dataset when the temporal decoder was applied. Our model also displayed improvements in temporal consistency up to 7.23%. CONCLUSIONS: This work demonstrates an advance in video segmentation of surgical scenes with potential applications in surgery with a view to improve patient outcomes. The proposed decoder can extend state-of-the-art static models, and it is shown that it can improve per-frame segmentation output and video temporal consistency.

Hierarchical segmentation of surgical scenes in laparoscopy.

PURPOSE: Segmentation of surgical scenes may provide valuable information for real-time guidance and post-operative analysis. However, in some surgical video frames there is unavoidable ambiguity, leading to incorrect predictions of class or missed detections. In this work, we propose a novel method that alleviates this problem by introducing a hierarchy and associated hierarchical inference scheme that allows broad anatomical structures to be predicted when fine-grained structures cannot be reliably distinguished. METHODS: First, we formulate a multi-label segmentation loss informed by a hierarchy of anatomical classes and then train a network using this. Subsequently, we use a novel leaf-to-root inference scheme ("Hiera-Mix") to determine the trade-off between label confidence and granularity. This method can be applied to any segmentation model. We evaluate our method using a large laparoscopic cholecystectomy dataset with 65,000 labelled frames. RESULTS: We observed an increase in per-structure detection F1 score for the critical structures, when evaluated across their sub-hierarchies, compared to the baseline method: 6.0% for the cystic artery and 2.9% for the cystic duct, driven primarily by increases in precision of 11.3% and 4.7%, respectively. This corresponded to visibly improved segmentation outputs, with better characterisation of the undissected area containing the critical structures and fewer inter-class confusions. For other anatomical classes, which did not stand to benefit from the hierarchy, performance was unimpaired. CONCLUSION: Our proposed hierarchical approach improves surgical scene segmentation in frames with ambiguity, by more suitably reflecting the model's parsing of the scene. This may be beneficial in applications of surgical scene segmentation, including recent advancements towards computer-assisted intra-operative guidance.

Nutritional management in newborn babies receiving therapeutic hypothermia: two retrospective observational studies using propensity score matching.

BACKGROUND: Therapeutic hypothermia is standard of care for babies with moderate to severe hypoxic-ischaemic encephalopathy. There is limited evidence to inform provision of nutrition during hypothermia. OBJECTIVES: To assess the association during therapeutic hypothermia between (1) enteral feeding and outcomes, such as necrotising enterocolitis and (2) parenteral nutrition and outcomes, such as late-onset bloodstream infection. DESIGN: A retrospective cohort study using data held in the National Neonatal Research Database and applying propensity score methodology to form matched groups for analysis. SETTING: NHS neonatal units in England, Wales and Scotland. PARTICIPANTS: Babies born at ≥ 36 gestational weeks between 1 January 2010 and 31 December 2017 who received therapeutic hypothermia for 72 hours or who died during treatment. INTERVENTIONS: Enteral feeding analysis - babies who were enterally fed during therapeutic hypothermia (intervention) compared with babies who received no enteral feeds during therapeutic hypothermia (control). Parenteral nutrition analysis - babies who received parenteral nutrition during therapeutic hypothermia (intervention) compared with babies who received no parenteral nutrition during therapeutic hypothermia (control). OUTCOME MEASURES: Primary outcomes were severe and pragmatically defined necrotising enterocolitis (enteral feeding analysis) and late-onset bloodstream infection (parenteral nutrition analysis). Secondary outcomes were survival at neonatal discharge, length of neonatal stay, breastfeeding at discharge, onset of breastfeeding, time to first maternal breast milk, hypoglycaemia, number of days with a central line in situ, duration of parenteral nutrition, time to full enteral feeds and growth. RESULTS: A total of 6030 babies received therapeutic hypothermia. Thirty-one per cent of babies received enteral feeds and 25% received parenteral nutrition. Seven babies (0.1%) were diagnosed with severe necrotising enterocolitis, and further comparative analyses were not conducted on this outcome. A total of 3236 babies were included in the matched enteral feeding analysis. Pragmatically defined necrotising enterocolitis was rare in both groups (0.5% vs. 1.1%) and was lower in babies who were fed during hypothermia (rate difference -0.5%, 95% confidence interval -1.0% to -0.1%; p = 0.03). Higher survival to discharge (96.0% vs. 90.8%, rate difference 5.2%, 95% confidence interval 3.9% to 6.6%; p < 0.001) and higher breastfeeding at discharge (54.6% vs. 46.7%, rate difference 8.0%, 95% confidence interval 5.1% to 10.8%; p < 0.001) rates were observed in enterally fed babies who also had a shorter neonatal stay (mean difference -2.2 days, 95% confidence interval -3.0 to -1.2 days). A total of 2480 babies were included in the matched parenteral nutrition analysis. Higher levels of late-onset bloodstream infection were seen in babies who received parenteral nutrition (0.3% vs. 0.9%, rate difference 0.6%, 95% confidence interval 0.1% to 1.2%; p = 0.03). Survival was lower in babies who did not receive parenteral nutrition (90.0% vs. 93.1%, rate difference 3.1%, 95% confidence interval 1.5% to 4.7%; p < 0.001). LIMITATIONS: Propensity score methodology can address imbalances in observed confounders only. Residual confounding by unmeasured or poorly recorded variables cannot be ruled out. We did not analyse by type or volume of enteral or parenteral nutrition. CONCLUSIONS: Necrotising enterocolitis is rare in babies receiving therapeutic hypothermia, and the introduction of enteral feeding is associated with a lower risk of pragmatically defined necrotising enterocolitis and other beneficial outcomes, including rates of higher survival and breastfeeding at discharge. Receipt of parenteral nutrition during therapeutic hypothermia is associated with a higher rate of late-onset infection but lower mortality. These results support introduction of enteral feeding during therapeutic hypothermia. FUTURE WORK: Randomised trials to assess parenteral nutrition during therapeutic hypothermia. TRIAL REGISTRATION: Current Controlled Trials ISRCTN474042962. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 25, No. 36. See the NIHR Journals Library website for further project information.

Every year, approximately 1200 babies in the UK suffer a lack of oxygen to the brain around birth. This is called hypoxic­ischaemic encephalopathy and can lead to brain injury or death. To treat hypoxic­ischaemic encephalopathy, babies receive cooling treatment in which their body temperature is lowered. Doctors do not know the best way to give nutrition to babies receiving cooling treatment. Babies can either be fed milk into their stomach (enteral nutrition) or be given nutrients through their veins (parenteral nutrition). We compared babies who were fed milk while they were being cooled with babies from whom milk was withheld while they were being cooled to see if there was a difference in the frequency of necrotising enterocolitis, a severe gut disease. In addition, we compared babies who received parenteral nutrition while they were being cooled with babies who did not to see if there was a difference in infections. Finally, we looked at other outcomes, including survival and breastfeeding. We used the National Neonatal Research Database, which holds de-identified (i.e. no baby can be identified) information on all babies who have received NHS neonatal care. We used a statistical approach to match babies in each group (i.e. fed babies and not fed babies) as closely as possible so that any difference in outcomes was because of different nutrition and not because of other differences. We included > 6000 babies with hypoxic­ischaemic encephalopathy. Approximately one in three babies received milk feeds and one in four babies received parenteral nutrition during cooling. Necrotising enterocolitis was very rare. More babies who were fed milk during cooling had good outcomes (e.g. being breastfed at discharge) and fewer had necrotising enterocolitis. Most of these babies received only a small amount of milk in the first 3 days. More babies given parenteral nutrition had infections, but also more survived. This suggests that it is probably safe and may be beneficial to feed babies milk during cooling. More research should look at milk feeding and parenteral nutrition during cooling.

Feasibility and design of a trial regarding the optimal mode of delivery for preterm birth: the CASSAVA multiple methods study.

BACKGROUND: Around 60,000 babies are born preterm (prior to 37 weeks' gestation) each year in the UK. There is little evidence on the optimal birth mode (vaginal or caesarean section). OBJECTIVE: The overall aim of the CASSAVA project was to determine if a trial to define the optimal mode of preterm birth could be carried out and, if so, determine what sort of trial could be conducted and how it could best be performed. We aimed to determine the specific groups of preterm women and babies for whom there are uncertainties about the best planned mode of birth, and if there would be willingness to recruit to, and participate in, a randomised trial to address some, but not all, of these uncertainties. This project was conducted in response to a Heath Technology Assessment programme commissioning call (17/22 'Mode of delivery for preterm infants'). METHODS: We conducted clinician and patient surveys (n = 224 and n = 379, respectively) to identify current practice and opinion, and a consensus survey and Delphi workshop (n = 76 and n = 22 participants, respectively) to inform the design of a hypothetical clinical trial. The protocol for this clinical trial/vignette was used in telephone interviews with clinicians (n = 24) and in focus groups with potential participants (n = 13). RESULTS: Planned sample size and data saturation was achieved for all groups except for focus groups with participants, as this had to be curtailed because of the COVID-19 pandemic and data saturation was not achieved. There was broad agreement from parents and health-care professionals that a trial is needed. The clinician survey demonstrated a variety of practice and opinion. The parent survey suggested that women and their families generally preferred vaginal birth at later gestations and caesarean section for preterm infants. The interactive workshop and Delphi consensus process confirmed the need for more evidence (hence the case for a trial) and provided rich information on what a future trial should entail. It was agreed that any trial should address the areas with most uncertainty, including the management of women at 26-32 weeks' gestation, with either spontaneous preterm labour (cephalic presentation) or where preterm birth was medically indicated. Clear themes around the challenges inherent in conducting any trial emerged, including the concept of equipoise itself. Specific issues were as follows: different clinicians and participants would be in equipoise for each clinical scenario, effective conduct of the trial would require appropriate resources and expertise within the hospital conducting the trial, potential participants would welcome information on the trial well before the onset of labour and minority ethnic groups would require tailored approaches. CONCLUSION: Given the lack of evidence and the variation of practice and opinion in this area, and having listened to clinicians and potential participants, we conclude that a trial should be conducted and the outlined challenges resolved. FUTURE WORK: The CASSAVA project could be used to inform the design of a randomised trial and indicates how such a trial could be carried out. Any future trial would benefit from a pilot with qualitative input and a study within a trial to inform optimal recruitment. LIMITATIONS: Certainty that a trial could be conducted can be determined only when it is attempted. TRIAL REGISTRATION: Current Controlled Trials ISRCTN12295730. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 25, No. 61. See the NIHR Journals Library website for further project information.

Around 60,000 babies are born preterm each year in the UK. We do not know what the safest mode of birth is for these babies. Birth options include a vaginal birth or a caesarean section (which involves an operation for the mother). Normally, the ideal way to find out what clinical options are best is to carry out a 'randomised trial' in which participants are allocated to a particular treatment group (in this case, vaginal birth or caesarean section) by chance. It is not clear if women who have their babies preterm would want to take part in such a trial or that the clinicians looking after the women would be happy to ask them to, as previous trials have failed to recruit sufficient participants. The purpose of the CASSAVA research project was to find out what people think is the best and safest method of delivering preterm babies, their views on doing a research trial and what sort of research trial could be carried out. We conducted a survey asking clinicians and women their views. We gathered clinicians and women together to discuss and agree the key questions for a trial to answer. We then developed a protocol (plan) for a possible trial. Using this trial protocol, we conducted telephone interviews with clinicians, asking them if they would be willing to be involved and if they would be willing to ask pregnant women to participate. We also conducted focus groups with women, using a vignette (storyboard) about a possible trial. We found that there is a lot of uncertainty about the best way for preterm babies to be born. Clinicians and women broadly agreed that it would be good to resolve this uncertainty through a trial. We were able to identify some areas of the greatest uncertainty where clinicians and women would consider participating in a study. We gained a lot of useful information about how we could best set up a trial and support clinicians and women to get involved.

Automated operative workflow analysis of endoscopic pituitary surgery using machine learning: development and preclinical evaluation (IDEAL stage 0).

OBJECTIVE: Surgical workflow analysis involves systematically breaking down operations into key phases and steps. Automatic analysis of this workflow has potential uses for surgical training, preoperative planning, and outcome prediction. Recent advances in machine learning (ML) and computer vision have allowed accurate automated workflow analysis of operative videos. In this Idea, Development, Exploration, Assessment, Long-term study (IDEAL) stage 0 study, the authors sought to use Touch Surgery for the development and validation of an ML-powered analysis of phases and steps in the endoscopic transsphenoidal approach (eTSA) for pituitary adenoma resection, a first for neurosurgery. METHODS: The surgical phases and steps of 50 anonymized eTSA operative videos were labeled by expert surgeons. Forty videos were used to train a combined convolutional and recurrent neural network model by Touch Surgery. Ten videos were used for model evaluation (accuracy, F1 score), comparing the phase and step recognition of surgeons to the automatic detection of the ML model. RESULTS: The longest phase was the sellar phase (median 28 minutes), followed by the nasal phase (median 22 minutes) and the closure phase (median 14 minutes). The longest steps were step 5 (tumor identification and excision, median 17 minutes); step 3 (posterior septectomy and removal of sphenoid septations, median 14 minutes); and step 4 (anterior sellar wall removal, median 10 minutes). There were substantial variations within the recorded procedures in terms of video appearances, step duration, and step order, with only 50% of videos containing all 7 steps performed sequentially in numerical order. Despite this, the model was able to output accurate recognition of surgical phases (91% accuracy, 90% F1 score) and steps (76% accuracy, 75% F1 score). CONCLUSIONS: In this IDEAL stage 0 study, ML techniques have been developed to automatically analyze operative videos of eTSA pituitary surgery. This technology has previously been shown to be acceptable to neurosurgical teams and patients. ML-based surgical workflow analysis has numerous potential uses-such as education (e.g., automatic indexing of contemporary operative videos for teaching), improved operative efficiency (e.g., orchestrating the entire surgical team to a common workflow), and improved patient outcomes (e.g., comparison of surgical techniques or early detection of adverse events). Future directions include the real-time integration of Touch Surgery into the live operative environment as an IDEAL stage 1 (first-in-human) study, and further development of underpinning ML models using larger data sets.

Refinement of inducible gene deletion in embryos of pregnant mice.

CreERT2-mediated gene recombination is widely applied in developmental biology research. Activation of CreERT2 is typically achieved by injection of tamoxifen in an oily vehicle into the peritoneal cavity of mid-gestation pregnant mice. This can be technically challenging and adversely impacts welfare. Here we characterize three refinements to this technique: Pipette feeding (not gavage) of tamoxifen, ex vivo CreERT2 activation in whole embryo culture and injection of cell-permeable TAT-Cre into Cre-negative cultured embryos. We demonstrate that pipette feeding of tamoxifen solution to the mother on various days of gestation reliably activates embryonic CreERT2, illustrated here using ß-Actin CreERT2 , Sox2 CreERT2 , T CreERT2 , and Nkx1.2 CreERT2 . Pipette feeding of tamoxifen induces dose-dependent recombination of Rosa26 mTmG reporters when administered at E8.5. Activation of two neuromesodermal progenitor-targeting Cre drivers, T CreERT2 , and Nkx1.2 CreERT2 , produces comparable neuroepithelial lineage tracing. Dose-dependent CreERT2 activation can also be achieved by brief exposure to 4OH-tamoxifen in whole embryo culture, allowing temporal control of gene deletion and eliminating the need to treat pregnant mice. Rosa26 mTmG reporter recombination can also be achieved regionally by injecting TAT-Cre into embryonic tissues at the start of culture. This allows greater spatial control over Cre activation than can typically be achieved with endogenous CreERT2, for example by injecting TAT-Cre on one side of the midline. We hope that our description and application of these techniques will stimulate refinement of experimental methods involving CreERT2 activation for gene deletion and lineage tracing studies. Improved temporal (ex vivo treatment) and spatial (TAT-Cre injection) control of recombination will also allow previously intractable questions to be addressed.

Mouse whole embryo culture: Evaluating the requirement for rat serum as culture medium.

BACKGROUND: Whole embryo culture is a valuable research method in mammalian developmental biology and birth defects research, enabling longitudinal studies of explanted organogenesis-stage rodent embryos. Rat serum is the primary culture medium, and can sustain growth and development over limited periods as in utero. However, the cost, labor, and time to produce culture serum are factors limiting the uptake of the methodology. The goal of replacing or at least reducing rat serum usage in culture would be in accordance with the principles of "replacement, reduction, and refinement" of animals in research (the 3Rs). METHODS: We performed cultures of mouse embryos for 24 hr from embryonic day 8.5 in serum-free media or in rat serum diluted with defined media, compared with 100% rat serum. Developmental parameters scored after culture included yolk sac circulation, dorsal axial length, somite number, protein content, and completion of cranial neural tube closure. RESULTS: A literature review revealed use of both serum-free and diluted rat serum-based media in whole embryo culture studies, but with almost no formal comparisons of culture success against 100% rat serum. Two serum-free media were tested, but neither could sustain development as in 100% rat serum. Dilution of rat serum 1:1 with Glasgow Minimum Essential Medium plus defined supplements supported growth and development as well as whole rat serum, whereas other diluent media yielded substandard outcomes. CONCLUSION: Rat serum usage cannot be avoided, to achieve high quality mouse embryo cultures, but rat usage can be reduced using medium containing diluted serum.

The WHEAT pilot trial-WithHolding Enteral feeds Around packed red cell Transfusion to prevent necrotising enterocolitis in preterm neonates: a multicentre, electronic patient record (EPR), randomised controlled point-of-care pilot trial.

INTRODUCTION: Necrotising enterocolitis (NEC) is a potentially devastating neonatal disease. A temporal association between red cell transfusion and NEC is well described. Observational data suggest that withholding enteral feeds around red cell transfusions may reduce the risk of NEC but this has not been tested in randomised trials; current UK practice varies. Prevention of NEC is a research priority but no appropriately powered trials have addressed this question. The use of a simplified opt-out consent model and embedding trial processes within existing electronic patient record (EPR) systems provide opportunities to increase trial efficiency and recruitment. METHODS AND ANALYSIS: We will undertake a randomised, controlled, multicentre, unblinded, pilot trial comparing two care pathways: continuing milk feeds (before, during and after red cell transfusions) and withholding milk feeds (for 4 hours before, during and for 4 hours after red cell transfusions), with infants randomly assigned with equal probability. We will use opt-out consent. A nested qualitative study will explore parent and health professional views. Infants will be eligible if born at <30+0 gestational weeks+days. Primary feasibility outcomes will be rate of recruitment, opt-out, retention, compliance, data completeness and data accuracy; clinical outcomes will include mortality and NEC. The trial will recruit in two neonatal networks in England for 9 months. Data collection will continue until all infants have reached 40+0 corrected gestational weeks or neonatal discharge. Participant identification and recruitment, randomisation and all trial data collection will be embedded within existing neonatal EPR systems (BadgerNet and BadgerEPR); outcome data will be extracted from routinely recorded data held in the National Neonatal Research Database. ETHICS AND DISSEMINATION: This study holds Research Ethics Committee approval to use an opt-out approach to consent. Results will inform future EPR-embedded and data-enabled trials and will be disseminated through conferences, publications and parent-centred information. TRIAL REGISTRATION NUMBER: ISRCTN registry ISRCTN62501859; Pre-results.

Neurovascular sequestration in paediatric P. falciparum malaria is visible clinically in the retina.

Retinal vessel changes and retinal whitening, distinctive features of malarial retinopathy, can be directly observed during routine eye examination in children with P. falciparum cerebral malaria. We investigated their clinical significance and underlying mechanisms through linked clinical, clinicopathological and image analysis studies. Orange vessels and severe foveal whitening (clinical examination, n = 817, OR, 95% CI: 2.90, 1.96-4.30; 3.4, 1.8-6.3, both p<0.001), and arteriolar involvement by intravascular filling defects (angiographic image analysis, n = 260, 2.81, 1.17-6.72, p<0.02) were strongly associated with death. Orange vessels had dense sequestration of late stage parasitised red cells (histopathology, n = 29; sensitivity 0.97, specificity 0.89) involving 360° of the lumen circumference, with altered protein expression in blood-retinal barrier cells and marked loss/disruption of pericytes. Retinal whitening was topographically associated with tissue response to hypoxia. Severe neurovascular sequestration is visible at the bedside, and is a marker of severe disease useful for diagnosis and management.