The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.

The empty pelvis syndrome: a core data set from the PelvEx collaborative

BACKGROUND

Empty pelvis syndrome (EPS) is a significant source of morbidity following pelvic exenteration (PE), but is undefined. EPS outcome reporting and descriptors of radicality of PE are inconsistent; therefore, the best approaches for prevention are unknown. To facilitate future research into EPS, the aim of this study is to define a measurable core outcome set, core descriptor set and written definition for EPS. Consensus on strategies to mitigate EPS was also explored.

METHOD

Three-stage consensus methodology was used: longlisting with systematic review, healthcare professional event, patient engagement, and Delphi-piloting; shortlisting with two rounds of modified Delphi; and a confirmatory stage using a modified nominal group technique. This included a selection of measurement instruments, and iterative generation of a written EPS definition.

RESULTS

One hundred and three and 119 participants took part in the modified Delphi and consensus meetings, respectively. This encompassed international patient and healthcare professional representation with multidisciplinary input. Seventy statements were longlisted, seven core outcomes (bowel obstruction, enteroperineal fistula, chronic perineal sinus, infected pelvic collection, bowel obstruction, morbidity from reconstruction, re-intervention, and quality of life), and four core descriptors (magnitude of surgery, radiotherapy-induced damage, methods of reconstruction, and changes in volume of pelvic dead space) reached consensus-where applicable, measurement of these outcomes and descriptors was defined. A written definition for EPS was agreed.

CONCLUSIONS

EPS is an area of unmet research and clinical need. This study provides an agreed definition and core data set for EPS to facilitate further research.

Anaesthetic management of people with multiple sclerosis

There is a lack of published guidelines on the management of patients with multiple sclerosis (MS) undergoing procedures that require anaesthesia and respective advice is largely based on retrospective studies or case reports. The aim of this paper is to provide recommendations for anaesthetists and neurologists for the management of patients with MS requiring anaesthesia. This review covers issues related to the anaesthetic management of patients with MS, with a focus on preoperative assessment, choice of anaesthetic techniques and agents, side-effects of drugs used during anaesthesia and their potential impact on the disease evolution, drug interactions that may occur, and the need to use monitoring devices. A systematic PubMed research was performed to retrieve relevant articles.

Quality of amoxicillin/clavulanic acid oral formulations for intended veterinary use in the UK, Malaysia, Serbia and Thailand

OBJECTIVES

Amoxicillin/clavulanate is the most commonly used oral antimicrobial drug in companion animals. The objective of the study was to detect types and frequency of deficits in the quality of veterinary oral formulations of amoxicillin/clavulanate in various countries.

MATERIALS AND METHODS

In a prospective study with purposive sampling, amoxicillin/clavulanate tablet formulations for canine use were collected in four countries (wholesalers or veterinary practice) and shipped to a central bioanalytical laboratory. Twenty-four samples were collected from the UK (nine), Malaysia (nine), Serbia (four) and Thailand (two), yielding 18 different formulations (10 veterinary). Packaging inspection, tablet disintegration and content assay were conducted (validated high-performance liquid chromatography with ultra-violet detection); content was acceptable when within the 90% to 120% pre-specified range (US Pharmacopeia).

RESULTS

Secondary packaging was present for 13 of 24 samples and primary packaging integrity was verified for all but one sample. Amoxicillin trihydrate/potassium clavulanate label ratio was 4:1, except for three formulations (2:1). Tablet dose strength ranged from 250 to 625 mg. All formulations contained both analytes. For amoxicillin, two of 24 samples were out of specification with 72.8% (Malaysia) and 82.3% (Thailand) of labelled content. For clavulanate, four of 24 samples were out of specification with 46.9% (Serbia), 79.0% (UK), 84.3% (Serbia) and 86.5% (Thailand) of labelled content. One formulation (Thailand) failed for both analytes.

CLINICAL SIGNIFICANCE

Antimicrobial formulations of substandard quality have negative consequences for efficacy in patients and potentially promote antimicrobial resistance. There was evidence of substandard formulations in all countries, not only for amoxicillin but especially for clavulanate; this could compromise equitable access to acceptable quality essential veterinary medicines worldwide.

Organic solvents and Multiple Sclerosis: the doubled risk dilemma

BACKGROUND

Compensation for industrial disease in the UK may be obtained in two ways. A State scheme includes a list of accepted associations between occupations and diseases with evidence of a causative association. Epidemiological evidence of a doubled risk in the occupation concerned is usually required. This takes no account of variation of exposures within occupations, excluding many occupations where risk is less than doubled. In such cases, compensation for a perceived industrial illness may be obtained in Civil Courts, where excessive exposures can be considered.

AIMS

To show that in the Civil Courts evidence of excessive exposure may lead to compensation for diseases which are not yet compensable as Industrial Injuries in the UK and to draw attention to the association of multiple sclerosis (MS) with solvent exposure.

METHODS

We report the case of an industrial spray painter, who claimed his MS had been caused by high-level exposure to organic solvents, and our examination of the epidemiological evidence submitted.

RESULTS

The painter received compensation by an out-of-court settlement, despite the overall epidemiological risk in relation to solvent exposure having been shown to be less than doubled. The evidence hinged on individual risk in relation to high exposure, genetic susceptibility and demonstration of a plausible mechanism.

CONCLUSIONS

High organic solvent exposure may lead to the development of MS. Those giving evidence in Court need to be able to discuss the epidemiological and toxicological issues in relation to exposure in the individual case.

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy

BACKGROUND

Protein-protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein-protein interactions and produce high-quality multimeric structural models.

RESULTS

Application of our method to the Human and Yeast genomes yield protein-protein interaction networks similar in quality to common experimental methods. We identified and modeled Human proteins likely to interact with the papain-like protease of SARS-CoV2's non-structural protein 3. We also produced models of SARS-CoV2's spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor and dipeptidyl peptidase-4.

CONCLUSIONS

The presented method is capable of confidently identifying interactions while providing high-quality multimeric structural models for experimental validation. The interactome modeling pipeline is available at usegalaxy.org and usegalaxy.eu.

Hallucinating symmetric protein assemblies

Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and C33 symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.

Robust deep learning-based protein sequence design using ProteinMPNN

Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning-based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo-electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.

987 Protocol Driven Reduction of Haematoma Following Symptomatic Carotid Endarterectomy (CEA) – a Prospective Cohort Study

Aim

Stroke is the third leading cause of death in developed nations and the leading cause of long-term disability. Carotid artery stenosis accounts for 20 to 30% of ischaemic strokes. Carotid Endarterectomy, has proven highly effective in preventing the development of strokes, TIAs and reducing death among patients with symptomatic carotid artery stenosis of 50–99%. The most common complication of CEA is wound haematomas. This study evaluates a protocol driven haemostasis pathway aimed to address the findings of a recent QI project that identified a significantly high neck haematoma rate as well as a high return to theatre rate for the complication.

Method

A prospective cohort outcome study between June 2019 and June 2020 was conducted, with the introduction of this stepwise pathway introduced as a quality improvement measure.

This was implemented at the end of successful patch closure, for each CEA.

Results

Post-CEA haematoma rates decreased from 7% to 3.6%. Return to theatre rates reduced from 6% to 0.9% with no increase in peri-operative stroke rates.

Conclusion

Our protocol appears to reduce post-CEA haematoma rates. Return to theatre rates had also dropped without an increase in peri-operative stroke rates despite using protamine and tranexemic acid when needed.

EP-681 Adherence to VTE prophylaxis guidelines in general surgical patients: a single-centre study

Introduction

Hospital acquired venous thromboembolism (VTE) is potentially preventable yet still accounts for 60% of all VTE seen. This study aimed to establish adherence to guidelines on VTE prevention including completion of VTE risk assessment within 24 hours of admission and appropriate prescription of mechanical and pharmacological VTE prophylaxis.

Methods

A database of all general surgical inpatients in our hospital at any point during the 48-hour period from 21/12/2021 to 22/12/2021 was obtained. Electronic records were examined to check for the presence of 11 established risk factors for VTE and to check for adherence to VTE guidelines. Every surgical patient was reviewed to check whether they were wearing anti-embolic stockings. Standard statistical analyses were undertaken.

Results

There were 107 general surgical patients in hospital during the study period. Of these, 33 (31%) had 3 or more risk factors on admission for VTE. 106 (99%) patients had VTE assessments completed within 24 hours of admission. Of these 107 patients, 93 (87%) had appropriate pharmacological VTE prophylaxis or had a documented reason why this was not prescribed. 14 (13%) patients had no pharmacological VTE prophylaxis prescribed. 84 patients were assessed as requiring anti-embolic stockings. Of these, 57 (68%) of patients were prescribed stockings, and 30 (36%) were physically wearing stockings.

Conclusions

This study has shown that adherence to VTE guidelines among surgical patients in our hospital is substandard. We suggest having a VTE safeguard during the ward round responsible for identifying any deficits in VTE prophylaxis and ensuring recommendations are acted upon.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Did it hurt? COVID-19 vaccination experience in people with multiple sclerosis

Background

Current guidelines recommend vaccination against SARS-CoV2 for people with multiple sclerosis (pwMS). The long-term review of the safety and effectiveness of COVID-19 vaccines in pwMS is limited.

Methods

Service re-evaluation. PwMS using the MS service at Barts Health National Health Service Trust were sent questionnaires via email to report symptoms following first and second COVID-19 vaccinations (n = 570). A retrospective review of electronic health records was conducted for clinical and safety data post-vaccination(s); cut-off was end of September 2021. Separate logistic regressions were carried out for symptoms experienced at each vaccination. Two sets of regressions were fitted with covariates: (i) Disease-modifying therapy type and (ii) patient characteristics for symptoms experienced.

Results

193/570 pwMS responded. 184 pwMS had both vaccinations. 144 received the AZD1222 and 49 the BNT162b2 vaccine. 87% and 75% of pwMS experienced any symptoms at first and second vaccinations, respectively. The majority of symptoms resolved within a short timeframe. No severe adverse effects were reported. Two pwMS subsequently died; one due to COVID-19 and one due to aspiration pneumonia. Males were at a reduced risk of reporting symptoms at first vaccination. There was evidence that pwMS in certain treatment groups were at reduced risk of reporting symptoms at second vaccination only.

Conclusions

Findings are consistent with our preliminary data. Symptoms post-vaccination were similar to the non-MS population and were mostly temporary. It is important to inform the MS community of vaccine safety data.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Computational design of mechanically coupled axle-rotor protein assemblies

Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.

Long-stay medical-surgical intensive care unit patients in South Africa: Quality of life and mortality 1 year after discharge

BACKGROUND

Although mortality is the primary measure of critical care outcome, the health-related quality of life (HRQOL) of survivors is often diminished. There is a paucity of South African research on HRQOL in intensive care unit (ICU) survivors.

OBJECTIVES

To evaluate the 1-year post-discharge data of long-stay ICU patients, a group known to consume 20 - 40% of ICU resources.

METHODS

A 1-year prospective observational study was conducted in a multidisciplinary medical-surgical ICU. Adult patients who were mechanically ventilated beyond 6 days were included. Clinical and mortality data were collected. Pre-admission and 6- and 12-month HRQOL were measured with the Short Form-36 questionnaire. Physical and mental component summary scores (PCS and MCS) were calculated. Associations between 12-month mortality and poor HRQOL scores were determined.

RESULTS

Of 119 patients enrolled, 40.3% had sustained trauma, 19.3% were post-surgical and 40.3% had medical conditions; 29.2% were HIV-positive (HIV status was known for 74.8% of the cohort). The hospital and 12-month mortality rates were 42.9% and 57.4% (n=66/115), respectively. Age, longer ICU stay, higher disease severity scores and vasopressor use were associated with 12-month mortality. The survivors' median PCS and MCS at 6 and 12 months were significantly lower compared with pre-admission scores (both p<0.001). At 12 months, 53.1% of survivors demonstrated a poor PCS and 42.9% a poor MCS. Associations with poor 12-month PCS included longer ICU stay, male gender and trauma, while trauma and sepsis were associated with a poor 12-month MCS. Among the 19 trauma survivors, 78.9% had a poor MCS and/or PCS. Of previously employed patients, 54.8% were unemployed at 12 months.

CONCLUSIONS

Patients ventilated beyond 6 days in a multidisciplinary ICU had a high mortality. Poor HRQOL at 12 months post discharge was frequently observed among survivors. Trauma was associated with poor 12-month outcomes. These findings highlight the need to further explore the outcomes of long-stay ICU patients in Africa.

56 A Quality Improvement Project to Assess and Refine the Handover Process at Morning Trauma Meetings

Aim

Poor handover and inadequate transmission of clinical information between shifts can result in patient harm. This study was designed to evaluate the impact of implementing a handover protocol on the quality of information exchanged in the trauma handover meetings in a UK district general hospital.

Method

A prospective single centre observational study was performed at an acute NHS trust, using the define, measure, analyse, improve and control (DMAIC) methodology. Ten consecutive weekday trauma meetings, involving 43 patients, were observed to identify poor practices in handover. This data was used in conjunction with the Royal College of Surgeon’s recommendations for effective handover (2007) to create a standard operating protocol (SOP). Following the implementation of the SOP, a further eight consecutive weekday trauma meetings, involving a further 47 patients, were observed. The data collection was performed by five trained independent observers. The data was analysed using t-test for quantitative variables and chi-square or Fisher’s exact tests for categorical variables.

Results

An improvement in the trauma handover was demonstrated in multiple aspects of handover including patient’s past medical history, injury date, results, diagnosis, consent, mark and starvation status (all p < 0.001). Subgroup analyses showed that handover of neck of femur patients including information on mobility (p = 0.04), Nottingham Hip Fracture Score (p = 0.01), next of kin discussion (p = 0.075) and resuscitation status (p = 0.001) all improved following our interventions.

Conclusions

These results demonstrate that the implementation of a well-structured handover protocol can improve the transmission of critical information in trauma meetings.

Barriers, Attitudes, and Influences Towards Dietary Intake Amongst Elite Rugby Union Players

Background: Dietary intakes can impact an athletes health and performance. Although evidence exists about what an athlete should eat, an athlete's nutritional intake is influenced by many factors. The limited research available suggests the main barriers preventing optimal nutritional intakes reported by athletes are lack of time, food accessibility, poor cooking skills, costs, taste, and time spent in “off-season.” Although these factors have been shown to influence dietary intake they remain relatively unexplored in Rugby Union. This study aimed to describe the nutritional influences on dietary intake amongst Rugby Union player's.

Methods: This was a qualitative study utilising in person individual interviews with all participants. Participants were Rugby Union players (n = 30) for either a Super Rugby franchise or one of their development squads in New Zealand. Participant's undertook recorded face to face interviews, which were later transcribed. A thematic approach was used to code the transcripts by the primary coder and the themes were subsequently evaluated by the research team.

Results: Childhood upbringing, organisational skills, time and food security also emerged as barriers. Body composition and sport nutrition knowledge emerged as both barriers and enablers to nutritional intake. Influence on performance was an enabler to optimal dietary intake. Fully professional rugby players have access to dietitians, whereas development and semi-professional rugby players only have limited if any access, and they were more likely to seek nutritional information via social media.

Conclusion: This study suggests a need for greater nutrition education at developmental levels with an emphasis on affordable food choices, meal planning and skills for interpreting online nutrition information.

High bone mass phenotype in a cohort of patients with Osteogenesis Imperfecta caused due to BMP1 and C-propeptide cleavage variants in COL1A1

OBJECTIVES

Osteogenesis Imperfecta (OI) is a heterogeneous condition mainly characterised by bone fragility; extra-skeletal features in OI include blue sclerae, dentinogenesis imperfecta, skin laxity and joint hyper-extensibility. Most patients with OI are thought to have a low bone mass but contrary to expectations there are certain forms of OI with high bone mass which this study explores in further detail.

METHOD

A cohort of n = 6 individuals with pathogenic variants in BMP1 and the C-propeptide cleavage variants in COL1A1 were included in this study. Detailed clinical and radiological phenotyping was done and correlated with genotype to identify patterns of clinical presentation and fracture history in this cohort of patients. This data was compared to previously reported literature in this group.

RESULTS

2 patients with BMP1 and 4 patients with pathogenic variants in C-propeptide region in COL1A1 were deep-phenotyped as part of this study and 1 patient with C-propeptide variant in COL1A1, showed low bone mineral density. In those with an elevated bone mineral density, this became even more apparent on bisphosphonate therapy. Patients in this cohort had variable clinical presentation ranging from antenatal presentation to more of an insidious course resulting in later confirmation of genetic diagnosis up to 19 years of age.

CONCLUSIONS

Patients with pathogenic variants in the C-propeptide region of COL1A1/A2 and BMP1 appear to have a high bone mass phenotype with increased sensitivity to bisphosphonate therapy. It is important to closely monitor patients with these genotypes to assess their response to therapy and tailor their treatment regime accordingly.

213 Can Styloid Process and Internal Carotid Artery Anatomy Be Used to Predict Carotid Artery Dissection?

Aim

Carotid artery dissection is a common cause of stroke in the young. It has been related to the association of the carotid artery with fixed neighbouring anatomical structures. This study assesses the association between styloid process length, internal carotid artery position and cervical carotid artery dissection (CCAD). This information would provide potential predicative radiological measurements, which could prevent delays in CCAD diagnosis.

Method

Retrospective data was collected from two central London hospitals over five years. CCAD cases were identified from individuals who underwent computer topography angiography (CTA) of the neck for suspected CCAD. The following data was collected: evidence of CCAD; bilateral styloid process length and presence of styloid-hyoid ligament calcification; bilateral styloid process-internal carotid distance; calcification of carotid arteries and whether their position was aberrant. Cases were dissection-side, age and gender matched with two non-dissection controls.

Results

Three hundred and fifty-five individuals were identified. Fifty individuals had CCAD, of which 4 had bilateral dissection. In individuals with CCAD, average styloid process length was 27.5mm and styloid process-internal carotid distance was 5.14mm. There was no significant association between styloid process length or styloid process-internal carotid distance, and CCAD when compared with matched controls. Internal carotid artery aberrancy was significant for non-dissection.

Conclusions

In this study, there was no association between styloid process length and styloid process-internal carotid distance with CCAD. These measurements cannot be used to predict the possibility of a CCAD following trauma.

O47 Safe delivery of surgical tracheostomies in COVID-19 patients during the pandemic

Introduction

During the corona virus disease (COVID-19) pandemic, frontline units worldwide faced the challenging task of providing high-risk services (like surgical tracheostomy) while safe-guarding the very people performing the high risk procedures. The aim of our study was to assess the incidence of COVID-19 infection among staff involved in surgical tracheostomy on COVID-19 patients

Method

A surgical tracheostomy protocol and operation theatre modifications were put in place at our centre, dictated by local resources, staff availability and previous tracheostomy experience. Between 26/03/2020 and 27/05/2020, staff participating in 71 tracheostomy procedures were sent a questionnaire. The presence of COVID-19 symptoms (new onset continuous cough, fever, loss of taste and/or loss of smell) in tracheostomy staff and patient related data were analysed.

Result

Among the responders (72/122), compliance with personal prophylaxis equipment use was 100%. Eleven (15%,11/72) reported key COVID-19 symptoms and self-isolated. 10 had a COVID-19 swab test and three tested positive. One staff attended (1/72) hospital for symptomatic treatment, none required hospitalisation. 43/72 staff (60%) underwent a COVID-19 antibody test, 18.6% (8/43) were positive. Among the tracheostomised patients, the mean age was 58 years(29–78) and 65.5% were males. The median time from intubation to ST was 15 days (range 5–33, IQR = 9). There were no tracheostomy related deaths and overall mortality was 11%(6/55).

Conclusion

Safe delivery of tracheostomy during a pandemic like COVID-19 is possible with strict adherence to personnel protective equipment, surgical protocols and regulation of traffic flow in theatres to mitigate the potential transmission of COVID-19 among surgical staff.

Take-home Message

Compliance with PPE, adherence to tracheostomy protocol and local modifications can mitigate potential COVID-19 transmission among health care personnel.

O28 Can styloid process and internal carotid artery anatomy be used to predict carotid artery dissection?

Introduction

Carotid artery dissection is a common cause of stroke in the young. It has been related to the association of the carotid artery with fixed neighbouring anatomical structures. This study assesses the association between styloid process length, internal carotid artery position and cervical carotid artery dissection (CCAD). This information would provide potential predicative radiological measurements, which could prevent delays in CCAD diagnosis.

Method

Retrospective data was collected from two central London hospitals over five years. CCAD cases were identified from individuals who underwent computer topography angiography (CTA) of the neck for suspected CCAD. The following data was collected: evidence of CCAD; bilateral styloid process length and presence of styloid-hyoid ligament calcification; bilateral styloid process-internal carotid distance; calcification of carotid arteries and whether their position was aberrant. Cases were dissection-side, age and gender matched with two non-dissection controls.

Result

Three hundred and fifty-five individuals were identified. Fifty individuals had CCAD, of which 4 had bilateral dissection. In individuals with CCAD, average styloid process length was 27.5 mm and styloid process-internal carotid distance was 5.14 mm. There was no significant association between styloid process length or styloid process-internal carotid distance, and CCAD when compared with matched controls. Internal carotid artery aberrancy was significant for non-dissection.

Conclusion

In this study, there was no association between styloid process length and styloid process-internal carotid distance with CCAD. These measurements can not be used to predict the possibility of a CCAD following trauma.

Take-home Message

Anatomy of the styloid process and calcification of the styloid-hyoid ligament are highly variable and many independent factors may contribute to the risk of cervical carotid artery dissection. Radiological measurements of the styloid process alone cannot be used to predict risk and likelihood of cervical carotid artery dissection.

Experience with the COVID-19 AstraZeneca vaccination in people with multiple sclerosis

Background

Some people with multiple sclerosis (pwMS) are at increased risk of severe Coronavirus disease 19 (COVID-19) and should be rapidly vaccinated. However, vaccine supplies are limited, and there are concerns about side-effects, particularly with the ChAdOx1nCoV-19 (AstraZeneca) vaccine.

Objectives

To report our first experience of pwMS receiving the AstraZeneca vaccine.

Methods

Service evaluation. pwMS using the MS service at Barts Health NHS Trust were sent questionnaires to report symptoms following vaccination.

Results

Thirty-three responses were returned, 29/33 pwMS received a first dose of AstraZeneca vaccine, the remaining four received a first dose of BioNTech/Pfizer vaccine.

All but two patients (94%) reported any symptoms including a sore arm (70%), flu-like symptoms (64%), fever (21%), fatigue (27%), and headache (21%). In more than 2/3 patients, symptoms lasted up to 48 hours, and with the exception of two pwMS reporting symptom duration of 10 and 12 days, respectively, symptoms in the remainder resolved within seven days. No severe adverse effects occurred.

Conclusions

pwMS report transient symptoms following AstraZeneca vaccination, characteristics of which were similar to those reported in the non-MS population. Symptoms may be more pronounced in pwMS due to the temperature-dependent delay in impulse propagation (Uhthoff's phenomenon) due to demyelination.

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org .

South African guidelines on the determination of death

Summary

Death is a medical occurrence that has social, legal, religious and cultural consequences requiring common clinical standards for its diagnosis and legal regulation. This document compiled by the Critical Care Society of Southern Africa outlines the core standards for determination of death in the hospital context. It aligns with the latest evidence-based research and international guidelines and is applicable to the South African context and legal system. The aim is to provide clear medical standards for healthcare providers to follow in the determination of death, thereby promoting safe practices and high-quality care through the use of uniform standards. Adherence to such guidelines will provide assurance to medical staff, patients, their families and the South African public that the determination of death is always undertaken with diligence, integrity, respect and compassion, and is in accordance with accepted medical standards and latest scientific evidence. The consensus guidelines were compiled using the AGREE II checklist with an 18-member expert panel participating in a three-round modified Delphi process. Checklists and advice sheets were created to assist with application of these guidelines in the clinical environment (https://criticalcare.org.za/resource/death-determination-checklists/).

Key points

Brain death and circulatory death are the accepted terms for defining death in the hospital context.

Death determination is a clinical diagnosis which can be made with complete certainty provided that all preconditions are met.

The determination of death in children is held to the same standard as in adults but cannot be diagnosed in children <36 weeks’ corrected gestation.

Brain-death testing while on extra-corporeal membrane oxygenation is outlined.

Recommendations are given on handling family requests for accommodation and on consideration of the potential for organ donation.

The use of a checklist combined with a rigorous testing process, comprehensive documentation and adequate counselling of the family are core tenets of death determination. This is a standard of practice to which all clinicians should adhere in end-of-life care.

Spectropolarimetric fluctuations in a sunspot chromosphere

The instrumental advances made in this new era of 4 m class solar telescopes with unmatched spectropolarimetric accuracy and sensitivity will enable the study of chromospheric magnetic fields and their dynamics with unprecedented detail. In this regard, spectropolarimetric diagnostics can provide invaluable insight into magneto-hydrodynamic (MHD) wave processes. MHD waves and, in particular, Alfvénic fluctuations associated with particular wave modes were recently recognized as important mechanisms not only for the heating of the outer layers of the Sun's atmosphere and the acceleration of the solar wind, but also for the elemental abundance anomaly observed in the corona of the Sun and other Sun-like stars (also known as first ionization potential) effect. Here, we take advantage of state-of-the-art and unique spectropolarimetric Interferometric BIdimensional Spectrometer observations to investigate the relation between intensity and circular polarization (CP) fluctuations in a sunspot chromosphere. Our results show a clear link between the intensity and CP fluctuations in a patch which corresponds to a narrow range of magnetic field inclinations. This suggests the presence of Alfvénic perturbations in the sunspot. This article is part of the Theo Murphy meeting issue 'High-resolution wave dynamics in the lower solar atmosphere'.

South African guidelines on the determination of death

Death is a medical occurrence that has social, legal, religious and cultural consequences requiring common clinical standards for its diagnosis and legal regulation. This document compiled by the Critical Care Society of Southern Africa outlines the core standards for determination of death in the hospital context. It aligns with the latest evidence-based research and international guidelines and is applicable to the South African context and legal system. The aim is to provide clear medical standards for healthcare providers to follow in the determination of death, thereby promoting safe practices and high-quality care through the use of uniform standards. Adherence to such guidelines will provide assurance to medical staff, patients, their families and the South African public that the determination of death is always undertaken with diligence, integrity, respect and compassion, and is in accordance with accepted medical standards and latest scientific evidence. The consensus guidelines were compiled using the AGREE II checklist with an 18-member expert panel participating in a three-round modified Delphi process. Checklists and advice sheets were created to assist with application of these guidelines in the clinical environment (https://criticalcare.org.za/resource/death-determination-checklists/). Key points • Brain death and circulatory death are the accepted terms for defining death in the hospital context. • Death determination is a clinical diagnosis which can be made with complete certainty provided that all preconditions are met. • The determination of death in children is held to the same standard as in adults but cannot be diagnosed in children <36 weeks' corrected gestation. • Brain-death testing while on extra-corporeal membrane oxygenation is outlined. • Recommendations are given on handling family requests for accommodation and on consideration of the potential for organ donation. • The use of a checklist combined with a rigorous testing process, comprehensive documentation and adequate counselling of the family are core tenets of death determination. This is a standard of practice to which all clinicians should adhere in end-of-life care.

Innate immunity during SARS-CoV-2: evasion strategies and activation trigger hypoxia and vascular damage

Innate immune sensing of viral molecular patterns is essential for development of antiviral responses. Like many viruses, SARS-CoV-2 has evolved strategies to circumvent innate immune detection, including low cytosine-phosphate-guanosine (CpG) levels in the genome, glycosylation to shield essential elements including the receptor-binding domain, RNA shielding and generation of viral proteins that actively impede anti-viral interferon responses. Together these strategies allow widespread infection and increased viral load. Despite the efforts of immune subversion, SARS-CoV-2 infection activates innate immune pathways inducing a robust type I/III interferon response, production of proinflammatory cytokines and recruitment of neutrophils and myeloid cells. This may induce hyperinflammation or, alternatively, effectively recruit adaptive immune responses that help clear the infection and prevent reinfection. The dysregulation of the renin-angiotensin system due to down-regulation of angiotensin-converting enzyme 2, the receptor for SARS-CoV-2, together with the activation of type I/III interferon response, and inflammasome response converge to promote free radical production and oxidative stress. This exacerbates tissue damage in the respiratory system, but also leads to widespread activation of coagulation pathways leading to thrombosis. Here, we review the current knowledge of the role of the innate immune response following SARS-CoV-2 infection, much of which is based on the knowledge from SARS-CoV and other coronaviruses. Understanding how the virus subverts the initial immune response and how an aberrant innate immune response contributes to the respiratory and vascular damage in COVID-19 may help to explain factors that contribute to the variety of clinical manifestations and outcome of SARS-CoV-2 infection.

COVID-19 vaccine-readiness for anti-CD20-depleting therapy in autoimmune diseases

Although most autoimmune diseases are considered to be CD4 T cell- or antibody-mediated, many respond to CD20-depleting antibodies that have limited influence on CD4 and plasma cells. This includes rituximab, oblinutuzumab and ofatumumab that are used in cancer, rheumatoid arthritis and off-label in a large number of other autoimmunities and ocrelizumab in multiple sclerosis. Recently, the COVID-19 pandemic created concerns about immunosuppression in autoimmunity, leading to cessation or a delay in immunotherapy treatments. However, based on the known and emerging biology of autoimmunity and COVID-19, it was hypothesised that while B cell depletion should not necessarily expose people to severe SARS-CoV-2-related issues, it may inhibit protective immunity following infection and vaccination. As such, drug-induced B cell subset inhibition, that controls at least some autoimmunities, would not influence innate and CD8 T cell responses, which are central to SARS-CoV-2 elimination, nor the hypercoagulation and innate inflammation causing severe morbidity. This is supported clinically, as the majority of SARS-CoV-2-infected, CD20-depleted people with autoimmunity have recovered. However, protective neutralizing antibody and vaccination responses are predicted to be blunted until naive B cells repopulate, based on B cell repopulation kinetics and vaccination responses, from published rituximab and unpublished ocrelizumab (NCT00676715, NCT02545868) trial data, shown here. This suggests that it may be possible to undertake dose interruption to maintain inflammatory disease control, while allowing effective vaccination against SARS-CoV-29, if and when an effective vaccine is available.

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.

From Old Wisdom to Future Trends

This article discusses educational services and programs provided by The New Mexico School for the Visually Handicapped. Many of these programs were being implemented before the enactment of EL. 94–142 and have been expanded since its passage.

The Critical Care Society of Southern Africa guidelines on the allocation of scarce critical care resources during the COVID-19 public health emergency in South Africa

Letter by Gopalan et al. on article by Singh and Moodley (Singh JA, Moodley K. Critical care triaging in the shadow of COVID-19: Ethics considerations. S Afr Med J 2020;110(5):355-359. https://doi.org/10.7196/SAMJ.2020.v110i5.14778); and response by Singh and Moodley.

Severe skin reactions associated with cladribine in people with multiple sclerosis

OBJECTIVE

To report three cases of severe skin reactions in patients treated with cladribine for multiple sclerosis.

METHODS

Case study.

RESULTS

Patients developed severe rash 3-192 days after receiving cladribine. All were effectively treated with steroids and antihistamines. Additional doses of cladribine were administered after pretreatment with steroids and anti-histamines. One patient developed mild recurrence following re-exposure, which resolved within three days, whilst another patient tolerated re-exposure without further adverse reaction.

CONCLUSION

Severe skin reactions, well described in patients receiving cladribine for treatment of haematological conditions, may occur in patients treated with this compound for multiple sclerosis. Neurologists need to be aware of this rare, but significant adverse reaction. Re-exposure may be safe with standard pre-treatment against allergic reactions.

Community-Driven Data Analysis Training for Biology

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

Electron microscopy in the diagnosis of Ehlers-Danlos syndromes: correlation with clinical and genetic investigations

BACKGROUND

The Ehlers-Danlos syndromes (EDS) consist of 13 subtypes with overlapping features including joint hypermobility, skin and vascular fragility and generalized connective tissue friability. As DNA analysis has become the gold standard for investigation of EDS, transmission electron microscopy (TEM) in clinical practice is decreasing. However, owing to the use of next-generation sequencing, the frequency of variants of uncertain significance (VUS) identified using DNA analysis is increasing. We hypothesized that TEM can provide evidence for or against pathogenicity of VUS.

OBJECTIVES

The aim of this study was to evaluate the role of TEM in the diagnosis of EDS subtypes.

METHODS

Data were collected from patients who underwent a skin biopsy between October 2012 and March 2017 at the London EDS National Diagnostic Service. TEM biopsies were categorized as 'normal' or 'abnormal' according to the description and conclusion in the TEM reports. Definitive diagnoses were reached via a combination of clinical features, structural and functional studies and DNA investigations.

RESULTS

The analysis included 177 patients, comprising 30 abnormal and 147 normal TEM reports. A definitive diagnosis of monogenic EDS subtypes was made in 24 patients. Overall, 17 of these 24 patients (71%) had an abnormal biopsy report and seven (29%) had a normal biopsy report. No TEM findings were specifically associated with any EDS subtype, although collagen flowers were present in most patients with a genetically confirmed diagnosis of classical EDS.

CONCLUSIONS

TEM analysis of collagen structure may have the potential to provide evidence for or against the pathogenicity of a VUS, but more work is needed to establish a clear role for TEM in this process. What's already known about this topic? Collagen fibril abnormalities can be seen in several Ehlers-Danlos syndrome (EDS) subtypes. What does this study add? This study provides clinical data, transmission electron microscopy (TEM) data and molecular data of one of the largest groups of patients suspected to have a monogenetic EDS subtype. No TEM findings were specifically associated with an EDS subtype. There was a higher percentage (71%) of abnormal biopsy findings in patients with a definitive diagnosis of a monogenetic EDS subtype and where a class 4/5 genetic variant was present.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

The EAACI/GA²LEN/EDF/WAO guideline for the definition, classification, diagnosis and management of urticaria

This evidence- and consensus-based guideline was developed following the methods recommended by Cochrane and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) working group. The conference was held on 1 December 2016. It is a joint initiative of the Dermatology Section of the European Academy of Allergology and Clinical Immunology (EAACI), the EU-founded network of excellence, the Global Allergy and Asthma European Network (GA²LEN), the European Dermatology Forum (EDF) and the World Allergy Organization (WAO) with the participation of 48 delegates of 42 national and international societies. This guideline was acknowledged and accepted by the European Union of Medical Specialists (UEMS). Urticaria is a frequent, mast cell-driven disease, presenting with wheals, angioedema, or both. The lifetime prevalence for acute urticaria is approximately 20%. Chronic spontaneous urticaria and other chronic forms of urticaria are disabling, impair quality of life and affect performance at work and school. This guideline covers the definition and classification of urticaria, taking into account the recent progress in identifying its causes, eliciting factors and pathomechanisms. In addition, it outlines evidence-based diagnostic and therapeutic approaches for the different subtypes of urticaria.

Disease activity in progressive multiple sclerosis can be effectively reduced by cladribine

BACKGROUND

Evidence suggests people with non-relapsing deteriorating ("progressive") multiple sclerosis (pwPMS) may benefit from disease-modifying immune therapy (DMT). However, only one such treatment (ocrelizumab) has been licensed and is highly restricted to pwPMS suffering from the primary progressive phenotype. The difficulties assessing treatment outcome in pwPMS is one important reason for the lack of respective DMT. The concentration of neurofilaments in the cerebrospinal fluid (CSF) provides a biomarker of neuro-axonal damage, and both neurofilament light (NfL) and heavy chain (NfH) levels have been used as outcome indices and to guide treatment choices.

METHODS

We report on two pwPMS, who were treated with subcutaneous cladribine undergoing CSF NfL testing, alongside MRI and clinical follow-up, before and after treatment.

RESULTS

Cladribine treatment was well tolerated without any side effects. CSF NfL after treatment revealed significant reduction (by 73% and 80%, respectively) corroborating the MRI detectable drop in disease activity. Disability mildly progressed in one, and remained stable in the other pwPMS.

CONCLUSIONS

pwPMS with detectable disease activity (MRI, elevated NfL) should be considered for DMT. NfL appears to be a sensitive index of treatment effect in pwPMS, and may be a useful outcome in clinical trials targeting this patient group. Over and above its licensed indication (relapsing MS), cladribine may be an effective treatment option for pwPMS.