The Expected Behaviors of Posterior Predictive Tests and Their Unexpected Interpretation

Poor fit between models of sequence or trait evolution and empirical data is known to cause biases and lead to spurious conclusions about evolutionary patterns and processes. Bayesian posterior prediction is a flexible and intuitive approach for detecting such cases of poor fit. However, the expected behavior of posterior predictive tests has never been characterized for evolutionary models, which is critical for their proper interpretation. Here, we show that the expected distribution of posterior predictive P-values is generally not uniform, in contrast to frequentist P-values used for hypothesis testing, and extreme posterior predictive P-values often provide more evidence of poor fit than typically appreciated. Posterior prediction assesses model adequacy under highly favorable circumstances, because the model is fitted to the data, which leads to expected distributions that are often concentrated around intermediate values. Nonuniform expected distributions of P-values do not pose a problem for the application of these tests, however, and posterior predictive P-values can be interpreted as the posterior probability that the fitted model would predict a dataset with a test statistic value as extreme as the value calculated from the observed data.

Reflective, pragmatic, and reactive decision-making by maternity service providers during the SARS-CoV-2 pandemic health system shock: a qualitative, grounded theory analysis

BACKGROUND

Pregnant and postpartum women were identified as having particular vulnerability to severe symptomatology of SARS-CoV-2 infection, so maternity services significantly reconfigured their care provision. We examined the experiences and perceptions of maternity care staff who provided care during the pandemic in South London, United Kingdom - a region of high ethnic diversity with varied levels of social complexity.

METHODS

We conducted a qualitative interview study, as part of a service evaluation between August and November 2020, using in-depth, semi-structured interviews with a range of staff (N = 29) working in maternity services. Data were analysed using Grounded Theory analysis appropriate to cross-disciplinary health research.

ANALYSIS & FINDINGS

Maternity healthcare professionals provided their views, experiences, and perceptions of delivering care during the pandemic. Analysis rendered three emergent themes regarding decision-making during reconfigured maternity service provision, organised into pathways: 1) 'Reflective decision-making'; 2) 'Pragmatic decision-making'; and 3) 'Reactive decision-making'. Whilst pragmatic decision-making was found to disrupt care, reactive-decision-making was perceived to devalue the care offered and provided. Alternatively, reflective decision-making, despite the difficult working conditions of the pandemic, was seen to benefit services, with regards to care of high-quality, sustainability of staff, and innovation within the service.

CONCLUSIONS

Decision-making within maternity care was found to take three forms - where at best changes to services could be innovative, at worst they could cause devaluation in care being delivered, and more often than not, these changes were disruptive. With regard to positive changes, healthcare providers identified staff empowerment, flexible working patterns (both for themselves and collectively as teams), personalised care delivery, and change-making in general, as key areas to capitalise on current and ongoing innovations borne out of the pandemic. Key learnings included a focus on care-related, meaningful listening and engagement of staff at all levels, in order to drive forward high-quality care and avoid care disruption and devaluation.

Clinical features and overall survival of osteosarcoma of the mandible

Osteosarcoma is the most common bone sarcoma and is typically found in the distal femur, proximal tibia, and proximal humerus. While several factors are known to influence survival, less is known regarding the influence of primary tumor location. This study describes the clinical features and prognosis of mandibular osteosarcoma. The SEER database was utilized to identify cases of mandibular osteosarcoma diagnosed between 2004 and 2015. Sex, age, grade, histological subtype, tumor size, tumor extension, presence of metastasis at diagnosis, and therapeutic intervention were determined. Osteosarcomas originating from other sites were assessed for comparison. There were 164 cases of mandibular osteosarcoma identified, representing 5.5% of all surveyed osteosarcomas. The 2-, 5-, and 10-year overall survival rates were 79.9%, 65.6% and 58.5%, respectively. Survival was worse for patients with older age, larger tumor size, metastatic disease, and absence of surgical resection. Compared to other sites, mandibular osteosarcomas were significantly smaller tumors and were far less likely to metastasize. Mandibular osteosarcoma manifested at an older age than the more common extremity osteosarcomas and presented with smaller tumors. Rates of metastasis of jaw osteosarcoma were much lower than osteosarcoma found in the extremities, while mortality rates were comparable.

A quantitative evaluation of aerosol generation during awake tracheal intubation

Aerosol-generating procedures are medical interventions considered high risk for transmission of airborne pathogens. Tracheal intubation of anaesthetised patients is not high risk for aerosol generation; however, patients often perform respiratory manoeuvres during awake tracheal intubation which may generate aerosol. To assess the risk, we undertook aerosol monitoring during a series of awake tracheal intubations and nasendoscopies in healthy participants. Sampling was undertaken within an ultraclean operating theatre. Procedures were performed and received by 12 anaesthetic trainees. The upper airway was topically anaesthetised with lidocaine and participants were not sedated. An optical particle sizer continuously sampled aerosol. Passage of the bronchoscope through the vocal cords generated similar peak median (IQR [range]) aerosol concentrations to coughing, 1020 (645-1245 [120-48,948]) vs. 1460 (390-2506 [40-12,280]) particles.l^-1 respectively, p = 0.266. Coughs evoked when lidocaine was sprayed on the vocal cords generated 91,700 (41,907-166,774 [390-557,817]) particles.l^-1 which was significantly greater than volitional coughs (p < 0.001). For 38 nasendoscopies in 12 participants, the aerosol concentrations were relatively low, 180 (120-525 [0-9552]) particles.l^-1 , however, five nasendoscopies generated peak aerosol concentrations greater than a volitional cough. Awake tracheal intubation and nasendoscopy can generate high concentrations of respiratory aerosol. Specific risks are associated with lidocaine spray of the larynx, instrumentation of the vocal cords, procedural coughing and deep breaths. Given the proximity of practitioners to patient-generated aerosol, airborne infection control precautions are appropriate when undertaking awake upper airway endoscopy (including awake tracheal intubation, nasendoscopy and bronchoscopy) if respirable pathogens cannot be confidently excluded.

Precarity and preparedness during the SARS-CoV-2 pandemic: A qualitative service evaluation of maternity healthcare professionals

Introduction

The SARS‐CoV‐2 pandemic has devastated populations, posing unprecedented challenges for healthcare services, staff and service‐users. In the UK, rapid reconfiguration of maternity healthcare service provision changed the landscape of antenatal, intrapartum and postnatal care. This study aimed to explore the experiences of maternity services staff who provided maternity care during the SARS‐CoV‐2 pandemic to inform future improvements in care.

Material and methods

A qualitative interview service evaluation was undertaken at a single maternity service in an NHS Trust, South London. Respondents (n = 29) were recruited using a critical case purposeful sample of maternity services staff. Interviews were conducted using video‐conferencing software, and were transcribed and analyzed using Grounded Theory Analysis appropriate for cross‐disciplinary health research. The focus of analysis was on staff experiences of delivering maternity services and care during the SARS‐CoV‐2 pandemic.

Results

A theory of “Precarity and Preparedness” was developed, comprising three main emergent themes: “Endemic precarity: A health system under pressure”; “A top‐down approach to managing the health system shock”; and “From un(der)‐prepared to future flourishing”.

Conclusions

Maternity services in the UK were under significant strain and were inherently precarious. This was exacerbated by the SARS‐CoV‐2 pandemic, which saw further disruption to service provision, fragmentation of care and pre‐existing staff shortages. Positive changes are required to improve staff retention and team cohesion, and ensure patient‐centered care remains at the heart of maternity care.

Quantitative evaluation of aerosol generation from upper airway suctioning assessed during tracheal intubation and extubation sequences in anaesthetized patients

BACKGROUND

Open respiratory suctioning is defined as an aerosol generating procedure (AGP). Laryngopharyngeal suctioning, used to clear secretions during anaesthesia, is widely managed as an AGP. However, it is uncertain whether upper airway suctioning should be designated as an AGP due to the lack of both aerosol and epidemiological evidence.

AIM

To assess the relative risk of aerosol generation by upper airway suctioning during tracheal intubation and extubation in anaesthetized patients.

METHODS

This prospective environmental monitoring study was undertaken in an ultraclean operating theatre setting to assay aerosol concentrations during intubation and extubation sequences, including upper airway suctioning, for patients undergoing surgery (N=19). An optical particle sizer (particle size 0.3-10 μm) sampled aerosol 20 cm above the patient's mouth. Baseline recordings (background, tidal breathing and volitional coughs) were followed by intravenous induction of anaesthesia with neuromuscular blockade. Four periods of laryngopharyngeal suctioning were performed with a Yankauer sucker: pre-laryngoscopy, post-intubation, pre-extubation and post-extubation.

FINDINGS

Aerosol was reliably detected {median 65 [interquartile range (IQR) 39-259] particles/L} above background [median 4.8 (IQR 1-7) particles/L, P<0.0001] when sampling in close proximity to the patient's mouth during tidal breathing. Upper airway suctioning was associated with a much lower average aerosol concentration than breathing [median 6.0 (IQR 0-12) particles/L, P=0.0007], and was indistinguishable from background (P>0.99). Peak aerosol concentrations recorded during suctioning [median 45 (IQR 30-75) particles/L] were much lower than during volitional coughs [median 1520 (IQR 600-4363) particles/L, P<0.0001] and tidal breathing [median 540 (IQR 300-1826) particles/L, P<0.0001].

CONCLUSION

Upper airway suctioning during airway management was not associated with a higher aerosol concentration compared with background, and was associated with a much lower aerosol concentration compared with breathing and coughing. Upper airway suctioning should not be designated as a high-risk AGP.

Six generations of CHMP2B-mediated Frontotemporal Dementia: Clinical features, predictive testing, progression, and survival

OBJECTIVES

Chromosome 3-linked frontotemporal dementia (FTD-3) is caused by a c.532-1G > C mutation in the CHMP2B gene. It is extensively studied in a Danish family comprising one of the largest families with an autosomal dominantly inherited frontotemporal dementia (FTD). This retrospective cohort study utilizes demographics to identify risk factors for onset, progression, life expectancy, and death in CHMP2B-mediated FTD. The pedigree of 528 individuals in six generations is provided, and clinical descriptions are presented. Choices of genetic testing are evaluated.

MATERIALS AND METHODS

Demographic and lifestyle factors were assessed in survival analysis in all identified CHMP2B mutation carriers (44 clinically affected FTD-3 patients and 16 presymptomatic CHMP2B mutation carriers). Predictors of onset and progression included sex, parental disease course, education, and vascular risk factors. Life expectancy was established by matching CHMP2B mutation carriers with average life expectancies in Denmark.

RESULTS

Disease course was not correlated to parental disease course and seemed unmodified by lifestyle factors. Diagnosis was recognized at an earlier age in members with higher levels of education, probably reflecting an early dysexecutive syndrome, unmasked earlier in people with higher work-related requirements. Carriers of the CHMP2B mutation had a significant reduction in life expectancy of 13 years. Predictive genetic testing was chosen by 20% of at-risk family members.

CONCLUSIONS

CHMP2B-mediated FTD is substantiated as an autosomal dominantly inherited disease of complete penetrance. The clinical phenotype is a behavioral variant FTD. The disease course is unpredictable, and life expectancy is reduced. The findings may be applicable to other genetic FTD subtypes.

OUP accepted manuscript

The scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount of information with which to draw inferences about evolutionary history. However, standard approaches to assessing confidence in those inferences (e.g., nonparametric bootstrap proportions [BP] and Bayesian posterior probabilities [PPs]) are still deeply influenced by statistical procedures and frameworks that were developed when information was much more limited. These approaches largely quantify uncertainty caused by limited amounts of data, which is often vanishingly small with modern, genome-scale sequence data sets. As a consequence, today’s phylogenomic studies routinely report near-complete confidence in their inferences, even when different studies reach strongly conflicting conclusions and the sites and loci in a single data set contain much more heterogeneity than our methods assume or can accommodate. Therefore, we argue that BPs and marginal PPs of bipartitions have outlived their utility as the primary means of measuring phylogenetic support for modern phylogenomic data sets with large numbers of sites relative to the number of taxa. Continuing to rely on these measures will hinder progress towards understanding remaining sources of uncertainty in the most challenging portions of the Tree of Life. Instead, we encourage researchers to examine the ideas and methods presented in this special issue of Systematic Biology and to explore the area further in their own work. The papers in this special issue outline strategies for assessing confidence and uncertainty in phylogenomic data sets that move beyond stochastic error due to limited data and offer promise for more productive dialogue about the challenges that we face in reaching our shared goal of understanding the history of life on Earth.[Big data; gene tree variation; genomic era; statistical bias.]

A quantitative evaluation of aerosol generation during supraglottic airway insertion and removal

Many guidelines consider supraglottic airway use to be an aerosol-generating procedure. This status requires increased levels of personal protective equipment, fallow time between cases and results in reduced operating theatre efficiency. Aerosol generation has never been quantitated during supraglottic airway use. To address this evidence gap, we conducted real-time aerosol monitoring (0.3-10-µm diameter) in ultraclean operating theatres during supraglottic airway insertion and removal. This showed very low background particle concentrations (median (IQR [range]) 1.6 (0-3.1 [0-4.0]) particles.l-1 ) against which the patient's tidal breathing produced a higher concentration of aerosol (4.0 (1.3-11.0 [0-44]) particles.l-1 , p = 0.048). The average aerosol concentration detected during supraglottic airway insertion (1.3 (1.0-4.2 [0-6.2]) particles.l-1 , n = 11), and removal (2.1 (0-17.5 [0-26.2]) particles.l-1 , n = 12) was no different to tidal breathing (p = 0.31 and p = 0.84, respectively). Comparison of supraglottic airway insertion and removal with a volitional cough (104 (66-169 [33-326]), n = 27), demonstrated that supraglottic airway insertion/removal sequences produced <4% of the aerosol compared with a single cough (p < 0.001). A transient aerosol increase was recorded during one complicated supraglottic airway insertion (which initially failed to provide a patent airway). Detailed analysis of this event showed an atypical particle size distribution and we subsequently identified multiple sources of non-respiratory aerosols that may be produced during airway management and can be considered as artefacts. These findings demonstrate supraglottic airway insertion/removal generates no more bio-aerosol than breathing and far less than a cough. This should inform the design of infection prevention strategies for anaesthetists and operating theatre staff caring for patients managed with supraglottic airways.

Novel use of social media to assess and improve coastal flood forecasts and hazard alerts

Coastal communities and infrastructure need protection from flooding and wave overtopping events. Assessment of hazard prediction methods, used in sea defence design, defence performance inspections and forecasting services, requires observations at the land-sea interface but these are rarely collected. Here we show how a database of hindcast overtopping events, and the conditions that cause them, can be built using qualitative overtopping information obtained from social media. We develop a database for a case study site at Crosby in the Northwest of England, use it to test the standard methods applied in operational flood forecasting services and new defence design, and suggest improvements to these methods. This novel approach will become increasingly important to deliver long-term, cost-effective coastal management solutions as sea-levels rise and coastal populations grow. At sites with limited, or no, monitoring or forecasting services, this approach, especially if combined with citizen science initiatives, could underpin the development of simplified early warning systems.

Systematic review of the use of translated patient-reported outcome measures in cancer trials

BACKGROUND

Patient-reported outcomes (PROs) are used in clinical trials to assess the effectiveness and tolerability of interventions. Inclusion of participants from different ethnic backgrounds is essential for generalisability of cancer trial results. PRO data collection should include appropriately translated patient-reported outcome measures (PROMs) to minimise missing data and sample attrition.

METHODS

Protocols and/or publications from cancer clinical trials using a PRO endpoint and registered on the National Institute for Health Research Portfolio were systematically reviewed for information on recruitment, inclusion of ethnicity data, and use of appropriately translated PROMs. Semi-structured interviews were conducted with key stakeholders to explore barriers and facilitators for optimal PRO trial design, diverse recruitment and reporting, and use of appropriately translated PROMs.

RESULTS

Eighty-four trials met the inclusion criteria, only 14 (17%) (n = 4754) reported ethnic group data, and ethnic group recruitment was low, 611 (13%). Although 8 (57%) studies were multi-centred and multi-national, none reported using translated PROMs, although available for 7 (88%) of the studies. Interviews with 44 international stakeholders identified a number of perceived barriers to ethnically diverse recruitment including diverse participant engagement, relevance of ethnicity to research question, prominence of PROs, and need to minimise investigator burden. Stakeholders had differing opinions on the use of translated PROMs, the impact of trial designs, and recruitment strategies on diverse recruitment. Facilitators of inclusive research were described and examples of good practice identified.

CONCLUSIONS

Greater transparency is required when PROs are used as primary or secondary outcomes in clinical trials. Protocols and publications should demonstrate that recruitment was accessible to diverse populations and facilitated by trial design, recruitment strategies, and appropriate PROM usage. The use of translated PROMs should be made explicit when used in cancer clinical trials.

Becoming the temporary surgeon: A grounded theory examination of anaesthetists performing emergency front of neck access in inter-disciplinary simulation-based training

The time-critical 'can't intubate, can't oxygenate' [CICO] emergency post-induction of anaesthesia is rare, but one which, should it occur, requires Anaesthetists to perform rapid emergency front of neck access [FONA] to the trachea, restoring oxygenation, and preventing death or brain hypoxia. The UK Difficult Airway Society [DAS] has directed all Anaesthetists to be trained with surgical cricothyroidotomy [SCT] as the primary emergency FONA method, sometimes referred to as 'Cric' as a shorthand. We present a longitudinal analysis using a classical approach to Grounded Theory methodology of ten Specialist Trainee Anaesthetists' data during a 6-month training programme delivered jointly by Anaesthetists and Surgeons. We identified with a critical realist ontology and an objectivist epistemology meaning data interpretation was driven by participants' narratives and accepted as true accounts of their experience. Our theory comprises three themes: 'Identity as an Anaesthetist'; 'The Role of a Temporary Surgeon'; and 'Training to Reconcile Identities', whereby training facilitated the psychological transition from a 'bloodless Doctor' (Anaesthetist) to becoming a 'temporary Surgeon'. The training programme enabled Specialist Trainees to move between the role of control and responsibility (Identity as an Anaesthetist), through self-described 'failure' and into a role of uncertainty about one's own confidence and competence (The Role of a Temporary Surgeon), and then return to the Anaesthetist's role once the airway had been established. Understanding the complexity of an intervention and providing a better insight into the training needs of Anaesthetic trainees, via a Grounded Theory approach, allows us to evaluate training programmes against the recognised technical and non-technical needs of those being trained.

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].

Trial of remote continuous versus intermittent NEWS monitoring after major surgery (TRaCINg): a feasibility randomised controlled trial

BACKGROUND

Despite medical advances, major surgery remains high risk with up to 44% of patients experiencing postoperative complications. Early recognition of postoperative complications is crucial in reducing morbidity and preventing long-term disability. The current standard of care is intermittent manual vital signs monitoring, but new wearable remote monitors offer the benefits of continuous vital signs monitoring without limiting the patient's mobility. The aim of this study was to evaluate the feasibility, acceptability and clinical outcomes of continuous remote monitoring after major surgery.

METHODS

The study was a randomised, controlled, unblinded, parallel group, feasibility trial. Adult patients undergoing elective major surgery were randomly assigned to receive continuous remote monitoring and normal National Early Warning Score (NEWS) monitoring (intervention group) or normal NEWS monitoring alone (control group). Continuous remote monitoring was achieved using the SensiumVitals® wireless patch which is worn on the patient's chest and monitors heart rate, respiratory rate and temperature continuously, and alerts the nurse when there is deviation from pre-set physiological norms. Feasibility was assessed by evaluating recruitment rate, adherence to protocol and randomisation and the amount of missing data. Clinical outcomes included time to antibiotics in cases of sepsis, length of hospital stay, number of critical care admissions and rate of hospital readmission within 30 days of discharge.

RESULTS

One hundred and thirty-six patients were randomised between October 2018 and April 2019: 67 to the control group and 69 to the intervention group. Recruitment was completed prior to the 12 month target with a high rate of eligibility and consent. Missing data was limited only to questionnaire responses; no participants were lost to follow-up and only one participant was withdrawn due to loss of capacity. The number of patients classed as 'drop-out' due to design (8.1%) were less than anticipated, and there were no participants who crossed over into the alternative trial allocation group. Seventeen participants in the intervention group (28%) did not adhere to the monitoring protocol. No formal comparisons between arms was undertaken; however, participants had fewer unplanned critical care admissions (1 versus 5) and had a shorter average length of hospital stay (11.6 days (95% confidence interval 9.5-13.7 days) versus 16.2 days (95% confidence interval 11.3-21.2 days)) in the continuous vital signs monitoring group. The time taken to receive antibiotics in cases of sepsis was similar in both arms. A cost-utility analysis indicated that the remote monitoring system was cost-saving when compared to standard NEWS monitoring alone.

CONCLUSIONS

It is feasible to perform a large-scale randomised controlled trial of continuous remote monitoring after major surgery. Progression to a definitive multicentre randomised controlled trial would be appropriate, taking consideration of factors, such as patient adherence, that might mask the potential benefit of additional monitoring.

TRIAL REGISTRATION

ISRCTN registry with study ID ISRCTN16601772 . Registered 30 August 2017.

An investigation into specialty trainee engagement with e-learning

AIM:

The objectives of this study were to determine paediatric specialty trainees' engagement with e-learning in Health Education England North West and the characteristics of sites accessed by specialty trainees, and to assess the quality of web interfaces being used and whether this aligns with the best evidence for e-learning provision.

METHODS:

A two-phase mixed methods design was used: a scoping exercise to elicit specialty trainees' preferred e-learning tools and a quality assessment of the named sites, and specialty trainee telephone interviews.

RESULTS:

A total of 135 respondents identified 86 sites. Quality assessment found considerable variation across sites and a number of barriers to access, one issue being uncertainty about quality and validity of sites.

CONCLUSIONS:

E-learning is viewed as an integral part of both mandatory and speciality training but there is considerable variation in access to and quality of sites. Specialty trainees value the convenience and breadth of e-learning available but express concerns about assessing the validity and legitimacy of such sites.

Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs

Approximately 80% of adults are infected with a member of the herpesviridae family. Herpesviruses establish life-long latent infections within neurons, which may reactivate into lytic infections due to stress or immune suppression. There are nine human herpesviruses (HHV) posing health concerns from benign conditions to life threatening encephalitis, including cancers associated with viral infections. The current treatment options for most HHV conditions mainly include several nucleoside and nucleotide analogs targeting viral DNA polymerase. Although these drugs help manage infections, their common mechanism of action may lead to the development of drug resistance, which is particularly devastating in immunocompromised patients. Therefore, new classes of drugs directed against novel targets in HHVs are necessary to alleviate this issue. We analyzed the conservation rates of all proteins in herpes simplex virus 1 (HHV-1), a representative of the HHV family and one of the most common viruses infecting the human population. Furthermore, we generated a full-length structure model of the most conserved HHV-1 protein, the DNA packaging terminase pUL15. A series of computational analyses were performed on the model to identify ATP and DNA binding sites and characterize the dynamics of the protein. Our study indicates that proteins involved in HHV-1 DNA packaging and cleavage are amongst the most conserved gene products of HHVs. Since the packaging protein pUL15 is the most conserved among all HHV-1 gene products, the virus will have a lower chance of developing resistance to small molecules targeting pUL15. A subsequent analysis of the structure of pUL15 revealed distinct ATP and DNA binding domains and the elastic network model identifies a functionally important hinge region between the two domains of pUL15. The atomic information on the active and allosteric sites in the ATP- and DNA-bound model of pUL15 presented in this study can inform the structure-based drug discovery of a new class of drugs to treat a wide range of HHVs.

Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling

Alphaherpesviruses are a subfamily of herpesviruses that include the significant human pathogens herpes simplex viruses (HSV) and varicella zoster virus (VZV). Glycoprotein K (gK), conserved in all alphaherpesviruses, is a multi-membrane spanning virion glycoprotein essential for virus entry into neuronal axons, virion assembly, and pathogenesis. Despite these critical functions, little is known about which gK domains and residues are most important for maintaining these functions across all alphaherpesviruses. Herein, we employed phylogenetic and structural analyses including the use of a novel model for evolutionary rate variation across residues to predict conserved gK functional domains. We found marked heterogeneity in the evolutionary rate at the level of both individual residues and domains, presumably as a result of varying selective constraints. To clarify the potential role of conserved sequence features, we predicted the structures of several gK orthologs. Congruent with our phylogenetic analysis, slowly evolving residues were identified at potentially structurally significant positions across domains. We found that using a quantitative measure of amino acid rate variation combined with molecular modeling we were able to identify amino acids predicted to be critical for gK protein structure/function. This analysis yields targets for the design of anti-herpesvirus therapeutic strategies across all alphaherpesvirus species that would be absent from more traditional analyses of conservation.

Correction to: Solochrome cyanine: A histological stain for cobalt-chromium wear particles in metal-on-metal periprosthetic tissues

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Test Your Memory (TYM) and Test Your Memory for Mild Cognitive Impairment (TYM-MCI): A Review and Update Including Results of Using the TYM Test in a General Neurology Clinic and Using a Telephone Version of the TYM Test

This paper summarises the current status of two novel short cognitive tests (SCT), known as Test Your Memory (TYM) and Test Your Memory for Mild Cognitive Impairment (TYM-MCI). The history of and recent research on the TYM and TYM-MCI are summarised in applications for Alzheimer's and non-Alzheimer's dementia and mild cognitive impairment. The TYM test can be used in a general neurology clinic and can help distinguish patients with Alzheimer's disease (AD) from those with no neurological cause for their memory complaints. An adapted tele-TYM test administered by telephone to patients produces scores which correlate strongly with the clinic-administered Addenbrookes Cognitive Examination revised (ACE-R) test and can identify patients with dementia. Patients with AD decline on the TYM test at a rate of 3.6-4.1 points/year.

Solochrome cyanine: A histological stain for cobalt-chromium wear particles in metal-on-metal periprosthetic tissues

Metal-on-metal (MoM) hip arthroplasties produce abundant implant-derived wear debris composed mainly of cobalt (Co) and chromium (Cr). Cobalt-chromium (Co-Cr) wear particles are difficult to identify histologically and need to be distinguished from other wear particle types and endogenous components (e.g., haemosiderin, fibrin) which may be present in MoM periprosthetic tissues. In this study we sought to determine whether histological stains that have an affinity for metals are useful in identifying Co-Cr wear debris in MoM periprosthetic tissues. Histological sections of periprosthetic tissue from 30 failed MoM hip arthroplasties were stained with haematoxylin-eosin (HE), Solochrome Cyanine (SC), Solochrome Azurine (SA) and Perls' Prussian Blue (PB). Sections of periprosthetic tissue from 10 cases of non-MoM arthroplasties using other implant biomaterials, including titanium, ceramic, polymethylmethacrylate (PMMA) and ultra-high molecular weight polyethylene (UHMWP) were similarly analysed. Sections of 10 cases of haemosiderin-containing knee tenosynovial giant cell tumour (TSGCT) were also stained with HE, SC, SA and PB. In MoM periprosthetic tissues, SC stained metal debris in phagocytic macrophages and in the superficial necrotic zone which exhibited little or no trichrome staining for fibrin. In non-MoM periprosthetic tissues, UHMWP, PMMA, ceramic and titanium particles were not stained by SC. Prussian Blue, but not SC or SA, stained haemosiderin deposits in MoM periprosthetic tissues and TSGT. Our findings show that SC staining (most likely Cr-associated) is useful in distinguishing Co-Cr wear particles from other metal/non-metal wear particles types in histological preparations of periprosthetic tissue and that SC reliably distinguishes haemosiderin from Co-Cr wear debris.

A mixed-methods pilot study to evaluate a collaborative anaesthetic and surgical training package for emergency surgical cricothyroidotomy

In a ‘can’t intubate, can’t oxygenate’ scenario, success of emergency front-of-neck access is dependent upon a clinician’s skill, competence and confidence to initiate the procedure. Surgical cricothyroidotomy is an important airway skill, as it can be employed as both the primary method of emergency front-of-neck access or as a rescue approach if a needle technique should fail. We designed a collaborative surgical and anaesthetic training package to address perceived anaesthetic reluctance to perform surgical cricothyroidotomy and undertook a pilot study of the package using a mixed-methods approach. The package consisted of three elements: theory teaching, surgical experience and repeated high-fidelity simulation. Ten anaesthetic trainees were trained using the package. Training comprised face-to-face tuition on the 2015 Difficult Airway Society guidelines, the Vortex cognitive aid, manikin-based surgical cricothyroidotomy instruction and surgical experience gained from an elective surgical tracheostomy. A standardised, high-fidelity in situ ‘can’t intubate, can’t oxygenate’ simulation was used to assess performance at baseline and at two weeks and six months after training. Participants scored their self-efficacy, underwent qualitative semi-structured interviews and had their performance quantitatively assessed to evaluate this training. Six months following training, participants’ performance had improved. They reported significantly increased self-efficacy and demonstrated significantly reduced deliberation time to initiate surgical cricothyroidotomy in the simulated ‘can’t intubate, can’t oxygenate’ emergency. Thematic framework analysis of interview transcripts revealed that reluctance to perform surgical cricothyroidotomy was related to fear and anxiety in regard to performing the procedure. These results support wider adoption of collaborative educational training packages, including hands-on surgical teaching, to improve trainees’ efficacy and confidence with surgical cricothyroidotomy and front-of-neck access in an emergency ‘can’t intubate, can’t oxygenate’ scenario.

Multi-disciplinary training hubs in North West England: the training hub lead perspective

Introduction: Increasing the capacity of Primary Care to meet the challenge of providing future complex and multi-disciplinary care in England has led to the increasing establishment of 'Training Hubs' [TH]. Other terms are used interchangeably to refer to TH activity: Advanced Training Practices, Enhanced Training Practices and Community Education Providers. The aim of this study was to gather the perceptions of TH Leads in North West England on how they established their TH and lessons learned. Methods: Five semi-structured telephone interviews were undertaken with TH Leads. Thematic analysis of the transcripts was undertaken. Findings: Four themes were identified: Motivation and Expectations of Establishing THs; Benefits to Learners and Practice Staff; Implementation Challenges and Barriers to Scale-Up; Sustainability and Wider Implementation. Discussion: TH Leads highlighted that the establishment of THs enhanced the multi-disciplinary learning experience. However, several barriers for sustaining the quality of the TH learning environments were identified. Difficulties recruiting 'Spoke Practices' were greater than expected. Findings identified the following factors for consideration for wider implementation: the maintenance of TH Lead support networks; appropriateness of funding to encourage practices who may be reluctant to take on this additional responsibility; the importance of communication channels between THs and HEIs; careful management of students numbers.

P3: Phylogenetic Posterior Prediction in RevBayes

Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian inference, posterior predictive simulations can be used to test absolute model fit. However, such tests have not been commonly practiced in phylogenetic inference due to a lack of convenient and flexible software. Here, we describe our newly implemented tests of model fit using posterior predictive testing, based on both data- and inference-based test statistics, in the phylogenetics software RevBayes. This new implementation makes a large spectrum of models available for use through a user-friendly and flexible interface.

Disseminating technology in global surgery

Background

Effective dissemination of technology in global surgery is vital to realize universal health coverage by 2030. Challenges include a lack of human resource, infrastructure and finance. Understanding these challenges, and exploring opportunities and solutions to overcome them, are essential to improve global surgical care.

Methods

This review focuses on technologies and medical devices aimed at improving surgical care and training in low- and middle-income countries. The key considerations in the development of new technologies are described, along with strategies for evaluation and wider dissemination. Notable examples of where the dissemination of a new surgical technology has achieved impact are included.

Results

Employing the principles of frugal and responsible innovation, and aligning evaluation and development to high scientific standards help overcome some of the challenges in disseminating technology in global surgery. Exemplars of effective dissemination include low-cost laparoscopes, gasless laparoscopic techniques and innovative training programmes for laparoscopic surgery; low-cost and versatile external fixation devices for fractures; the LifeBox pulse oximeter project; and the use of immersive technologies in simulation, training and surgical care delivery.

Conclusion

Core strategies to facilitate technology dissemination in global surgery include leveraging international funding, interdisciplinary collaboration involving all key stakeholders, and frugal scientific design, development and evaluation.

Evaluating Model Performance in Evolutionary Biology

Many fields of evolutionary biology now depend on stochastic mathematical models. These models are valuable for their ability to formalize predictions in the face of uncertainty and provide a quantitative framework for testing hypotheses. However, no mathematical model will fully capture biological complexity. Instead, these models attempt to capture the important features of biological systems using relatively simple mathematical principles. These simplifications can allow us to focus on differences that are meaningful, while ignoring those that are not. However, simplification also requires assumptions, and to the extent that these are wrong, so is our ability to predict or compare. Here, we discuss approaches for evaluating the performance of evolutionary models in light of their assumptions by comparing them against reality. We highlight general approaches, how they are applied, and remaining opportunities. Absolute tests of fit, even when not explicitly framed as such, are fundamental to progress in understanding evolution.

The Behavior of Metropolis-Coupled Markov Chains When Sampling Rugged Phylogenetic Distributions

Bayesian phylogenetic inference relies on the use of Markov chain Monte Carlo (MCMC) to provide numerical approximations of high-dimensional integrals and estimate posterior probabilities. However, MCMC performs poorly when posteriors are very rugged (i.e., regions of high posterior density are separated by regions of low posterior density). One technique that has become popular for improving numerical estimates from MCMC when distributions are rugged is Metropolis coupling (MC$^3$). In MC$^3$, additional chains are employed to sample flattened transformations of the posterior and improve mixing. Here, we highlight several underappreciated behaviors of MC3. Notably, estimated posterior probabilities may be incorrect but appear to converge, when individual chains do not mix well, despite different chains sampling trees from all relevant areas in tree space. Counterintuitively, such behavior can be more difficult to diagnose with increased numbers of chains. We illustrate these surprising behaviors of MC$^3$ using a simple, non-phylogenetic example and phylogenetic examples involving both constrained and unconstrained analyses. To detect and mitigate the effects of these behaviors, we recommend increasing the number of independent analyses and varying the temperature of the hottest chain in current versions of Bayesian phylogenetic software. Convergence diagnostics based on the behavior of the hottest chain may also help detect these behaviors and could form a useful addition to future software releases.

Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

The use of large genomic data sets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological vs. methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

Trial of Remote Continuous versus Intermittent NEWS monitoring after major surgery (TRaCINg): protocol for a feasibility randomised controlled trial

Background

Despite medical advances, major surgery remains high risk. Up to 44% of patients experience postoperative complications, which can have huge impacts for patients and the healthcare system. Early recognition of postoperative complications is crucial in reducing morbidity and preventing long-term disability. The current standard of care is intermittent manual vital signs monitoring, but new wearable remote monitors offer the benefits of continuous vital signs monitoring without limiting the patient's mobility. The aim of this study is to evaluate the feasibility, acceptability and clinical impacts of continuous remote monitoring after major surgery.

Methods

The study is a randomised, controlled, unblinded, parallel group, feasibility trial. Adult patients undergoing elective major surgery will be invited to participate if they have the capacity to provided informed, written consent and do not have a cardiac pacemaker or an allergy to adhesives. Participants will be randomly assigned to receive continuous remote monitoring and normal National Early Warning Score (NEWS) monitoring (intervention group) or normal NEWS monitoring alone (control group). Continuous remote monitoring will be achieved using the SensiumVitals® wireless patch which is worn on the patient's chest and monitors heart rate, respiratory rate and temperature continuously and alerts the nurse when there is deviation from pre-set physiological norms. Participants will be followed up throughout their hospital admission and for 30 days after discharge. Feasibility will be assessed by evaluating recruitment rate, adherence to protocol and randomisation, and the amount of missing data. The acceptability of the patch to nursing staff and patients will be assessed using questionnaires and interviews. Clinical outcomes will include time to antibiotics in cases of sepsis, length of hospital stay, number of critical care admissions and rate of readmission within 30 days of discharge.

Discussion

Early detection and treatment of complications minimises the need for critical care, improves patient outcomes, and produces significant cost savings for the healthcare system. Remote continuous monitoring systems have the potential to allow earlier detection of complications, but evidence from the literature is mixed. Demonstrating significant benefit over intermittent monitoring to offset the practical and economic implications of continuous monitoring requires well-controlled studies in high-risk populations to demonstrate significant differences in clinical outcomes; this feasibility trial seeks to provide evidence of how best to conduct such a confirmatory trial.

Trial registration

This study is listed on the ISRCTN registry with study ID ISRCTN16601772.

The impact of continuous versus intermittent vital signs monitoring in hospitals: A systematic review and narrative synthesis

BACKGROUND

Continuous vital signs monitoring on general hospital wards may allow earlier detection of patient deterioration and improve patient outcomes. This systematic review will assess if continuous monitoring is practical outside of the critical care setting, and whether it confers any clinical benefit to patients.

METHODS

MEDLINE^®, MEDLINE^® In-Process, EMBASE, CINAHL and The Cochrane Library were searched for articles that evaluated the clinical or non-clinical outcomes of continuous vital signs monitoring in adults outside of the critical care setting. The protocol was registered with PROSPERO (CRD42017058098).

FINDINGS

Twenty-four studies met the inclusion criteria and reported outcomes on a total of 40,274 patients and 59 ward staff in nine countries. The majority of studies showed benefits in terms of critical care use and length of hospital stay. Larger studies were more likely to demonstrate clinical benefit, particularly critical care use and length of hospital stay. Three studies showed cost-effectiveness. Barriers to implementation included nursing and patient satisfaction and the burden of false alerts.

CONCLUSIONS

Continuous vital signs monitoring outside the critical care setting is feasible and may provide a benefit in terms of improved patient outcomes and cost efficiency. Large, well-controlled studies in high-risk populations are required to evaluate the clinical benefit of continuous monitoring systems.

Ethical dilemmas and reflexivity in qualitative research

CONTEXT

For medical education researchers, a key concern may be the practicalities of gaining ethical approval where this is a national or local requirement. However, in qualitative studies, where the dynamics of human interaction pervade, ethical considerations are an ongoing process which continues long after approval has been granted. Responding to ethical dilemmas arising 'in the moment' requires a reflexive approach whereby the researcher questions his/her own motivations, assumptions and interests. Drawing on empirical studies and their experiences in academic and clinical research practice, the authors share their reflections on adhering to ethical principles throughout the research process to illustrate the complexities and nuances involved.

OBJECTIVES AND FINDINGS

These reflections offer critical insights into dilemmas arising in view of the ethical principles driving good conduct, and through domains which distinguish between procedural ethics, situational ethics, ethical relationships and ethical issues in exiting the study. The accounts consider integrity and altruism in research, gatekeeping and negotiating access, consent and confidentiality, power dynamics and role conflict, and challenges in dissemination of findings. The experiences are based on a range of examples of research in a UK context from managing difficult conversations in the classroom to video-ethnography in the operating theatre.

DISCUSSION AND CONCLUSIONS

These critical reflections make visible the challenges encountered and decisions that must be taken in the moment and on reflection after the event. Through sharing our experiences and debating the decisions we made, we offer insights into reflexivity in qualitative research which will be of value to others.

Patient attitudes towards remote continuous vital signs monitoring on general surgery wards: An interview study

BACKGROUND

Vital signs monitoring is used to identify deteriorating patients in hospital. The most common tool for vital signs monitoring is an early warning score, although emerging technologies allow for remote, continuous patient monitoring. A number of reviews have examined the impact of continuous monitoring on patient outcomes, but little is known about the patient experience. This study aims to discover what patients think of monitoring in hospital, with a particular emphasis on intermittent early warning scores versus remote continuous monitoring, in order to inform future implementations of continuous monitoring technology.

METHODS

Semi-structured interviews were undertaken with 12 surgical inpatients as part of a study testing a remote continuous monitoring device. All patients were monitored with both an early warning score and the new device. Interviews were audio-recorded, transcribed verbatim and analysed using thematic analysis.

FINDINGS

Patients can see the value in remote, continuous monitoring, particularly overnight. However, patients appreciate the face-to-face aspect of early warning score monitoring as it allows for reassurance, social interaction, and gives them further opportunity to ask questions about their medical care.

CONCLUSION

Early warning score systems are widely used to facilitate detection of the deteriorating patient. Continuous monitoring technologies may provide added reassurance. However, patients value personal contact with their healthcare professionals and remote monitoring should not replace this. We suggest that remote monitoring is best introduced in a phased manner, and initially as an adjunct to usual care, with careful consideration of the patient experience throughout.

Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent

The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent (MSC) to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the MSC model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across data sets. Posterior predictive tests find the poorest model performance in data sets that were hypothesized to be impacted by model violations. We also show that while the inferences assuming the MSC are robust to minor model violations, such inferences can be biased under some biologically plausible scenarios. Taken together, these results suggest that researchers can identify individual data sets in which species delimitation under the MSC is likely to be problematic, thereby highlighting the cases where additional lines of evidence to identify species boundaries are particularly important to collect. Our study supports a growing body of work highlighting the importance of model checking in phylogenetics, and the usefulness of tailoring tests of model fit to assess the reliability of particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].

Bayes Factors Unmask Highly Variable Information Content, Bias, and Extreme Influence in Phylogenomic Analyses

As the application of genomic data in phylogenetics has become routine, a number of cases have arisen where alternative data sets strongly support conflicting conclusions. This sensitivity to analytical decisions has prevented firm resolution of some of the most recalcitrant nodes in the tree of life. To better understand the causes and nature of this sensitivity, we analyzed several phylogenomic data sets using an alternative measure of topological support (the Bayes factor) that both demonstrates and averts several limitations of more frequently employed support measures (such as Markov chain Monte Carlo estimates of posterior probabilities). Bayes factors reveal important, previously hidden, differences across six "phylogenomic" data sets collected to resolve the phylogenetic placement of turtles within Amniota. These data sets vary substantially in their support for well-established amniote relationships, particularly in the proportion of genes that contain extreme amounts of information as well as the proportion that strongly reject these uncontroversial relationships. All six data sets contain little information to resolve the phylogenetic placement of turtles relative to other amniotes. Bayes factors also reveal that a very small number of extremely influential genes (less than 1% of genes in a data set) can fundamentally change significant phylogenetic conclusions. In one example, these genes are shown to contain previously unrecognized paralogs. This study demonstrates both that the resolution of difficult phylogenomic problems remains sensitive to seemingly minor analysis details and that Bayes factors are a valuable tool for identifying and solving these challenges.

Acute intravenous exposure to silver nanoparticles during pregnancy induces particle size and vehicle dependent changes in vascular tissue contractility in Sprague Dawley rats

The use of silver nanoparticles (AgNP) raises safety concerns during susceptible life stages such as pregnancy. We hypothesized that acute intravenous exposure to AgNP during late stages of pregnancy will increase vascular tissue contractility, potentially contributing to alterations in fetal growth. Sprague Dawley rats were exposed to a single dose of PVP or Citrate stabilized 20 or 110nm AgNP (700μg/kg). Differential vascular responses and EC50 values were observed in myographic studies in uterine, mesenteric arteries and thoracic aortic segments, 24h post-exposure. Reciprocal responses were observed in aortic and uterine vessels following PVP stabilized AgNP with an increased force of contraction in uterine artery and increased relaxation responses in aorta. Citrate stabilized AgNP exposure increased contractile force in both uterine and aortic vessels. Intravenous AgNP exposure during pregnancy displayed particle size and vehicle dependent moderate changes in vascular tissue contractility, potentially influencing fetal blood supply.

The Test Your Memory for Mild Cognitive Impairment (TYM-MCI)

BACKGROUND

To validate a short cognitive test: the Test Your Memory for Mild Cognitive Impairment (TYM-MCI) in the diagnosis of patients with amnestic mild cognitive impairment or mild Alzheimer's disease (aMCI/AD).

METHODS

Two hundred and two patients with mild memory problems were recruited. All had 'passed' the Mini-Mental State Examination (MMSE). Patients completed the TYM-MCI, the Test Your Memory test (TYM), MMSE and revised Addenbrooke's Cognitive Examination (ACE-R), had a neurological examination, clinical diagnostics and multidisciplinary team review.

RESULTS

As a single test, the TYM-MCI performed as well as the ACE-R in the distinction of patients with aMCI/AD from patients with subjective memory impairment with a sensitivity of 0.79 and specificity of 0.91. Used in combination with the ACE-R, it provided additional value and identified almost all cases of aMCI/AD. The TYM-MCI correctly classified most patients who had equivocal ACE-R scores. Integrated discriminant improvement analysis showed that the TYM-MCI added value to the conventional memory assessment. Patients initially diagnosed as unknown or with subjective memory impairment who were later rediagnosed with aMCI/AD scored poorly on their original TYM-MCI.

CONCLUSION

The TYM-MCI is a powerful short cognitive test that examines verbal and visual recall and is a valuable addition to the assessment of patients with aMCI/AD. It is simple and cheap to administer and requires minimal staff time and training.

Short Communication: Lack of Support for Socially Connected HIV-1 Transmission Among Young Adult Black Men Who Have Sex with Men

We explore the phylogenetic relationships among HIV sequences sampled from young adult black men who have sex with men (YAB-MSM), who are connected through peer referral/social ties and who attend common venues. Using 196 viral sequences sampled from the peripheral blood mononuclear cells of 10 individuals, our preliminary phylogenetic results indicate that these socially connected YAB-MSM are infected with distantly related viruses and provide no evidence for viral transmission between network members. Our results suggest that HIV-prevention strategies that target young adult MSM should extend beyond their network members and local community.

TMEM106B and ApoE polymorphisms in CHMP2B-mediated frontotemporal dementia (FTD-3)

Single-nucleotide polymorphisms in the TMEM106B gene have been identified as a risk factor in frontotemporal dementia (FTD). The major allele of SNP rs3173615 is a risk factor in sporadic FTD, whereas the minor allele seems protective in GRN- and C9orf72-mediated FTD. The role of apolipoprotein E (ApoE) in FTD is uncertain, though an established risk factor in Alzheimer's disease. In a unique Danish family, inherited FTD is caused by a mutation in the CHMP2B gene located on chromosome 3 (FTD-3). In this family, both risk factors TMEM106B and ApoE were analyzed and correlated to age at onset (AAO) and progression in terms of age at institutionalization (AAI) and age at death (AAD). Although TMEM106B and CHMP2B share cellular function in that both localize to endolysosomes, TMEM106B genotypes appeared to have no influence on the clinical disease course. ApoE ε4 was found to be a protective factor with later AAO and AAI, whereas ε2 seemed to aggravate the disease with earlier AAO and AAD. These results indicate ApoE ε2 as a risk factor in FTD-3 and suggest a protective role of ε4.

Water-carbon dioxide solid phase equilibria at pressures above 4 GPa

A solid phase in the mixed water-carbon dioxide system, previously identified as carbonic acid, was observed in the high-pressure diamond-anvil cell. The pressure-temperature paths of both its melting and peritectic curves were measured, beginning at 4.4 GPa and 165 °C (where it exists in a quadruple equilibrium, together with an aqueous fluid and the ices H₂O(VII) and CO₂(I)) and proceeding to higher pressures and temperatures. Single-crystal X-ray diffraction revealed a triclinic crystal with unit cell parameters (at 6.5 GPa and 20 °C) of a = 5.88 Å, b = 6.59 Å, c = 6.99 Å, α = 88.7°, β = 79.7°, and γ = 67.7°. Raman spectra exhibit a major line at ~1080 cm⁻¹ and lattice modes below 300 cm⁻¹.

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees

Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License.

Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years

Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep “tension zone,” in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30 years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.

EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics

Background

Branch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informative and lead to branch- and tree-length estimates that are unreasonable. Alternatively, priors may be uninformative, but lead to diffuse posterior estimates. Despite the widespread availability of relevant datasets from other groups, biologists rarely leverage outside information to specify branch-length priors that are specific to the analysis they are conducting.

Results

We developed the software package EmpPrior to facilitate the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics. EmpPrior efficiently queries TreeBASE to find data that are similar to focal data, in terms of taxonomic and genetic sampling, and uses them to inform branch-length priors for the focal analysis. EmpPrior consists of two components: EmpPrior-search, written in Java to query TreeBASE, and EmpPrior-fit, written in R to parameterize branch-length distributions. In an example analysis, we show how the use of relevant, outside data is made possible by EmpPrior and improves tree-length estimates from a focal dataset.

Conclusion

EmpPrior is easy to use, fast, and improves both the accuracy and precision of branch-length estimates in many circumstances. While EmpPrior’s focus is on branch lengths, the strategy it employs could easily be extended to address other prior parameterization problems in phylogenetics.